@article {pmid40472788,
year = {2025},
author = {Lunde, TM and Tansirichaiya, S and Xue, Y and Al-Haroni, M},
title = {Evolutionary dynamics of Tn916 in Streptococcus oralis: Fitness cost and persistent metabolic shifts post-acquisition.},
journal = {Archives of oral biology},
volume = {177},
number = {},
pages = {106317},
doi = {10.1016/j.archoralbio.2025.106317},
pmid = {40472788},
issn = {1879-1506},
abstract = {OBJECTIVES: The acquisition and transfer of mobile genetic elements (MGEs) are major drivers of antibiotic resistance in bacterial populations. Despite the fitness cost associated with the acquisition of MGEs, the mechanisms underlying their persistence remain poorly understood. This study investigates the evolutionary dynamics of the integrative conjugative element (ICE) Tn916 in a naïve Streptococcus oralis host, focusing on growth rates and metabolic activity.

METHODS: We tracked the evolutionary trajectory of Tn916 in S. oralis by monitoring changes in growth rates and maximum metabolic activities over 1000 generations. Comparative analyses were conducted between Tn916-free and Tn916-carrying populations to assess fitness cost and evolutionary adaptations.

RESULTS: Following Tn916 integration, the S. oralis host exhibited a significant initial fitness cost, characterized by reduced growth rates and maximum metabolic activity. However, within 500 generations, the fitness cost was mitigated, and by 1000 generations, evolved Tn916- transconjugant populations outcompeted their unevolved counterparts. Despite the restoration of growth rates, a persistent reduction in maximum metabolic rate was observed, suggesting resource reallocation favoring growth and ICE maintenance.

CONCLUSION: The acquisition of Tn916 imposes initial fitness cost on S. oralis, but the cost is rapidly mitigated through evolution, leading to competitive advantages in the long term. However, the persistence of lower maximum metabolic rate indicates that Tn916 acquisition affects cellular functions beyond growth, underscoring the need to monitor metabolic activity to fully understand the impact of horizontal gene transfer, MGEs, and ICEs on bacterial populations.},
}

@article {pmid40471191,
year = {2025},
author = {Ramirez, P and Martinez Montoya, H and Aramayo, R and Mateos, M},
title = {Diverse toxin repertoire but limited metabolic capacities inferred from the draft genome assemblies of three Spiroplasma (Citri clade) strains associated with Drosophila.},
journal = {Microbial genomics},
volume = {11},
number = {6},
pages = {},
doi = {10.1099/mgen.0.001408},
pmid = {40471191},
issn = {2057-5858},
mesh = {Animals ; *Drosophila/microbiology ; Phylogeny ; *Spiroplasma/genetics/metabolism/classification ; *Genome, Bacterial ; *Bacterial Toxins/genetics/metabolism ; Symbiosis ; },
abstract = {Spiroplasma (class Mollicutes) is a diverse wall-less bacterial genus whose members are strictly dependent on eukaryotic hosts (mostly arthropods and plants), with which they engage in pathogenic to mutualistic interactions. Spiroplasma are generally fastidious to culture in vitro, especially those that are vertically transmitted by their hosts, which include flies in the genus Drosophila. Drosophila has been invaded by at least three independent clades of Spiroplasma: Poulsonii (the best studied, contains reproductive manipulators and defensive mutualists associated with two major clades of Drosophila and has amongst the highest substitution rates within bacteria), Citri (restricted to the repleta group of Drosophila) and Ixodetis. We report the first genome drafts of Drosophila-associated Citri clade Spiroplasma: strain sMoj from Drosophila mojavensis, strain sAld-Tx from Drosophila aldrichi from Texas (newly discovered; also associated with Drosophila mulleri) and strain sHy2 from Drosophila hydei (the only Drosophila species known to naturally also harbour a Poulsonii clade strain, thereby providing an arena for horizontal gene transfer). Compared to their Poulsonii clade counterparts, we infer that the three Citri clade strains have the following: (1) equal or worse DNA repair abilities; (b) more limited metabolic capacities, which may underlie their comparatively lower titres and transmission efficiency; and (c) similar content of toxin domains, including at least one ribosome-inactivating protein, which is implicated in the Poulsonii-conferred defence against natural enemies. As a byproduct of our phylogenomic analyses and exhaustive search for certain toxin domains in public databases, we document the toxin repertoire in close relatives of Drosophila-associated Spiroplasma, and in a very divergent newly discovered lineage (i.e. 'clade X'). Phylogenies of toxin-encoding genes or domains imply substantial exchanges between closely and distantly related strains. Surprisingly, despite encoding several toxin genes and achieving relatively high prevalences in certain natural populations (sAld-Tx in this study; sMoj in prior work), fitness assays of sMoj (this study) and sAld-Tx (prior work) in the context of wasp parasitism fail to detect a beneficial effect to their hosts. Thus, how Citri clade strains persist in their Drosophila host populations remains elusive.},
}

Animals
*Drosophila/microbiology
Phylogeny
*Spiroplasma/genetics/metabolism/classification
*Genome, Bacterial
*Bacterial Toxins/genetics/metabolism
Symbiosis

@article {pmid40471045,
year = {2025},
author = {Hayward, C and Whiley, H and Ashbolt, NJ},
title = {The plumbing problem: rising antimicrobial resistance in building water systems.},
journal = {Current opinion in infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1097/QCO.0000000000001119},
pmid = {40471045},
issn = {1473-6527},
abstract = {PURPOSE OF REVIEW: This review examines the interplay between biological and anthropogenic factors in the development and persistence of antimicrobial resistance (AMR) within building plumbing systems, which is of particular concern in high risk setting such as healthcare facilities. The review highlights the role of biofilms and amoeba as reservoirs for AMR and explores how engineering and design decisions, governance structures, and cleaning protocols influence microbial resistance dynamics.

RECENT FINDINGS: Biofilms provide a protective environment that facilitates horizontal gene transfer and enhances bacterial resistance to disinfection. Amoeba-hosted bacteria can evade standard cleaning practices, further promoting AMR persistence. Emerging technologies, such as digital twin modelling, offer new opportunities to optimize risk mitigation strategies. However, more consideration is needed to be given to design or management decision that may have unintended consequences, such as unintended design outcomes, such as increased biofilm growth from tap mixers and low-flow fixtures, and ineffective cleaning protocols, which can inadvertently worsen AMR.

SUMMARY: Effectively managing AMR in plumbing systems requires a multidisciplinary approach that integrates microbiology, engineering, and policy. Data driven risk assessments can identify high-risk areas that may require design changes but also can enable targeted cleaning strategies, reducing reliance on widespread disinfection that may drive resistance. Future policies must consider system-wide implications to prevent unintended consequences. By addressing both biological and anthropogenic drivers, we can develop sustainable solutions to mitigate AMR risks in healthcare and beyond.},
}

@article {pmid40468151,
year = {2025},
author = {Pourrostami Niavol, K and Bordoloi, A and McKelvey, S and Suri, RPS},
title = {How does food waste to municipal sludge ratio affect anaerobic digestion: performance evaluation and fate of antibiotic resistance genes.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {40468151},
issn = {1614-7499},
abstract = {Anaerobic co-digestion of food waste (FW) and sewage sludge (SS) has shown superior performance over anaerobic mono-digestion. However, the fate of antibiotic resistance genes (ARGs) under various co-digestion ratios has been rarely reported to date. Thus, this study investigates the effects of FW:SS ratios on the digester's performance and the fate of ARGs at different FW:SS ratios. The results demonstrated that at a 50:50 FW:SS ratio, 738 mL.g[-1] VS of biogas and 393 mL.g[-1] VS of methane were produced in the system on day 18. Response surface methodology (RSM) was also used for optimization, showing 42.5% FW is the optimal FW content for maximum biogas and minimum H2S production. The distribution of select ARGs (qnrS, tetA, emrB, blaTEM, ampR) was tracked in the liquid and solid fraction of the digestate. Results illustrated a decrease (83-99% reduction) in the overall abundance of the ARGs in the solid fraction after AD. A similar trend was observed for the ARGs in the liquid fractions (65-99% reduction), except for ermB which became 1.74-10.6-fold higher in the final digestate. Also, at 50% FW, the abundance of intl1 increased in the liquid and solid fraction of digestate, indicating increased potential of ARG dissemination via horizontal gene transfer.},
}

@article {pmid40467884,
year = {2025},
author = {Jung, G and Zin, H and Son, B and Shin, H and Kim, J},
title = {Characterization of a plasmid dependent DNA phage targeting Escherichia coli harboring a conjugative plasmid and its impact on gut microbiota.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {19701},
pmid = {40467884},
issn = {2045-2322},
support = {2022R1A6A1A03055869//National Research Foundation of Korea/ ; R2024057//National Institute of Fisheries Science/ ; },
mesh = {*Escherichia coli/virology/genetics ; *Plasmids/genetics ; *Gastrointestinal Microbiome/genetics ; Humans ; Phylogeny ; *Bacteriophages/genetics ; Conjugation, Genetic ; Feces/microbiology ; Gene Transfer, Horizontal ; },
abstract = {The emergence and spread of antimicrobial resistance in bacteria pose a significant global threat to public health. One of the main drivers of this spread is the horizontal transfer of antimicrobial resistance genes via conjugative plasmids. In this study, we isolated a novel phage, PDP46, which specifically targets Escherichia coli strains carrying a conjugative plasmid that encodes antibiotic resistance genes. PDP46 requires a conjugative IncF plasmid for infection, enabling it to selectively target bacterial strains capable of plasmid-mediated gene transfer. Phylogenetic analysis based on the major capsid protein revealed that PDP46 clusters with several phages that use O-antigen as a receptor. However, the tail fiber of PDP46 differs from those of the clustered phages, suggesting that the tail fiber structure of PDP46 may play a key role in its plasmid-dependent infectivity. Furthermore, to explore its therapeutic potential, we evaluated PDP46's effects on the gut microbiota using an in vitro human fecal incubation model. Our findings suggest that phage PDP46 could inhibit the growth of target bacteria harboring conjugative plasmids without disrupting overall microbial diversity. By inhibiting the growth of donor cells carrying antibiotic resistance-associated plasmids, PDP46 may serve as a targeted gut microbiota modulator.},
}

*Escherichia coli/virology/genetics
*Plasmids/genetics
*Gastrointestinal Microbiome/genetics
Humans
Phylogeny
*Bacteriophages/genetics
Conjugation, Genetic
Feces/microbiology
Gene Transfer, Horizontal

@article {pmid40467487,
year = {2025},
author = {Nakayama, T and Harada, R and Yabuki, A and Nomura, M and Shiba, K and Inaba, K and Inagaki, Y},
title = {Marked Genome Reduction Driven by a Parasitic Lifestyle: Two Complete Genomes of Endosymbiotic Bacteria Possibly Hosted by a Dinoflagellate.},
journal = {Microbes and environments},
volume = {40},
number = {2},
pages = {},
doi = {10.1264/jsme2.ME25005},
pmid = {40467487},
issn = {1347-4405},
mesh = {*Symbiosis ; Phylogeny ; *Genome, Bacterial ; *Dinoflagellida/microbiology/physiology ; *Gammaproteobacteria/genetics/classification/isolation & purification/physiology ; Base Composition ; Gene Transfer, Horizontal ; Genome Size ; },
abstract = {Bacteria with endosymbiotic lifestyles often show marked genome reduction. While the shrinkage of genomes in intracellular symbionts of animals, including parasitic bacteria, has been extensively exami-ned, less is known about symbiotic bacteria associated with single-celled eukaryotes. We herein report the genomes of two novel gammaproteobacterial lineages, RS3 and XS4, identified as putative parasitic endosymbionts of the dinoflagellate Citharistes regius. Phylogenetic ana-lyses suggest that RS3 and XS4 belong to the family Fastidiosibacteraceae within the order Beggiatoales, forming independent lineages therein. The genomes of RS3 and XS4 are 529 and 436‍ ‍kbp in size, respectively, revealing marked reductions from related bacterial genomes. XS4, which has a very reduced genome with a low GC content, uses a different genetic code, in which UGA assigned tryptophan. The small genomes of RS3 and XS4 encode a limited number of proteins, retaining only approximately 20% of the predicted ancestral proteome. Metabolic reconstruction suggests that RS3 and XS4 are parasitic symbionts that are heavily dependent on their host for essential metabolites. Furthermore, we found that the ancestor of both genomes likely acquired an ADP:ATP antiporter gene via horizontal gene transfer, an event that may have enabled their evolution as energy parasites by facilitating the acquisition of ATP from their host. These results on novel bacteria with highly reduced genomes expand our understanding of the phylogenetic and genomic diversities of endosymbiotic bacteria in protists.},
}

*Symbiosis
Phylogeny
*Genome, Bacterial
*Dinoflagellida/microbiology/physiology
*Gammaproteobacteria/genetics/classification/isolation & purification/physiology
Base Composition
Gene Transfer, Horizontal
Genome Size

@article {pmid40158282,
year = {2025},
author = {Feng, Y and Li, T and Zhao, S and Li, X and Zhai, Y and Yuan, L and Liu, J and Hu, G and He, D and Pan, Y},
title = {Genetic characterization and transmission of the multidrug resistance gene cfr in fecal and environmental pathways on a chicken farm in China.},
journal = {Poultry science},
volume = {104},
number = {6},
pages = {105079},
pmid = {40158282},
issn = {1525-3171},
mesh = {Animals ; China ; *Chickens ; *Drug Resistance, Multiple, Bacterial/genetics ; *Escherichia coli/genetics/drug effects ; Feces/microbiology ; Plasmids ; *Klebsiella pneumoniae/genetics/drug effects ; *Poultry Diseases/microbiology/transmission/epidemiology ; Phylogeny ; Anti-Bacterial Agents/pharmacology ; *Bacterial Proteins/genetics/metabolism ; Gene Transfer, Horizontal ; },
abstract = {The emergence and spread of the multidrug-resistant gene cfr have raised significant public health concerns worldwide. To investigate its prevalence and dissemination dynamics, 18 cfr-positive strains were isolated in 2021 from fecal and environmental samples. Antimicrobial susceptibility testing showed that all strains were 100 % multidrug-resistant. Conjugation experiments demonstrated that a cfr- carrying IncFII(K)-IncR-IncFIB multi-replicon plasmid could transfer to E. coli J53. S1-nuclease digestion and Southern blotting identified cfr on plasmids of varying sizes, while whole-genome sequencing confirmed its presence on multiple plasmid types: IncX4, IncN, IncFII(K)-IncR-IncFIB, IncFIB-IncFII-IncR-IncHI2-IncHI2A multi-replicon plasmids, and two plasmids of unknown types. Genetic environment analysis revealed that cfr is categorized into five distinct structures (Types I-V). Reverse PCR results showed that Types I, II, and IV can form three circular intermediates of varying lengths (cfr-IS26). Network analysis further indicated strong association between cfr, tet(M), and dfrA14 mediated by IS26. Phylogenetic analysis revealed that the four ST1140 E. coli strains and all nine K. pneumoniae strains showed minimal genetic divergence. These findings suggest both clonal and horizontal transmission of cfr within the poultry farm. Continuous monitoring of cfr in animal-related environments is essential to mitigate its potential transfer to humans.},
}

Animals
China
*Chickens
*Drug Resistance, Multiple, Bacterial/genetics
*Escherichia coli/genetics/drug effects
Feces/microbiology
Plasmids
*Klebsiella pneumoniae/genetics/drug effects
*Poultry Diseases/microbiology/transmission/epidemiology
Phylogeny
Anti-Bacterial Agents/pharmacology
*Bacterial Proteins/genetics/metabolism
Gene Transfer, Horizontal

@article {pmid40466317,
year = {2025},
author = {Li, W and Zeng, J and Zheng, N and Ge, C and Li, Y and An, X and Yao, H},
title = {Astragalus polysaccharide slows the dissemination of antibiotic resistance genes and reduces the prevalence of opportunistic pathogens in the fish gut.},
journal = {Journal of environmental management},
volume = {389},
number = {},
pages = {126058},
doi = {10.1016/j.jenvman.2025.126058},
pmid = {40466317},
issn = {1095-8630},
abstract = {There is irrefutable evidence that the overuse of antibiotics in aquaculture contributes to the propagation and dissemination of antibiotic resistance genes (ARGs). In recent years, traditional Chinese medicines such as astragalus polysaccharide (APS) have been widely used as feed additives in aquaculture because of their ability to promote growth and enhance immunity and disease resistance. However, few studies have assessed whether APS exacerbates the ecological and health risk of ARG transmission. In this study, microcosm experiments were conducted with different concentrations of APS to assess the effects on the gut resistome and microbial community of a fish (Cyprinus carpio) using amplicon sequencing technology and high-throughput quantitative PCR. The results indicated that APS significantly reduced the total abundance of ARGs and mobile genetic elements (MGEs) in the gut (26.67 %-38.24 %). APS exposure led to a decrease in the abundance of Chlamydiae and opportunistic pathogens of the genus Aeromonas (41.54 %-87.86 %) in the gut. Network analysis revealed that Aeromonas is a potential host for most ARGs and MGEs, which exhibited similar trends in abundance changes. Functional analysis via PICRUSt2 indicated that APS markedly downregulated pathway activity related to drug resistance: antimicrobial, infectious diseases: bacterial and biofilm formation. The structural equation model based on partial least-squares path model indicated that the bacterial community, MGEs, and functional modules collectively determined the composition and distribution of gut ARGs under APS exposure. In summary, our study evaluated the health risks of the use of APS as a feed supplement, ensuring its appropriate use and sustainable aquaculture practices.},
}

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

@article {pmid40462285,
year = {2025},
author = {Ding, P and Lu, J and Lei, T and Guo, Y and Zhu, B and Zhao, Y and Wang, Y and Engelstädter, J and Schembri, MA and Guo, J},
title = {Antidepressant drugs promote the spread of broad-host-range plasmid in mouse and human gut microbiota.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2514138},
doi = {10.1080/19490976.2025.2514138},
pmid = {40462285},
issn = {1949-0984},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects/genetics ; Humans ; Mice ; *Plasmids/genetics ; *Antidepressive Agents/pharmacology ; *Bacteria/genetics/drug effects/classification/isolation & purification ; *Gene Transfer, Horizontal/drug effects ; RNA, Ribosomal, 16S/genetics ; Duloxetine Hydrochloride/pharmacology ; Drug Resistance, Bacterial/genetics ; Male ; Mice, Inbred C57BL ; },
abstract = {Antibiotic resistance is a global public health challenge. The gut microbiota serves as a reservoir for antibiotic resistance genes (ARGs), facilitating their transfer between bacteria. With the rising incidence of major depressive disorders (MDD), antidepressant prescriptions have surged. Previous pure-culture studies suggest that antidepressants exhibit antibiotic-like side effects, but their impact on gene transfer in microbial communities remains unclear. Here, we report that clinically relevant doses of antidepressants duloxetine and sertraline enhance the transfer of a broad-host range conjugative plasmid across bacterial phyla from mice gut microbiota. Tests in human gut simulators confirmed that duloxetine facilitates plasmid transfer in human gut microbiota. Mechanistic analyses revealed that antidepressants increase reactive oxygen species levels and alter bacterial cell membrane permeability. Using fluorescence-activated cell sorting and 16S rRNA gene sequencing, we discovered that antidepressants alter plasmid transfer patterns at both phylum and genus levels, driving ARG exchange among opportunistic pathogens. Our findings suggest that antidepressant use may promote the spread of antibiotic resistance between commensal and pathogenic bacteria, raising important public health concerns.},
}

Animals
*Gastrointestinal Microbiome/drug effects/genetics
Humans
Mice
*Plasmids/genetics
*Antidepressive Agents/pharmacology
*Bacteria/genetics/drug effects/classification/isolation & purification
*Gene Transfer, Horizontal/drug effects
RNA, Ribosomal, 16S/genetics
Duloxetine Hydrochloride/pharmacology
Drug Resistance, Bacterial/genetics
Male
Mice, Inbred C57BL

@article {pmid40458482,
year = {2025},
author = {Islam, MS and Polash, MA and Haque, MH},
title = {First Molecular Characterization and Antibiogram of Bacteria Isolated From Dairy Farm Wastewater in Bangladesh.},
journal = {Veterinary medicine international},
volume = {2025},
number = {},
pages = {7253393},
pmid = {40458482},
issn = {2090-8113},
abstract = {This pioneering study in Bangladesh combines phenotypic and genotypic approaches to characterize antibiotic-resistant bacteria in dairy farm wastewater, addressing a critical gap in regional antimicrobial resistance (AMR) research. Dairy farming is integral to global food production, yet the wastewater generated by these operations is a significant source of environmental and public health concerns, particularly in the context of antibiotic resistance. This study aimed to isolate and identify antibiotic-resistant bacteria from dairy farm wastewater and evaluate their antibiogram profiles to inform effective management strategies. A total of 60 wastewater samples were collected and subjected to conventional bacterial characterization, followed by molecular detection via PCR and 16S rRNA gene sequencing. The study identified Pseudomonas aeruginosa (35%), Escherichia coli (30%), Bacillus subtilis (16.67%), and Acinetobacter junii (8.33%) as the predominant bacterial species. Sequencing results demonstrated high compatibility with reference sequences, confirming the identities of the isolates. Antibiogram analysis revealed significant resistance patterns: P. aeruginosa exhibited the highest resistance to penicillin (85.71%) and amoxicillin (76.19%), while demonstrating greater sensitivity to ciprofloxacin and cotrimoxazole. E. coli showed notable resistance to penicillin (88.89%), amoxicillin, and ceftriaxone, while B. subtilis and A. junii also demonstrated high levels of resistance to multiple antibiotics. Notably, a substantial proportion of the isolates exhibited multidrug resistance (MDR), with MAR indices ranging from 0.37 to 0.75. Moreover, several antibiotic resistance genes (ARGs) including penA, bla TEM , bla CTX-M , tetA, tetB, tetC, and ermB were detected across the bacterial species, with high prevalence rates in P. aeruginosa and A. junii, suggesting the potential for horizontal gene transfer and further spread of resistance. These findings underscore the critical need for a One Health approach to mitigate the risks posed by antibiotic-resistant bacteria in dairy farm wastewater, emphasizing the critical importance of responsible antibiotic use and sustainable farming practices to protect public health and environmental integrity.},
}

@article {pmid40457174,
year = {2025},
author = {Okuno, M and Yamamoto, T and Ogura, Y},
title = {Blastn2dotplots: multiple dot-plot visualizer for genome comparisons.},
journal = {BMC bioinformatics},
volume = {26},
number = {1},
pages = {146},
pmid = {40457174},
issn = {1471-2105},
support = {24K10210//Japan Society for the Promotion of Science/ ; },
mesh = {*Software ; *Genomics/methods ; *Sequence Alignment/methods ; *Genome ; Computer Graphics ; },
abstract = {BACKGROUND: Dot-plots, along with linear comparisons, are fundamental visualization methods in genome comparisons, widely used for analyzing structural variations, repeat regions, and sequence similarities. However, existing tools often have limitations in visualization flexibility, particularly requiring the concatenation of multiple sequences into a single continuous axis. This constraint can make it difficult to apply highlights or user-defined grid lines effectively, reducing interpretability in comparative genomic analyses.

RESULTS: We developed blastn2dotplots, a Python 3-based tool that utilizes the Matplotlib library to generate customizable dot-plots from local blastn results. Unlike traditional approaches, blastn2dotplots treats each alignment as a separate subplot, allowing for independent axis labeling, adjustable spacing between plots, and enhanced visualization flexibility. Users can highlight specific regions of interest, apply custom grid lines, and tailor the display to suit different genomic analyses. This tool is particularly useful for chromosomal structure analyses, detection of horizontal gene transfer events, and visualization of repetitive elements, offering an intuitive and adaptable framework for sequence comparison.

CONCLUSIONS: By addressing key limitations of existing dot-plot visualization tools, blastn2dotplots enhances the clarity and flexibility of comparative genomic analyses. Its ability to handle multiple alignments separately while preserving independent axis control and customization options makes it a valuable resource for a wide range of genomic studies. This tool provides a novel and effective solution for researchers needing precise and adaptable visualization of sequence alignments, thereby maximizing the potential of dot-plots in bioinformatics.},
}

*Software
*Genomics/methods
*Sequence Alignment/methods
*Genome
Computer Graphics

@article {pmid40455052,
year = {2025},
author = {Zhang, YQ and Cheng, LC and Zhao, FJ and Chen, MM and Wang, P},
title = {Chiral Pesticides Selectively Influence the Dissemination of Antibiotic Resistance Genes: An Overlooked Environmental Risk.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c13010},
pmid = {40455052},
issn = {1520-5851},
abstract = {The global spread of antibiotic resistance genes (ARGs) poses a critical threat to public health and environmental safety. Among environmental factors, the widespread use of chiral pesticides has raised ecological concerns, yet their enantioselective impacts on ARG propagation remain largely unexplored. Here, we investigate how chiral pesticides influence microbial ARG dissemination at the enantiomeric level. Using flurtamone as a model, we successfully separated and quantitatively analyzed its enantiomers (R-flurtamone and S-flurtamone) and evaluated their effects at environmentally relevant concentrations (0-80 μg/L). Remarkably, R-flurtamone significantly enhanced the horizontal transfer of ARGs, surpassing the effects of Rac-flurtamone, whereas S-flurtamone exerted a negligible influence. Mechanistic insights revealed that R-flurtamone is more easily recognized by bacterial cells and induces more cellular stress responses. Additionally, R-flurtamone induced an increase in cell membrane permeability, excessive reactive oxygen species (ROS) production, SOS responses, and boosted ATP levels, further accelerating ARG propagation. By integrating experimental findings with molecular simulations, we elucidated the enantioselective mechanisms underpinning ARG transfer. This study highlights the overlooked risks associated with racemic chiral pesticides at the enantiomeric level and provides a foundation for mitigating ARG dissemination in agricultural and environmental systems.},
}

@article {pmid40453648,
year = {2025},
author = {},
title = {Correction to 'Current state and future prospects of Horizontal Gene Transfer detection'.},
journal = {NAR genomics and bioinformatics},
volume = {7},
number = {2},
pages = {lqaf078},
doi = {10.1093/nargab/lqaf078},
pmid = {40453648},
issn = {2631-9268},
mesh = {*Gene Transfer, Horizontal ; Humans ; },
abstract = {[This corrects the article DOI: 10.1093/nar/lqaf005.].},
}

*Gene Transfer, Horizontal
Humans

@article {pmid40451789,
year = {2025},
author = {Yue, X and Yang, J and Qi, J and Gao, S and Huo, Q and Guo, X and Guo, H and Luo, J and Wang, Y and Zhao, Y and Liu, R and Wang, H and Yi, S and Fu, Y and Ji, X and Wei, Y and He, W and Guo, B},
title = {Loss of Pathogenicity and Evidence of Horizontal Gene Transfer in Colletotrichum gloeosporioides From a Medicinal Plant.},
journal = {Molecular plant pathology},
volume = {26},
number = {6},
pages = {e70098},
doi = {10.1111/mpp.70098},
pmid = {40451789},
issn = {1364-3703},
support = {GX2346//Xi'an Beilin District Science and Technology Plan Project/ ; 2018ZDXM-SF-016//Key Research and Development Plan Project of Shaanxi Province/ ; 23JHQ056//Shaanxi Institute of Basic Sciences Project/ ; 2023-JC-YB-165//Natural Science Basis Research Plan in Shaanxi Province of China/ ; },
mesh = {*Colletotrichum/pathogenicity/genetics ; *Gene Transfer, Horizontal/genetics ; *Plants, Medicinal/microbiology ; Phylogeny ; *Huperzia/microbiology ; Virulence/genetics ; },
abstract = {Colletotrichum gloeosporioides is a major agricultural pathogen of crops that has also been identified as an endophyte of the medicinal plant Huperzia serrata. Both H. serrata and C. gloeosporioides produce huperzine A, a potential treatment for Alzheimer's disease. In this study, a nonpathogenic C. gloeosporioides strain (NWUHS001) was isolated and its genome sequenced. Gene structure prediction identified 15,413 protein-coding genes and 879 noncoding RNAs. Through PHI-base database prediction, we found that NWUHS001 lacks two key pathogenicity genes CgDN3 and cap20, which may be the cause of its nonpathogenicity. Comparative genomic analysis showed that the number of genes encoding pectin lyase B (pelB), pectin lyase (pnl) and polygalacturonase (pg) in NWUHS001 was significantly lower than that in pathogenic strains during the expansion of mycelium into host tissues. This caused slow growth and incapability to penetrate host cells. In contrast, in NWUHS001, genes involved in carbon acquisition such as ribose and amino sugar metabolic pathways were enriched, indicating active metabolite exchange with the host. In addition, by comparing the genome of NWUHS001 with that of the host H. serrata, we found that polyketosynthetase (pksIII), a key gene in the host huperzine A biosynthetic pathway, may possibly have been acquired from the fungus by horizontal gene transfer (HGT). This study explained the possible genetic evolution mechanism of C. gloeosporioides from pathogenicity to nonpathogenicity, which is of value for studying the interaction between microorganisms and plants. It also provided clues to the genetic evolution of the biosynthetic pathway of huperzine A.},
}

*Colletotrichum/pathogenicity/genetics
*Gene Transfer, Horizontal/genetics
*Plants, Medicinal/microbiology
Phylogeny
*Huperzia/microbiology
Virulence/genetics

@article {pmid40451201,
year = {2025},
author = {Spirin, S and Grishin, A and Rusinov, I and Alexeevski, A and Karyagina, A},
title = {Restriction-Modification Systems Specific toward GGATC, GATGC, and GATGG. Part 2. Functionality and Structure.},
journal = {Biochemistry. Biokhimiia},
volume = {90},
number = {4},
pages = {513-521},
doi = {10.1134/S0006297925600152},
pmid = {40451201},
issn = {1608-3040},
mesh = {*DNA Restriction-Modification Enzymes/metabolism/chemistry ; DNA Modification Methylases/metabolism/chemistry ; Substrate Specificity ; },
abstract = {The structural and functional basics of protein functionality of restriction-modification systems recognizing GGATC/GATCC, GATGC/GCATC, and GATGG/CCATC sites have been studied using bioinformatics methods. Such systems include a single restriction endonuclease and either two separate DNA methyltransferases or a single fusion DNA methyltransferase with two catalytic domains. It is known that some of these systems methylate both adenines in the recognition sites to 6-methyladenine, but the role of each of the two DNA methyltransferases remained unknown. In this work, we proved the functionality of most known systems. Based on the analysis of structures of related DNA methyltransferases, we hypothesized which of the adenines within the recognition site is modified by each of the DNA methyltransferases and suggested a possible molecular mechanism of changes in the DNA methyltransferase specificity from GATGG to GATGC during horizontal transfer of its gene.},
}

*DNA Restriction-Modification Enzymes/metabolism/chemistry
DNA Modification Methylases/metabolism/chemistry
Substrate Specificity

@article {pmid40451200,
year = {2025},
author = {Spirin, S and Rusinov, I and Makarikova, O and Alexeevski, A and Karyagina, A},
title = {Restriction-Modification Systems Specific toward GGATC, GATGC, and GATGG. Part 1. Evolution and Ecology.},
journal = {Biochemistry. Biokhimiia},
volume = {90},
number = {4},
pages = {502-512},
doi = {10.1134/S0006297925600115},
pmid = {40451200},
issn = {1608-3040},
mesh = {*Evolution, Molecular ; *DNA Restriction-Modification Enzymes/metabolism/genetics/chemistry ; *DNA Restriction Enzymes/metabolism/genetics/chemistry ; Phylogeny ; },
abstract = {The article presents the results of studies on the evolution of proteins from restriction-modification systems consisting of restriction endonucleases with the REase_AlwI family domain and either two DNA methyltransferases, each with the MethyltransfD12 family domain, or a single DNA methyltransferase with two domains of this family. It was found that all such systems recognized one of the three DNA sequences, namely GGATC, GATGC or GATGG. Based on the sequence similarity, restriction endonucleases of these systems could be attributed to three clades that unambiguously corresponded to the RM system specificity. The DNA methyltransferase domains of these systems were classified into two groups based on sequence similarity, with the two domains of each system belonging to different groups. Within each group, the domains were attributed to three clades according to their specificity. An evidence of multiple interspecific horizontal transfer of entire restriction-modification systems has been found, as well as the transfer of individual genes between the systems (including the transfer of one of DNA methyltransferases accompanied by changes in its specificity). Evolutionary relationships of DNA methyltransferases from the studied systems with other DNA methyltransferases, including orphan DNA methyltransferases, have been revealed.},
}

*Evolution, Molecular
*DNA Restriction-Modification Enzymes/metabolism/genetics/chemistry
*DNA Restriction Enzymes/metabolism/genetics/chemistry
Phylogeny

@article {pmid40445756,
year = {2025},
author = {Holt, JD and Peng, Y and Dalia, TN and Dalia, AB and Nadell, CD},
title = {Environmental DNA adsorption to chitin can promote horizontal gene transfer by natural transformation.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {22},
pages = {e2420708122},
doi = {10.1073/pnas.2420708122},
pmid = {40445756},
issn = {1091-6490},
support = {826672//Simons Foundation (SF)/ ; R35GM151158//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; R35GM128674//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; },
mesh = {*Chitin/metabolism/chemistry ; *Gene Transfer, Horizontal ; *Vibrio cholerae/genetics/metabolism ; *DNA, Environmental/genetics/chemistry ; Adsorption ; Fimbriae, Bacterial/metabolism/genetics ; *Transformation, Bacterial ; },
abstract = {Horizontal gene transfer by natural transformation (NT) is induced in Vibrio cholerae upon attachment to chitin surfaces in the aquatic environment. Here, we show that free environmental DNA adsorbs to chitin surfaces under physiologically realistic conditions. Using live-cell imaging and a fluorescent NT reporter, we demonstrate with cellular resolution microscopy that V. cholerae utilizes chitin-bound DNA as a reservoir for genetic exchange. Additionally, we demonstrate that uptake of DNA from this chitin-bound reservoir requires the forceful retraction of competence type IV pili. These findings uncover a role for retraction force in driving pilus-dependent NT and suggest that chitin particle surfaces can act as hotspots for horizontal gene transfer.},
}

*Chitin/metabolism/chemistry
*Gene Transfer, Horizontal
*Vibrio cholerae/genetics/metabolism
*DNA, Environmental/genetics/chemistry
Adsorption
Fimbriae, Bacterial/metabolism/genetics
*Transformation, Bacterial

@article {pmid40444634,
year = {2025},
author = {Ellison, TJ and Ellison, CK},
title = {Improved DNA binding to a type IV minor pilin increases natural transformation.},
journal = {Nucleic acids research},
volume = {53},
number = {10},
pages = {},
pmid = {40444634},
issn = {1362-4962},
support = {R35GM150916/NH/NIH HHS/United States ; DFS6023/DRCRF/Damon Runyon Cancer Research Foundation/United States ; },
mesh = {*Acinetobacter/genetics/metabolism ; *Fimbriae Proteins/metabolism/genetics/chemistry ; Gene Transfer, Horizontal ; *Transformation, Bacterial ; *DNA, Bacterial/metabolism ; Protein Binding ; Fimbriae, Bacterial/metabolism/genetics ; DNA-Binding Proteins/metabolism ; },
abstract = {Bacteria take up environmental DNA using dynamic appendages called type IV pili (T4P) to elicit horizontal gene transfer in a process called natural transformation. Natural transformation is widespread amongst bacteria yet the parameters that enhance or limit this process across species are poorly understood. We show that the most naturally transformable species known, Acinetobacter baylyi, owes this property to uniquely high levels of DNA binding by its orphan minor pilin, FimT. Expression of A. baylyi FimT in a closely related Acinetobacter pathogen substantially improves its capacity for natural transformation, showing that the acquisition of a single gene is sufficient to increase rates of horizontal gene transfer. We show that, compared with its homologs, A. baylyi FimT contains multiple regions of positively charged residues that additively promote DNA binding efficiency. These results demonstrate the importance of T4P-DNA binding in establishing natural transformation rates and provide a basis for improving or limiting this mechanism of horizontal gene transfer in different species.},
}

*Acinetobacter/genetics/metabolism
*Fimbriae Proteins/metabolism/genetics/chemistry
Gene Transfer, Horizontal
*Transformation, Bacterial
*DNA, Bacterial/metabolism
Protein Binding
Fimbriae, Bacterial/metabolism/genetics
DNA-Binding Proteins/metabolism

@article {pmid40443099,
year = {2025},
author = {Chen, H and Qin, X and Chen, Y and Zhang, H and Feng, Y and Tan, J and Chen, X and Hu, L and Xie, J and Xie, J and Yang, Z},
title = {Chromosome-level genome assembly of Pinus massoniana provides insights into conifer adaptive evolution.},
journal = {GigaScience},
volume = {14},
number = {},
pages = {},
doi = {10.1093/gigascience/giaf056},
pmid = {40443099},
issn = {2047-217X},
support = {Guike AD19254004//Guangxi Science and Technology Base and Talent/ ; 2024YFD2201301-1//National Key R&D Program of China/ ; No.2022YFD2201600//National Key R&D Program of China/ ; 2022YFD2200602//National Key R&D Program of China/ ; 2019A26//Bagui Scholar/ ; 2019AQ17//Bagui Young Scholar/ ; 32371906//National Natural Science Foundation of China/ ; 32022057//National Natural Science Foundation of China/ ; 2020132607//Forestry and Grassland Science and Technology Innovation Youth Top Talent/ ; QNTD202305//Fundamental Research Funds for the Central Universities/ ; BFUKF202413//Fundamental Research Funds for the Central Universities/ ; },
mesh = {*Pinus/genetics/metabolism ; *Genome, Plant ; *Evolution, Molecular ; *Chromosomes, Plant/genetics ; *Adaptation, Physiological/genetics ; Genomics/methods ; Phylogeny ; },
abstract = {Pinus massoniana, a conifer of significant economic and ecological value in China, is renowned for its wide adaptability and oleoresin production. We sequenced and assembled the chromosomal-level P. massoniana genome, revealing 80,366 protein-coding genes and significant gene family expansions associated with stress response and plant-pathogen interactions. Long-intron genes, which are predominantly presented in low-copy gene families, are strongly linked to the recent long terminal repeat burst in the Pinus genome. By reanalyzing population transcriptomic data, we identified genetic markers linked to oleoresin synthesis, including those within the CYP450 and TPS gene families. The results suggest that the genes of the resin terpene biosynthesis pathway can be activated in several cell types, and the oleoresin yield may depend on the rate-limiting enzymes. Using a multiomics algorithm, we identified several regulatory factors, including PmMYB4 and PmbZIP2, that interact with TPS and CYP450 genes, potentially playing a role in oleoresin production. This was further validated through molecular genetics analyses. We observed signatures of adaptive evolution in dispersed duplicates and horizontal gene transfer events that have contributed to the species adaptation. This study provides insights for further research into the evolutionary biology of conifers and lays the groundwork for genomic-assisted breeding and sustainable management of Masson pine.},
}

*Pinus/genetics/metabolism
*Genome, Plant
*Evolution, Molecular
*Chromosomes, Plant/genetics
*Adaptation, Physiological/genetics
Genomics/methods
Phylogeny

@article {pmid40440992,
year = {2025},
author = {Zhao, H and Zhao, HM and Wu, F and Liu, BL and Li, H and Li, YW and Cai, QY and Xiang, L and Mo, CH and Li, QX},
title = {Perfluorooctane sulfonate (PFOS) promotes transformational transfer of antibiotic resistance genes and cross-resistance between antibiotics and PFOS.},
journal = {Water research},
volume = {284},
number = {},
pages = {123868},
doi = {10.1016/j.watres.2025.123868},
pmid = {40440992},
issn = {1879-2448},
abstract = {Both per- and polyfluoroalkyl substances (PFASs) pollution and antibiotic resistance genes (ARGs) dissemination pose significant threats to global public health. PFASs and ARGs coexist in the environment, but little research was done on associations between PFASs and ARGs dissemination. This study demonstrated that perfluorooctane sulfonate (PFOS) increased ARGs transformation by 1.5-1.7-fold in Escherichia coli DH5α carrying pBR322 plasmid as a model. Moreover, pre-exposure of DH5α to PFOS increased ARGs transformation up to 7-fold. PFOS triggered up-regulation of the gene of outer membrane protein A (OmpA), enhancing cell membrane permeability and thus increasing ARGs transformation. Interestingly, the presence of ARGs decreased ompA gene expression and consequently lowered the accumulation and toxicity response of transformants to PFOS, which established cross-resistance between antibiotics and PFOS. This cross-resistance is attributed to the multifunctional role of the OmpA that acted as a major channel for ARGs entry into cells and facilitated cellular accumulation of PFOS. The OmpA-mediated cellular accumulation was also observed in structurally analogous PFASs (perfluorohexylsulfonic acid and pentadecafluorooctanoic acid), indicating a potential universality in the cross-resistance between antibiotics and PFASs. The United States, Canada and China are likely being confronted with high risks of PFOS-induced ARGs dissemination based on the global risk assessments. These findings demonstrate the overlooked eco-environmental risks associated with the interactions among PFASs, ARGs, and microorganisms, highlighting adaptability of organisms to chemical stress.},
}

@article {pmid40440354,
year = {2025},
author = {Marcarian, HQ and Sivakoses, A and Arias, AM and Ihedioha, OC and Lee, BR and Bishop, MC and Bothwell, ALM},
title = {Renal cancer cells acquire immune surface protein through trogocytosis and horizontal gene transfer.},
journal = {PloS one},
volume = {20},
number = {5},
pages = {e0325043},
pmid = {40440354},
issn = {1932-6203},
mesh = {Humans ; *Kidney Neoplasms/genetics/immunology/pathology/metabolism ; *Carcinoma, Renal Cell/genetics/immunology/pathology/metabolism ; *Gene Transfer, Horizontal ; Gene Expression Regulation, Neoplastic ; Carbonic Anhydrase IX ; Tumor Microenvironment/immunology ; Leukocyte Common Antigens/metabolism/genetics ; Cell Line, Tumor ; *Membrane Proteins/metabolism/genetics ; Biomarkers, Tumor/metabolism ; },
abstract = {Trogocytosis is an underappreciated phenomenon that shapes the immune microenvironment surrounding many types of solid tumors. The consequences of membrane-bound proteins being deposited from a donor immune cell to a recipient cancer cell via trogocytosis are still unclear. Here, we report that human clear cell renal carcinoma tumors stably express the lymphoid markers CD45, CD56, CD14, and CD16. Flow cytometry performed on fresh kidney tumors revealed consistent CD45 expression on tumor cells, as well as varying levels of the other markers mentioned previously. These results were consistent with our immunofluorescent analysis, which also revealed colocalization of lymphoid markers with carbonic anhydrase 9, a standard kidney tumor marker. RNA analysis showed a significant upregulation of genes typically associated with immune cells by tumor cells. Finally, we show evidence of chromosomal DNA being transferred from immune cells to tumor cells through physical contact. This horizontal gene transfer has transcriptional consequences in the recipient tumor cell, resulting in a fusion phenotype that expresses both immune and cancer specific proteins. This work demonstrates a novel mechanism by which tumor cell protein expression is altered through the acquisition of surface membrane fragments and genomic DNA from infiltrating lymphocytes. These results alter the way in which we understand tumor-immune cell interactions and may reveal new insights into the mechanisms by which tumors develop. Additionally, further studies into trogocytosis and other mechanisms of contact-mediated cellular transfer will help push the field towards the next generation of immunotherapies and biomarkers for treating renal cell carcinoma and other cancers.},
}

Humans
*Kidney Neoplasms/genetics/immunology/pathology/metabolism
*Carcinoma, Renal Cell/genetics/immunology/pathology/metabolism
*Gene Transfer, Horizontal
Gene Expression Regulation, Neoplastic
Carbonic Anhydrase IX
Tumor Microenvironment/immunology
Leukocyte Common Antigens/metabolism/genetics
Cell Line, Tumor
*Membrane Proteins/metabolism/genetics
Biomarkers, Tumor/metabolism

@article {pmid40438350,
year = {2025},
author = {Peng, H and Fu, J},
title = {Unveiling horizontal gene transfer in the gut microbiome: bioinformatic strategies and challenges in metagenomics analysis.},
journal = {National science review},
volume = {12},
number = {6},
pages = {nwaf128},
pmid = {40438350},
issn = {2053-714X},
}

@article {pmid40436596,
year = {2025},
author = {Tan, G and Lin, K and Hu, M and Wang, Y and Li, X and Li, X and Chen, S and Zhang, Q and Zheng, Z},
title = {Uncovering the resistome and mobilome across different types of ready-to-eat fermented foods.},
journal = {Food research international (Ottawa, Ont.)},
volume = {213},
number = {},
pages = {116577},
doi = {10.1016/j.foodres.2025.116577},
pmid = {40436596},
issn = {1873-7145},
mesh = {*Fermented Foods/microbiology ; *Food Microbiology ; *Fast Foods/microbiology ; Interspersed Repetitive Sequences ; Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/drug effects ; *Drug Resistance, Bacterial/genetics ; Metagenomics ; Dairy Products/microbiology ; Vegetables/microbiology ; },
abstract = {Antimicrobial resistance in food poses a significant threat to public health, and the persistence of antibiotic resistance genes (ARGs) in ready-to-eat fermented foods (RTE-FFs) is a growing concern. However, information on the diversity, origins, and transferability of ARGs in RTE-FFs is limited. This study investigated the distribution of ARGs and mobile genetic elements (MGEs) in four types of RTE-FFs: soybean, dairy, meat, and vegetable products. Using whole metagenomic sequencing, we identified significant variations in the bacterial diversity, ARG profiles, and MGE profiles among these food types. Bean-based RTE-FFs exhibited the highest diversity of ARGs and MGEs, while dairy products showed the lowest diversity (p < 0.05). Eight types of ARGs were significantly more prevalent in bean-based foods than in the other food categories (p < 0.05). Several ARGs were highly abundant in the RTE-FFs, including aphA2, blaTEM-116, PBP1a, PBP1b, OqxA, OqxBgb, lsa(A), tet(34), and tet(58). Plasmids carried the highest number of ARGs among all MGEs, particularly those associated with beta-lactam, macrolide-lincosamide-streptogramin, tetracycline, and aminoglycoside resistance, suggesting a higher risk with plasmid-mediated transfer, especially in bean-based RTE-FFs. Metagenomic binning analysis recovered 76 high-quality metagenome-assembled genomes (MAGs), including four novel species. A total of 13 types of ARGs, encompassing 95 subtypes, were identified across the MAGs; Bacillus paranthracis, Enterococcus casseliflavus, and Enterococcus gallinarum had the most ARGs (16, 12, and 14, respectively). Dairy RTE-FFs (yogurt and cheese) contained a high abundance of Streptococcus thermophilus resistant to beta-lactams (PBP1b) and tetracycline (tetB(60)), raising concerns about ARG transfer in these food products. Bean RTE-FFs (sufu) harbored two pathogenic Acinetobacter species carrying carbapenem resistance genes (blaOXA-180, blaOXA-211, and blaOXA-230). No ARGs were found in the MGEs (prophages, insertion sequences, or transposons) within the MAGs. Overall, our results provide valuable insights into the antibiotic resistome and mobilome of various RTE-FFs to inform food production and management practices.},
}

*Fermented Foods/microbiology
*Food Microbiology
*Fast Foods/microbiology
Interspersed Repetitive Sequences
Anti-Bacterial Agents/pharmacology
*Bacteria/genetics/drug effects
*Drug Resistance, Bacterial/genetics
Metagenomics
Dairy Products/microbiology
Vegetables/microbiology

@article {pmid40436163,
year = {2025},
author = {Gagneja, S and Capalash, N and Sharma, P},
title = {Whole genome sequence analysis of an environmental isolate Bacillus subtilis K3C: Genome plasticity and acquisition of hyaluronic acid capsule traits through horizontal multigene transfer.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {144696},
doi = {10.1016/j.ijbiomac.2025.144696},
pmid = {40436163},
issn = {1879-0003},
abstract = {B. subtilis K3C was isolated from an environmental sample. Genomic analysis revealed that the GRAS strain harbors a circular chromosome of 4,120,051 bp composed of 4361 protein coding sequences with a GC content of 43.4 %, 80 tRNA, and 3 rRNA genes. Two regions containing complete assembly of prophages encoded by 83 prophage genes were present suggesting the role of bacteriophage infection in evolutionary accumulation of strain-specific genes contributing towards strain diversification. Strong recombination, repair, transfer and competence systems were identified, suggesting their role in strain fitness and evolutionary process. Pan-genomic analysis revealed 3824 protein homologs as the bacterial core genome shared among different strains and 390 singletons in the pan-genome orthologous groups. The hyaluronic acid capsule trait in the isolate seems to be acquired through selective pressure to adapt in environmentally stressed niches. Phyloproteomic analysis showed that the acquired genes responsible for HA production were phylogenetically closer to Streptococcal clade, evidencing the role of horizontal gene transfer. The bacterial genome showed the presence of multiple HA genes translating HasB and HasC proteins suggesting gene dosage in the strain. However, no gene rearrangement events seem to have taken course as the HA genes were integrated in different contigs of the genome.},
}

@article {pmid40433443,
year = {2025},
author = {Dahal, U and Bansal, A},
title = {Unravelling Prokaryotic Codon Usage: Insights from Phylogeny, Influencing Factors and Pathogenicity.},
journal = {Current genomics},
volume = {26},
number = {2},
pages = {81-94},
pmid = {40433443},
issn = {1389-2029},
abstract = {Analyzing prokaryotic codon usage trends has become a crucial topic of study with significant ramifications for comprehending microbial genetics, classification, evolution, and the control of gene expression. This review study explores the numerous facets of prokaryotic codon usage patterns, looking at different parameters like habitat and lifestyle across broad groups of prokaryotes by emphasizing the role of codon reprogramming in adaptive strategies and its integration into systems biology. We also explored the numerous variables driving codon usage bias, including natural selection, mutation, horizontal gene transfer, codon-anticodon interaction, and genomic composition in prokaryotes through a thorough study of current literature. Furthermore, a special session on codon usage on pathogenic prokaryotes and the role of codon usage in the phylogeny of prokaryotes has been discussed. We also looked at the various software and indices that have been recently applied to prokaryotic genomes. The promising directions that lay ahead to map the future of codon usage research on prokaryotes have been emphasized. Codon usage variations across prokaryotic communities could be better understood by combining environmental, metagenomic, and system biology approaches.},
}

@article {pmid40431712,
year = {2025},
author = {Nikulina, AN and Nikulin, NA and Suzina, NE and Zimin, AA},
title = {Treatment of E. coli Infections with T4-Related Bacteriophages Belonging to Class Caudoviricetes: Selecting Phage on the Basis of Their Generalized Transduction Capability.},
journal = {Viruses},
volume = {17},
number = {5},
pages = {},
doi = {10.3390/v17050701},
pmid = {40431712},
issn = {1999-4915},
support = {№24-64-00017//Russian Science Foundation/ ; },
mesh = {*Phage Therapy/methods ; *Escherichia coli/virology ; *Escherichia coli Infections/therapy ; *Bacteriophage T4/genetics/physiology ; *Transduction, Genetic ; Humans ; Gene Transfer, Horizontal ; *Coliphages/genetics/physiology ; Animals ; },
abstract = {The problem of the multidrug resistance of pathogenic bacteria is a serious concern, one which only becomes more pressing with every year that passes, motivating scientists to look for new therapeutic agents. In this situation, phage therapy, i.e., the use of phages to combat bacterial infections, is back in the spotlight of research interest. Bacterial viruses are highly strain-specific towards their hosts, which makes them particularly valuable for targeting pathogenic variants amidst non-pathogenic microflora, represented by such commensals of animals and humans as E. coli, S. aureus, etc. However, selecting phages for the treatment of bacterial infections is a complex task. The prospective candidates should meet a number of criteria; in particular, the selected phage must not contain potentially dangerous genes (e.g., antibiotic resistance genes, genes of toxins and virulence factors etc.)-or be capable of transferring them from their hosts. This work introduces a new approach to selecting T4-related coliphages; it allows one to identify strains which may be safer in terms of involvement in the horizontal gene transfer. The approach is based on the search for genes that reduce the frequency of genetic transduction.},
}

*Phage Therapy/methods
*Escherichia coli/virology
*Escherichia coli Infections/therapy
*Bacteriophage T4/genetics/physiology
*Transduction, Genetic
Humans
Gene Transfer, Horizontal
*Coliphages/genetics/physiology
Animals

@article {pmid40431550,
year = {2025},
author = {Elbir, H},
title = {No Genomic Signatures Were Found in Escherichia coli Isolates from Camels With or Without Clinical Endometritis.},
journal = {Veterinary sciences},
volume = {12},
number = {5},
pages = {},
doi = {10.3390/vetsci12050457},
pmid = {40431550},
issn = {2306-7381},
abstract = {Clinical endometritis is a leading cause of infertility in she-camels. We commonly isolate E. coli from camel uteri with and without endometritis during our routine diagnosis of conception failure. From an epidemiological standpoint, it is critical to know if certain E. coli genotypes and virulence factors are specifically associated with endometritis. Thus, we aimed to compare the abundance of virulence elements and genotypes in uterine E. coli from camels with and without endometritis and understand their evolution. For this investigation, we retrieved data from the genomes of 28 E. coli isolates from humans, cats, dogs, horses, cows, and birds and 14 sequenced genomes of camel uterine E. coli isolates. We found no specific E. coli genotype or virulence factor associated with endometritis. Instead, multiple genotypes and high genomic diversity were observed. Moreover, horizontal gene transfer driven by genomic islands and plasmids contributed to the genetic diversity of the isolates, resulting in the acquisition of virulence genes, metabolic characteristics, and antibiotic resistance determinants to trimethoprim, sulfonamide, streptomycin, and tetracycline. Additionally, the phylogenetic position of the E. coli isolates from camel uteri suggests that they originated from intestinal strains. In conclusion, there was no evidence of E. coli specialization, and E. coli alone may not be able to develop endometritis, as other factors are required. Also, we elucidated the mechanism behind the diversity of the gene repertoire of E. coli isolated from camel uteri. These findings provide insight into the evolutionary origins of E. coli isolates from camel uteri.},
}

@article {pmid40431301,
year = {2025},
author = {Wang, K and Zhang, C and Munang'andu, HM and Xu, C and Cai, W and Yan, X and Tao, Z},
title = {Comparative Genomic Analysis of Two Vibrio harveyi Strains from Larimichthys crocea with Divergent Virulence Profiles.},
journal = {Microorganisms},
volume = {13},
number = {5},
pages = {},
doi = {10.3390/microorganisms13051129},
pmid = {40431301},
issn = {2076-2607},
support = {42376108//National Natural Science Foundation of China/ ; },
abstract = {Vibrio harveyi is a significant pathogen in marine aquaculture, causing vibriosis in various marine species. This study presents a comparative genomic analysis of two V. harveyi strains, N8T11 and 45T2, which exhibit differing virulence profiles. Virulence assays revealed that N8T11 caused 92% mortality in infected fish, while 45T2 resulted in 0% mortality. Whole-genome sequencing revealed that strain N8T11 harbors five plasmids (pN8T11a, pN8T11b, pN8T11c, pN8T11d and pN8T11e) absent in 45T2, encoding genes potentially linked to virulence, such as siderophore-mediated iron acquisition and stress response mechanisms. Pan-genome analysis highlighted substantial genomic plasticity within V. harveyi, with mobile genetic elements, including plasmids and prophages, contributing to horizontal gene transfer. Conjugation experiments demonstrated that all five N8T11 plasmids can transfer to 45T2 with efficiencies up to 87%, with pN8T11b remaining stable across multiple subcultures, enabling the dissemination of virulence-associated genes. These findings suggest that plasmid-mediated gene transfer plays a role in the virulence variability observed between V. harveyi strains. This study contributes to understanding the genomic factors underlying pathogenicity in V. harveyi and provides insights for future research aimed at controlling vibriosis in aquaculture.},
}

@article {pmid40431267,
year = {2025},
author = {Duarte, MLO and Rodrigues, DLN and de Lima, GBV and Ariute, JC and Gouveia, GV and de Simoni Gouveia, JJ and Azevedo, V and Brenig, B and Guédon, E and Tavares, GC and da Costa, MM and Pereira, UP and Aburjaile, FF},
title = {In Silico Characterization of Resistance and Virulence Genes in Aeromonas jandaei Strains Isolated from Oreochromis niloticus in Brazil.},
journal = {Microorganisms},
volume = {13},
number = {5},
pages = {},
doi = {10.3390/microorganisms13051094},
pmid = {40431267},
issn = {2076-2607},
support = {408898/2022-4//CNPq/MCTI/CT-Saúde nº 52/2022/ ; },
abstract = {Understanding the genetic characteristics of Aeromonas jandaei in Brazilian aquaculture is crucial for developing effective control strategies against this fish pathogen. The present study conducted a genomic analysis of Brazilian A. jandaei strains with the objective of investigating their virulence potential and resistance profiles. Four Brazilian isolates were subjected to sequencing, and comparative genomic analyses were conducted in conjunction with 48 publicly available A. jandaei genomes. The methods employed included quality assessment, de novo assembly, annotation, and analyses of antimicrobial resistance and virulence factors. The results demonstrated the presence of fluoroquinolone resistance genes within the core genome. Notably, these antibiotics are not authorized for use in aquaculture in Brazil, suggesting that their resistance determinants may originate from other selective pressures or horizontal gene transfer unrelated to aquaculture practices. The analysis identified significant virulence mechanisms, including T2SS, T3SS, and notably T6SS (vgrG3 gene), which was more prevalent in Brazilian isolates. Additionally, genes associated with motility, adhesion, and heavy metal resistance were identified. These findings highlight the enhanced adaptability of Brazilian A. jandaei strains and raise concerns about antimicrobial resistance in aquaculture, emphasizing the need for improved regulatory oversight and control strategies.},
}

@article {pmid40428151,
year = {2025},
author = {Müller, GA},
title = {The Transformation Experiment of Frederick Griffith II: Inclusion of Cellular Heredity for the Creation of Novel Microorganisms.},
journal = {Bioengineering (Basel, Switzerland)},
volume = {12},
number = {5},
pages = {},
doi = {10.3390/bioengineering12050532},
pmid = {40428151},
issn = {2306-5354},
abstract = {So far, synthetic biology approaches for the construction of artificial microorganisms have fostered the transformation of acceptor cells with genomes from donor cells. However, this strategy seems to be limited to closely related bacterial species only, due to the need for a "fit" between donor and acceptor proteomes and structures. "Fitting" of cellular regulation of metabolite fluxes and turnover between donor and acceptor cells, i.e. cybernetic heredity, may be even more difficult to achieve. The bacterial transformation experiment design 1.0, as introduced by Frederick Griffith almost one century ago, may support integration of DNA, macromolecular, topological, cybernetic and cellular heredity: (i) attenuation of donor Pneumococci of (S) serotype fosters release of DNA, and hypothetically of non-DNA structures compatible with subsequent transfer to and transformation of acceptor Pneumococci from (R) to (S) serotype; (ii) use of intact donor cells rather than of subcellular or purified fractions may guarantee maximal diversity of the structural and cybernetic matter and information transferred; (iii) "Blending" or mixing and fusion of donor and acceptor Pneumococci may occur under accompanying transfer of metabolites and regulatory circuits. A Griffith transformation experiment design 2.0 is suggested, which may enable efficient exchange of DNA as well as non-DNA structural and cybernetic matter and information, leading to unicellular hybrid microorganisms with large morphological/metabolic phenotypic differences and major features compared to predeceding cells. The prerequisites of horizontal gene and somatic cell nuclear transfer, the molecular mechanism of transformation, the machineries for the biogenesis of bacterial cytoskeleton, micelle-like complexes and membrane landscapes are briefly reviewed on the basis of underlying conceptions, ranging from Darwin's "gemmules" to "stirps", cytoplasmic and "plasmon" inheritance, "rhizene agency", "communicology", "transdisciplinary membranology" to up to Kirschner's "facilitated variation".},
}

@article {pmid40426537,
year = {2025},
author = {Touaitia, R and Mairi, A and Ibrahim, NA and Basher, NS and Idres, T and Touati, A},
title = {Staphylococcus aureus: A Review of the Pathogenesis and Virulence Mechanisms.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {5},
pages = {},
doi = {10.3390/antibiotics14050470},
pmid = {40426537},
issn = {2079-6382},
support = {grant number IMSIU-DDRSP2501//Deanship of Scientific Research at Imam Mohammad Ibn Saud Islamic University (IMSIU)/ ; },
abstract = {Staphylococcus aureus is a formidable human pathogen responsible for infections ranging from superficial skin lesions to life-threatening systemic diseases. This review synthesizes current knowledge on its pathogenesis, emphasizing colonization dynamics, virulence mechanisms, biofilm formation, and antibiotic resistance. By analyzing studies from PubMed, Scopus, and Web of Science, we highlight the pathogen's adaptability, driven by surface adhesins (e.g., ClfB, SasG), secreted toxins (e.g., PVL, TSST-1), and metabolic flexibility in iron acquisition and amino acid utilization. Nasal, skin, and oropharyngeal colonization are reservoirs for invasive infections, with biofilm persistence and horizontal gene transfer exacerbating antimicrobial resistance, particularly in methicillin-resistant S. aureus (MRSA). The review underscores the clinical challenges of multidrug-resistant strains, including vancomycin resistance and decolonization strategies' failure to target single anatomical sites. Key discussions address host-microbiome interactions, immune evasion tactics, and the limitations of current therapies. Future directions advocate for novel anti-virulence therapies, multi-epitope vaccines, and AI-driven diagnostics to combat evolving resistance. Strengthening global surveillance and interdisciplinary collaboration is critical to mitigating the public health burden of S. aureus.},
}

@article {pmid40426515,
year = {2025},
author = {Olanrewaju, TO and Dooley, JSG and Coleman, HM and McGonigle, C and Arnscheidt, J},
title = {Bacterivorous Ciliate Tetrahymena pyriformis Facilitates vanA Antibiotic Resistance Gene Transfer in Enterococcus faecalis.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {5},
pages = {},
doi = {10.3390/antibiotics14050448},
pmid = {40426515},
issn = {2079-6382},
abstract = {Background: Wastewater treatment plants (WWTPs) are hotspots for the emergence and spread of antibiotic resistance genes (ARGs). In activated sludge treatment systems, bacterivorous protozoa play a crucial role in biological processes, yet their impact on the horizontal gene transfer in Gram-positive enteric bacteria remains largely unexplored. This study investigated whether the ciliate Tetrahymena pyriformis facilitates the transfer of antibiotic resistance genes between Enterococcus faecalis strains. Methods: Conjugation assays were conducted under laboratory conditions using a vanA-carrying donor and a rifampicin-resistant recipient at an initial bacterial concentration of 10[9] CFU/mL and ciliate density of 10[5] N/mL. Results: Transconjugant numbers peaked at 2 h when experiments started with recipient bacteria harvested in the exponential growth phase, and at 24 h when bacteria were in the stationary phase. In both cases, vanA gene transfer frequency was highest at 24 h (10[-4]-10[-5] CFU/mL), and the presence of energy sources increased gene transfer frequency by one order of magnitude. Conclusions: These findings suggest that ciliate grazing may contribute to vanA gene transfer in WWTP effluents, potentially facilitating its dissemination among permissive bacteria. Given the ecological and public health risks associated with vanA gene persistence in wastewater systems, understanding protozoan-mediated gene transfer is crucial for mitigating the spread of antibiotic resistance in aquatic environments.},
}

@article {pmid40425158,
year = {2025},
author = {Chrismas, N and Bird, K and Laundon, D and Lieng, C and Hesketh-Best, P and Cunliffe, M},
title = {Adaptive traits for chitin utilization in the saprotrophic aquatic chytrid fungus Rhizoclosmatium globosum.},
journal = {Proceedings. Biological sciences},
volume = {292},
number = {2047},
pages = {20250337},
doi = {10.1098/rspb.2025.0337},
pmid = {40425158},
issn = {1471-2954},
support = {//HORIZON EUROPE European Research Council/ ; //Natural Environment Research Council/ ; },
mesh = {*Chitin/metabolism ; Chitinases/metabolism/genetics ; *Chytridiomycota/genetics/physiology/metabolism/enzymology ; Genome, Fungal ; Phylogeny ; Fungal Proteins/metabolism/genetics ; },
abstract = {The Chytridiomycota (chytrids) are early diverging fungi, many of which function in ecosystems as saprotrophs; however, associated adaptive traits are poorly understood. We focused on chitin degradation, a common ecosystem function of aquatic chytrids, using the model chitinophilic Rhizoclosmatium globosum and comparison of other chytrid genomes. Zoospores are chemotactic to the chitin monomer N-acetylglucosamine and accelerate development when grown with chitin. The R. globosum secretome is dominated by different glycoside hydrolase (GH) family GH18 chitinases, with abundance matching reciprocal transcriptome mRNA sequences. Models of the secreted chitinases indicate a range of sizes and domain configurations. Along with R. globosum, the genomes of other chitinophilic chytrids also have expanded inventories of GH-encoding genes responsible for chitin processing. Several R. globosum GH18 chitinases have bacteria-like chitin-binding module domains, also present in the genomes of other chitinophilic chytrids yet absent in non-chitinophilic chytrids. Chemotaxis, increased abundance and diversity of secreted chitinases, complemented with the acquisition of novel chitin-binding capability, are probably adaptive traits that facilitate chitin saprotrophy. Our study reveals the underpinning mechanisms that have supported the niche expansion of some chytrids to utilize lucrative chitin-rich particles in aquatic ecosystems and is a demonstration of the adaptive ability of this successful fungal group.},
}

*Chitin/metabolism
Chitinases/metabolism/genetics
*Chytridiomycota/genetics/physiology/metabolism/enzymology
Genome, Fungal
Phylogeny
Fungal Proteins/metabolism/genetics

@article {pmid40422289,
year = {2025},
author = {Derriche, M and Nouvel, LX and Gaudino, M and Sagné, E and Simon, E and Robert, H and Pot, G and Meyer, G and de la Fe, C and Arfi, Y and Maillard, R and Citti, C and Baranowski, E},
title = {Bacterial conjugation in the ruminant pathogen Mycoplasma agalactiae is influenced by eukaryotic host factors.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0086825},
doi = {10.1128/aem.00868-25},
pmid = {40422289},
issn = {1098-5336},
abstract = {Horizontal gene transfer (HGT) plays a pivotal role in the evolution and adaptation of genome-reduced mycoplasmas. The conjugative properties of these organisms are key in this phenomenon but are largely understudied, particularly in vivo. In the present study, the ruminant pathogen Mycoplasma agalactiae was used as a model organism to document mycoplasma conjugation in environments of increasing complexity, from axenic to cell and organotypic culture conditions. Compared to axenic mating conditions, mycoplasma co-cultivation with goat epithelial cells or bovine precision-cut lung slices resulted in enhanced mating frequencies with high rates of M. agalactiae integrative and conjugative element (ICEA) self-dissemination. These results were conditioned by the presence of eukaryotic cells in the culture and influenced by competition between mating partners but were not limited to M. agalactiae, as similar results were observed with Mycoplasma bovis. Mycoplasma conjugation ex vivo was further characterized by analyzing mycoplasma chromosomal transfer (MCT), a newly discovered mechanism of horizontal exchange of chromosomal DNA that generates mosaic genomes. Compared to ICEA transfer, MCT was detected at lower rates under cell and organotypic culture conditions, suggesting a negative impact of these cellular environments on MCT or its progeny. Finally, mating experiments under nutrient-deprived conditions identified nucleotide stress as a potential factor influencing the modulation of mycoplasma conjugation by eukaryotic host cells. In conclusion, these results suggest that HGT in vivo is likely underestimated and provide valuable models to further study mycoplasma conjugation ex vivo.IMPORTANCEConjugation is an evolutionary shortcut that bacteria use to exchange genetic information with their neighbors. Despite the fast evolution rate of the genome-reduced mycoplasmas, their conjugative properties remain largely understudied, particularly in vivo. Here we used the ruminant pathogen Mycoplasma agalactiae to study how mycoplasmas conjugate in co-culture with host-derived cells and tissues. Interestingly, conjugation was stimulated when mycoplasmas were co-cultured with eukaryotic cells. This was documented by monitoring the self-propagation of a mobile genetic element known as integrative and conjugative element (ICE) and the exchange of chromosomal DNA leading to the formation of mosaic genomes. While ICE transfer was observed at high frequency, only a few mosaic genomes were detected in the presence of eukaryotic cells. Further data point toward nucleotide stress as a possible factor modulating mycoplasma conjugation in cellular environments. These results suggest that mycoplasma-host interactions may stimulate conjugation in vivo.},
}

@article {pmid40419976,
year = {2025},
author = {Vidal-Quist, JC and Ortego, F and Lambrecht, BN and Rombauts, S and Hernández-Crespo, P},
title = {Stage-specific transcriptomic analysis reveals insights into the development, reproduction and biological function of allergens in the European house dust mite Dermatophagoides pteronyssinus.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {527},
pmid = {40419976},
issn = {1471-2164},
support = {01M01521//Fonds Wetenschappelijk Onderzoek/ ; },
mesh = {Animals ; Female ; Male ; *Allergens/genetics/metabolism ; *Gene Expression Profiling ; *Dermatophagoides pteronyssinus/genetics/growth & development/physiology ; Reproduction/genetics ; *Transcriptome ; Gene Expression Regulation, Developmental ; },
abstract = {BACKGROUND: House dust mites (HDMs) such as Dermatophagoides pteronyssinus are major allergy elicitors worldwide, yet their gene expression across developmental stages remains underexplored. Herein, we report a comprehensive RNAseq analysis of larvae, nymphs, and adult males and females, mapped to a recently published high-quality genome with extended functional annotations.

RESULTS: Analysis of differentially expressed genes (DEG) revealed that female-biased expression was the most prevalent profile (16% of genes), while males exhibited the highest fold-change differences. DEG data, combined with network clustering and functional enrichment analysis, highlighted distinct genes and biological processes for each stage and sex: females showed upregulation of genes related to cell division and oogenesis, with vitellogenins among the most abundant transcripts; males exhibited increased expression of genes encoding putative seminal fluid proteins (e.g. endopeptidases, serpins, antimicrobial peptides), and those involved in reproductive regulation (e.g. testis-specific serine kinases); while juveniles displayed enhanced expression of genes related to energy metabolism and growth. Further analysis of endocrine pathways revealed non-canonic mechanisms compared to insect models, particularly in ecdysteroid and sesquiterpenoid biosynthesis and regulation. Expression patterns in genes involved in cuticle formation were also identified, reflecting their role in developmental transitions and sexual differentiation. Allergen and allergen-related gene expression showed an overall increase in feeding juveniles, as well as sex-biased expression, with Der p 27 upregulated in females. These findings provide insight into the physiological roles of allergens in digestion, immunity, and muscle formation, among other functions. Additionally, seven new horizontally transferred genes, including a DNA-repair photolyase linked to females, and novel multigene families (e.g. 119 male-specific beta-propeller proteins, 70 hypothetical cuticular proteins, 23 tetraspanin-like proteins, 5 female-associated putative odorant-binding proteins) were identified.

CONCLUSIONS: This study provides the first genome-wide transcriptomic analysis of a HDM across life stages and sexes, expanding our understanding of the molecular mechanisms underlying mite development, sexual reproduction, and allergen expression. The generated data, fully available via supplementary spreadsheet and the ORCAE online platform, provide a valuable foundation for future allergy research and the development of new mite control strategies.},
}

Animals
Female
Male
*Allergens/genetics/metabolism
*Gene Expression Profiling
*Dermatophagoides pteronyssinus/genetics/growth & development/physiology
Reproduction/genetics
*Transcriptome
Gene Expression Regulation, Developmental

@article {pmid40305681,
year = {2025},
author = {Bennett, BD and Meier, DAO and Lanclos, VC and Asrari, H and Coates, JD and Thrash, JC},
title = {Polyhydroxybutyrate production by freshwater SAR11 (LD12).},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
doi = {10.1093/ismejo/wraf087},
pmid = {40305681},
issn = {1751-7370},
mesh = {Phylogeny ; *Fresh Water/microbiology ; *Hydroxybutyrates/metabolism ; *Polyhydroxyalkanoates/metabolism/biosynthesis ; Escherichia coli/genetics/metabolism ; *Alphaproteobacteria/metabolism/genetics/classification ; Bacterial Proteins/genetics/metabolism ; Gene Transfer, Horizontal ; Polyhydroxybutyrates ; },
abstract = {SAR11 bacteria (order Pelagibacterales) are oligotrophs and often the most abundant bacterioplankton in aquatic environments. A subset of sequenced SAR11 genomes, predominantly in the brackish and freshwater SAR11 subclades, contain homologs of pha genes, which in other organisms confer the ability to store carbon and energy via polyhydroxyalkanoate (PHA) polymers. Here, we investigated the relevance of PHA production to SAR11 biology. Phylogenetics showed that Pha proteins occurred on a long branch and provided evidence for origin at the common ancestor of the brackish IIIa and freshwater LD12 subclades, followed by horizontal transfer within SAR11. Using the LD12 representative "Candidatus Fonsibacter ubiquis" strain LSUCC0530, we found that many LSUCC0530 cells contained a single Nile red-staining granule, confirmed that the cells produced polyhydroxybutyrate, a common form of PHA, and estimated the total polyhydroxybutyrate content in the cells. We heterologously expressed the LSUCC0530 phaCAB locus in Escherichia coli, finding it to be functional and the likely origin of the polyhydroxybutyrate. We also determined that, irrespective of changes to carbon, nitrogen, and phosphorus concentrations, a similar fraction of LSUCC0530 cells generated polyhydroxybutyrate granules and expression of the phaCAB locus remained constant. We suggest that polyhydroxybutyrate synthesis in LSUCC0530 may be constitutively active due to the slow growth dynamics and minimal regulation that characterize SAR11 bacteria. This work characterizes polymer storage in SAR11, providing new insights into the likely fitness advantage for cells harboring this metabolism.},
}

Phylogeny
*Fresh Water/microbiology
*Hydroxybutyrates/metabolism
*Polyhydroxyalkanoates/metabolism/biosynthesis
Escherichia coli/genetics/metabolism
*Alphaproteobacteria/metabolism/genetics/classification
Bacterial Proteins/genetics/metabolism
Gene Transfer, Horizontal
Polyhydroxybutyrates

@article {pmid40417658,
year = {2025},
author = {Bhuvaragavan, S and Sruthi, K and Nivetha, R and Keerthana, CB and Marieshwari, BN and Janarthanan, S},
title = {PacBio-based de novo transcriptomics of the coconut rhinoceros beetle Oryctes rhinoceros identifies physiologically important full-length genes and sheds insights into the molecular relationship (chitin synthase) between Scarabaeidae (Coleoptera) and Hymenoptera.},
journal = {3 Biotech},
volume = {15},
number = {6},
pages = {182},
pmid = {40417658},
issn = {2190-572X},
abstract = {UNLABELLED: The sparser molecular data in non-model insects such as Oryctes rhinoceros prompted us to investigate and identify its physiologically important genes using the novel PacBio Iso-Seq Sequel II platform with single-molecule real-time (SMRT) technology. SMRT library was prepared from various tissues and sequenced. In total, 16,916,297 subreads clustered into 17,547 contigs which collapsed to form 8708 full-length sequences out of which 4352 functionally annotated transcripts were identified. Genes involved in innate immunity, growth and development, hormonal regulation, cellular process, peritrophic membrane, melanogenesis, integument, circulation, cuticle formation, glycan metabolism, etc., were identified. The transcripts' orthologues were identified predominantly in Coleoptera and Hymenoptera in which chitin synthase (CHS), toll, haemocytin, serine protease/limulus clotting factor c, vitellogenin and trehalose transporter exhibited significant molecular relationships between these two insect orders. Chitin synthase 8 (CHS-8) found in ant has been identified for the first time in the order Coleoptera. (O. rhinoceros) at the translational level and projected a potential to explore evolution (horizontal gene transfer) of CHS in insects. The findings will bridge the molecular data between the genome and transcriptome of O. rhinoceros, thus helping develop molecular targets for its control and management.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-025-04348-9.},
}

@article {pmid40409398,
year = {2025},
author = {Zhang, Y and Zou, D and Ji, Y and Liu, S and Jiang, Y and Fan, F and Zou, C},
title = {The combined effect of microplastics and tetracycline on soil microbial communities and ARGs.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {126482},
doi = {10.1016/j.envpol.2025.126482},
pmid = {40409398},
issn = {1873-6424},
abstract = {Microplastics (MPs), due to their difficult degradation and adsorption characteristics, are highly prone to form compound contamination with antibiotic residues in the soil environment, thereby disrupting the soil ecosystem. To address this issue of compound contamination, this study investigated the effects of compound contamination composed of three common MPs-polyethylene (PE), polyamide (PA), and polyvinyl chloride (PVC)-combined with tetracycline(TC), on the structure of soil microbial communities and resistance genes. The results showed that the effects of composite pollution on soil physicochemical properties, enzyme activities, bacterial communities, and antibiotic resistance genes (ARGs) were more significant compared to single-contaminant pollution. Among the composite contaminants, TC combined with PVC and PE significantly increased the absolute abundance of the tetC gene, while the composite contamination of TC with PA had the greatest effect on bacterial diversity. This also increased the relative abundance of the phylum Actinobacteria and significantly affected the relative abundance of the phylum Ascomycetes. In addition, significant correlations were found between soil physicochemical properties, enzyme activities, microbial communities, and ARGs. A positive correlation between the intl1 integrator gene and all target genes suggests that horizontal gene transfer contributes to the enrichment of ARGs. Furthermore, the bacterial genera correlated with ARGs-Ascomycetes, Acidobacteria, Actinobacteria, and Anaplasma-are the major bacterial hosts for ARGs in soil samples. This study provides data to support the investigation of combined microplastic and antibiotic contamination in soil.},
}

@article {pmid40408144,
year = {2025},
author = {Quiñonero-Coronel, MDM and Cabello-Yeves, PJ and Haro-Moreno, JM and Rodriguez-Valera, F and Garcillán-Barcia, MP},
title = {The type IV secretion system of Patescibacteria is homologous to the bacterial monoderm conjugation machinery.},
journal = {Microbial genomics},
volume = {11},
number = {5},
pages = {},
doi = {10.1099/mgen.0.001409},
pmid = {40408144},
issn = {2057-5858},
mesh = {Phylogeny ; *Type IV Secretion Systems/genetics/metabolism ; Bacterial Proteins/genetics/metabolism ; *Conjugation, Genetic ; Computational Biology ; },
abstract = {The Candidate Phyla Radiation, also known as Patescibacteria, represents a vast and diverse division of bacteria that has come to light via culture-independent 'omics' technologies. Their limited biosynthetic capacity, along with evidence of their growth as obligate epibionts on other bacteria, suggests a broad reliance on host organisms for their survival. Nevertheless, our understanding of the molecular mechanisms governing their metabolism and lifestyle remains limited. The type IV secretion system (T4SS) represents a superfamily of translocation systems with a wide range of functional roles. T4SS genes have been identified in the Patescibacteria class Saccharimonadia as essential for their epibiotic growth. In this study, we used a comprehensive bioinformatics approach to investigate the diversity and distribution of T4SS within Patescibacteria. The phylogenetic analysis of the T4SS signature protein VirB4 suggests that most of these proteins cluster into a distinct monophyletic group with a shared ancestry to the MPFFATA class of T4SS. This class is found in the conjugative elements of Firmicutes, Actinobacteria, Tenericutes and Archaea, indicating a possible horizontal gene transfer from these monoderm micro-organisms to Patescibacteria. We identified additional T4SS components near virB4, particularly those associated with the MPFFATA class, as well as homologues of other T4SS classes, such as VirB2-like pilins, and observed their varied arrangements across different Patescibacteria classes. The absence of a relaxase in most of these T4SS clusters suggests that the system has been co-opted for other functions in Patescibacteria. The proximity of T4SS components to the origin of replication (gene dnaA) in some Patescibacteria suggests a potential mechanism for increased expression. The broad ubiquity of a phylogenetically distinct T4SS, combined with its chromosomal location, underscores the significance of T4SS in the biology of Patescibacteria.},
}

Phylogeny
*Type IV Secretion Systems/genetics/metabolism
Bacterial Proteins/genetics/metabolism
*Conjugation, Genetic
Computational Biology

@article {pmid40407872,
year = {2025},
author = {Suhajda, Á and Al-Nussairawi, M and Amara, I and Sörös, C and Tömösközi-Farkas, R and Kriszt, B and Farkas, M and Cserháti, M},
title = {Co-Occurrence of Beauvericin and Fumonisin Producing Ability of Fusarium Strains Isolated from Crop Plants in Hungary.},
journal = {Current microbiology},
volume = {82},
number = {7},
pages = {302},
pmid = {40407872},
issn = {1432-0991},
support = {TKP2021-NVA-22//"The feasibility of the circular economy during national defense activities" of 2021 Thematic Excellence Programme of the National Research Development and Innovation Office/ ; TKP2021-NVA-22//"The feasibility of the circular economy during national defense activities" of 2021 Thematic Excellence Programme of the National Research Development and Innovation Office/ ; TKP2021-NVA-22//"The feasibility of the circular economy during national defense activities" of 2021 Thematic Excellence Programme of the National Research Development and Innovation Office/ ; TKP2021-NVA-22//"The feasibility of the circular economy during national defense activities" of 2021 Thematic Excellence Programme of the National Research Development and Innovation Office/ ; TKP2021-NVA-22//"The feasibility of the circular economy during national defense activities" of 2021 Thematic Excellence Programme of the National Research Development and Innovation Office/ ; },
mesh = {*Depsipeptides/metabolism ; *Fusarium/metabolism/isolation & purification/genetics/classification ; *Fumonisins/metabolism/analysis ; *Zea mays/microbiology ; Hungary ; Mycotoxins/metabolism ; Fungal Proteins/genetics/metabolism ; *Crops, Agricultural/microbiology ; Peptide Synthases/genetics ; },
abstract = {Beauvericin (BEA) is an emerging mycotoxin with wide-ranging bioactivity (antimicrobial and insecticide), making it a potential target for drug and pesticide development. BEA primarily produced by Beauveria, Isaria, and Fusarium species. The BEA-producing abilities of a collection of 100 Fusarium strains isolated from maize were tested using a gene-specific primer (Beas_1, Beas_2) by PCR. Among all, 23 were found to have the beauvericin synthetase (BEAS) gene sequence, which is responsible for the production of BEA. Fusarium proliferatum (6) and F. verticillioides (14) strains were producing the highest BEA concentrations. The toxin-producing ability of the strains was investigated in small bioreactors. Parallel with BEA, the most frequent Fusarium toxins such as deoxynivalenol (DON), T2, HT-2, zearalenone (ZEA), fumonisin B1 (FB1), and fumonisin B2 (FB2) were also measured. Only FB1 and FB2 were observed above the detection limit, the coexistence of the FBs and BEA was measured in high concentration. In all BEA-producing strains, the FBs production could be detected. The highest BEA concentration was 3131 mg/kg, and the highest FB1 and FB2 concentrations were 4393 mg/kg and 1390 mg/kg, respectively. In the present study, the gene sequences responsible for the production of BEA in F. verticilloides isolates have not only been detected but also demonstrated with UHPLC-ESI-MS/MS to be capable of biosynthesis. From the phylogenic analysis of the BEAS gene sequences, the assumption could be made that the ability to produce BEA was conferred via horizontal gene transfer.},
}

*Depsipeptides/metabolism
*Fusarium/metabolism/isolation & purification/genetics/classification
*Fumonisins/metabolism/analysis
*Zea mays/microbiology
Hungary
Mycotoxins/metabolism
Fungal Proteins/genetics/metabolism
*Crops, Agricultural/microbiology
Peptide Synthases/genetics

@article {pmid40407325,
year = {2025},
author = {Mom, J and Valette, O and Pieulle, L and Pelicic, V},
title = {Unraveling the molecular mechanisms of DNA capture by the Com pilus in naturally transformable monoderm bacteria.},
journal = {mBio},
volume = {},
number = {},
pages = {e0085125},
doi = {10.1128/mbio.00851-25},
pmid = {40407325},
issn = {2150-7511},
abstract = {UNLABELLED: Transformation is a mechanism of horizontal gene transfer widespread in bacteria. The first step in transformation-capture of exogenous DNA-is mediated by surface-exposed filaments belonging to the type 4 filament (T4F) superfamily. How these protein polymers, composed of major and minor pilin subunits, interact with DNA remains poorly understood. Here, we address this question for the Com pilus, a widespread T4F mediating DNA capture in competent monoderm species. Our functional analysis, performed in Streptococcus sanguinis, was guided by a complete structural model of the Com pilus. We show that the major pilin ComGC does not bind DNA. In contrast, a systematic mutational analysis of electropositive residues exposed at the filament surface in the four minor pilins (ComGD, ComGE, ComGF, and ComGG) reveals that the interface between ComGD and ComGF is important for DNA capture. Sequential mutations in these two interacting subunits lead to complete abolition of transformation, without affecting piliation. We further demonstrate the physical interaction between ComGD and ComGF using disulfide crosslinking, upon mutagenesis of two strategically positioned residues into cysteines. A structural model of the Com pilus tip interacting with DNA recapitulates all these findings and highlights a novel mode of DNA-binding, conserved in hundreds of monoderm species.

IMPORTANCE: Bacteria are capable of evolving and diversifying very rapidly by acquiring new genetic material via horizontal gene transfer (HGT). Transformation is a widespread mechanism of HGT, which results from the capture of extracellular DNA by surface-exposed pili belonging to the type 4 filament (T4F) superfamily. How T4F-composed of major and minor pilins-interact with DNA remains poorly understood, especially in monoderm species that use a unique T4F for DNA capture, known as Com pilus or T4dP. The significance of this work is in characterizing a novel mode of DNA-binding by showing that the interface between two minor pilins, part of a tip-located complex of four pilins-found in different T4F-has been functionalized in monoderms to capture DNA. This is an evolutionary mechanism promoting the exceptional functional versatility of T4F.},
}

@article {pmid40403929,
year = {2025},
author = {Shin, JI and Park, SH and Park, C and Jung, SH and Lee, DG},
title = {Genomic investigation of NDM-1 producing Enterobacterales transmission in a South Korean hospital.},
journal = {Journal of global antimicrobial resistance},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jgar.2025.05.010},
pmid = {40403929},
issn = {2213-7173},
abstract = {OBJECTIVES: Prolonged detection of multispecies New Delhi metallo-β-lactamase (NDM)-1-producing Enterobacterales was observed previously in clinical and environmental samples collected from a South Korean hospital. This study aimed to investigate the transmission mechanisms of blaNDM-1 and assess the role of environmental reservoirs in its persistence.

METHODS: Epidemiological data were collected, and antibiotic susceptibility testing, carbapenemases detection, and whole-genome sequencing were performed on 42 clinical and 13 environmental isolates collected between November 2018 and February 2021, during the pre-outbreak, outbreak (July-September 2019), and post-outbreak periods. Long-read complete-genome sequencing was performed on four clinical and four environmental isolates to characterize plasmids carrying blaNDM-1 and associated mobile genetic elements (MGEs). Phylogenetic analyses were also performed.

RESULTS: blaNDM-1 was detected in 15 different species across clinical and environmental isolates. During the 2019 outbreak, clonal spread of Klebsiella pneumoniae and Klebsiella quasipneumoniae in the hospital was the primary mechanism of dissemination. During the post-outbreak period, horizontal gene transfer (HGT), mediated by the IncX3 plasmid carrying blaNDM-1, was the dominant transmission mechanism. This plasmid, detected in both clinical and environmental isolates, showed high genetic conservation with IncX3 plasmids reported worldwide. These plasmids contained conserved MGEs, including the IS26-dsbD-trpF-ble-blaNDM-1 structure.

CONCLUSION: This study highlights the dual roles of clonal spread and plasmid-mediated HGT in the dissemination of blaNDM-1 in hospital settings. The persistence of highly conserved IncX3 plasmids in environmental isolates underscores the complexity of carbapenem resistance control. Comprehensive infection control strategies targeting patient-to-patient transmission and environmental reservoirs are crucial for mitigating the spread of NDM-producing Enterobacterales.},
}

@article {pmid40402828,
year = {2025},
author = {Bremer, N and Martin, WF and Steel, M},
title = {Surprising effects of differential loss in genome evolution: the last-one-out.},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnaf051},
pmid = {40402828},
issn = {1574-6968},
abstract = {Gene loss is an important process in genome evolution, though its power is often underestimated. If a gene is present at the root of a phylogenetic tree and can be lost in one lineage across the tree, it can potentially be lost in all, leading to gene extinction. Just before gene extinction, there will be one lineage that still retains the gene, generating a 'last-one-out' distribution. Such an isolated gene presence will emulate the result of recent lateral gene acquisition, even though its distribution was generated by loss. How probable is it to observe 'last-one-out' distributions in real data? Here we mathematically derive this probability and find that it is surprisingly high, depending upon the tree and the gene loss rate. Examples from real data show that loss can readily account for observed frequencies of last-one-out gene distributions that might otherwise be attributed to lateral gene transfer.},
}

@article {pmid40402243,
year = {2025},
author = {Gozashti, L and Nakamoto, A and Russell, S and Corbett-Detig, R},
title = {Horizontal transmission of functionally diverse transposons is a major source of new introns.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {21},
pages = {e2414761122},
doi = {10.1073/pnas.2414761122},
pmid = {40402243},
issn = {1091-6490},
support = {R35GM128932//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; R00GM135583//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; GRFP//NSF | NSF Graduate Research Fellowship Program (GRFP)/ ; },
mesh = {*Introns/genetics ; *DNA Transposable Elements/genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Phylogeny ; Genome ; Retroelements/genetics ; Eukaryota/genetics ; Animals ; Humans ; },
abstract = {Since the discovery of spliceosomal introns in eukaryotic genomes, the proximate molecular and evolutionary processes that generate new introns have remained a critical mystery. Specialized transposable elements (TEs), introners, are thought to be one of the major drivers of intron gain in diverse eukaryotes. However, the molecular mechanism(s) and evolutionary processes driving introner propagation within and between lineages remain elusive. Here, we analyze 8,716 genomes, revealing 1,093 introner families in 201 species spanning 1.7 billion years of evolution. Introners are derived from functionally diverse TEs including families of terminal-inverted-repeat DNA TEs, retrotransposons, cryptons, and helitrons as well as mobile elements with unknown molecular mechanisms. We identify eight cases where introners recently transferred between divergent host species and show that giant viruses that integrate into genomes may facilitate introner transfer across lineages. We propose that ongoing intron gain is primarily a consequence of TE activity in eukaryotes, thereby resolving a key mystery of genome structure evolution.},
}

*Introns/genetics
*DNA Transposable Elements/genetics
*Evolution, Molecular
*Gene Transfer, Horizontal
Phylogeny
Genome
Retroelements/genetics
Eukaryota/genetics
Animals
Humans

@article {pmid40401976,
year = {2025},
author = {Qamar, MU and Sierra, R and Jabeen, K and Rizwan, M and Rashid, A and Dar, YF and Andrey, DO},
title = {Genomic characterization of plasmids harboring blaNDM-1, blaNDM-5, and blaNDM-7 carbapenemase alleles in clinical Klebsiella pneumoniae in Pakistan.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0235924},
doi = {10.1128/spectrum.02359-24},
pmid = {40401976},
issn = {2165-0497},
abstract = {UNLABELLED: Klebsiella pneumoniae is notorious for causing healthcare-associated infections, which become more complicated by the acquisition of blaNDM genes via mobile genetic elements. Although Pakistan is a well-established hot spot of blaNDM-positive K. pneumoniae, detailed molecular descriptions of blaNDM-carrying plasmids are scarce. Seven K. pneumoniae isolates harboring blaNDM were recovered from clinical sample sources during a 6 month period and tested for antimicrobial susceptibility. A long-read approach was used for whole-genome sequencing to obtain circularized plasmids and chromosomes for typing, annotation, and comparative analysis. The isolates were susceptible to colistin and tigecycline only among the tested antibiotics. We identified five sequence types (STs): ST11, ST16, ST716, ST464, and ST2856. Notably, three strains possessed the hypervirulent capsule KL2, while five were classified as O locus type O2a. Evidence of genetic diversity was further highlighted by the presence of four IncC plasmids harboring blaNDM-1, two IncX3 plasmids harboring blaNDM-5, and a single hybrid IncFIB/IncHI1B plasmid harboring blaNDM-7. These plasmids also carried additional antimicrobial resistance (AMR) genes conferring resistance to aminoglycosides, cephalosporins, and fluoroquinolones. We identified the plasmidome of the K. pneumoniae isolates and characterized the New Delhi metallo-beta-lactamase (NDM)-carrying plasmids. Genetic analysis confirmed the presence of blaNDM-1 and blaNDM-5 on broad host range plasmids and blaNDM-7 in a previously unreported hybrid plasmid backbone. We emphasized the critical role of plasmids in spreading blaNDM in the clinical setting in Pakistan. Hence, we stressed the urgent need for enhanced surveillance, not least in low-middle income countries, infection control measures, and adherence to the "Access," "Watch," and "Reserve" guidelines in antibiotics use.

IMPORTANCE: Infections caused by NDM-producing Klebsiella pneumoniae are a significant challenge to treat and represent a crucial health burden in low- and middle-income countries (LMICs). Most of the blaNDM are located on plasmids that promote horizontal gene transfer. However, there is a lack of comprehensive information on the genetic context of the NDM-carrying plasmids in Pakistan. This study presents a detailed analysis of seven NDM-plasmids in clinical K. pneumoniae isolates, shedding light on their high-risk sequence types and multiple resistance determinants. We also describe the plasmid-bearing NDM alleles (blaNDM-1, blaNDM-5, and blaNDM-7). Notably, we are the first to report blaNDM-7 on the hybrid IncFIB/IncHI1B backbone in Pakistan, a plasmid that has rarely been reported previously globally. Understanding the plasmid genomic landscape is paramount to comprehensively understanding the AMR scenario in this LMIC.},
}

@article {pmid40400687,
year = {2025},
author = {Guerrero-Flores, S and Contreras-Peruyero, H and Ibarra-Rodríguez, JM and Lovaco-Flores, JA and Nieto-de la Rosa, FS and Fontove-Herrera, F and Sélem-Mojica, N},
title = {Topological data analysis captures horizontal gene transfer in antimicrobial resistance gene families among clinically relevant bacteria.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1461293},
pmid = {40400687},
issn = {1664-302X},
abstract = {Antibiotic resistance, projected to cause 10 million deaths annually by 2050, remains a critical health threat. Hospitals drive multidrug resistance via horizontal gene transfer. The 2023 Critical Assessment of Massive Data Analysis challenge presents resistance markers from 146 Johns Hopkins bacterial isolates, aiming to analyze resistomes without metadata or genomic sequences. Persistent homology, a topological data analysis method, effectively captures processes beyond vertical inheritance. A 1-hole is a topological feature representing a loop or gap in the data, where relationships form a circular structure rather than a linear one. Unlike vertical inheritance, which lacks topological 1-holes, horizontal gene transfer generates distinct patterns. Since antimicrobial resistance genes often spread via horizontal gene transfer, we simulated vertical and horizontal inheritance in bacterial resistomes. The number of 1-holes from simulations and a documented horizontal gene transfer case was analyzed using persistence barcodes. In a simulated population of binary sequences, we observed that, on average, two 1-holes form for every three genomes undergoing horizontal gene transfer. Using a presence-absence gene table, we confirmed the existence of 1-holes in a documented case of horizontal gene transfer between two bacterial genera in a Pittsburgh hospital. Notably, the Critical Assessment of Massive Data Analysis resistomes of Klebsiella and Escherichia exhibit 1-holes, while Enterobacter shows none. Lastly, we provide a mathematical example of a non-tree-like space that contains no 1-holes. Persistent homology provides a framework for uncovering complex clinical patterns, offering an alternative to understanding resistance mobility using presence-absence data, which could be obtained through methods beyond genomic sequencing.},
}

@article {pmid40400517,
year = {2025},
author = {Ohata, Y and Sugimoto, TN and Wybouw, N and Tagami, Y},
title = {Suppression of cytoplasmic incompatibility in the leaf-mining fly Liriomyza sativae with a nuclear Wolbachia insert.},
journal = {Royal Society open science},
volume = {12},
number = {5},
pages = {242137},
pmid = {40400517},
issn = {2054-5703},
abstract = {Cytoplasmic incompatibility (CI) drives maternally transmitted endosymbionts such as Wolbachia through insect populations by inducing embryonic mortality when infected males fertilize uninfected females. CI is controlled by Wolbachia cif operons that are categorized into multiple phylogenetic types. CI strength is further shaped by poorly understood host factors, including development and genetic background. To study the strength of CI across different host species, we genotyped a Japanese field population of Liriomyza sativae. By uncovering paternal transmission of Wolbachia genic elements, we collected strong evidence of horizontal genome transfer, including Type I and Type V cif operons, from Wolbachia into the nuclear genome of L. sativae. We established a transinfection of wLtri in L. sativae, a Wolbachia variant that induces strong CI in Liriomyza trifolii. No CI was observed in both intraspecific and interspecific reciprocal crosses with L. trifolii, suggesting that both uninfected females and infected males of L. sativae completely suppress wLtri-mediated CI. Our results raise the appealing hypothesis that host suppression of Wolbachia-induced CI might evolve owing to horizontal transfer of cif operons into the host nuclear genome.},
}

@article {pmid40398027,
year = {2025},
author = {Zhang, J and Li, B and Shen, Z and Zhang, Z and Feng, J and Wong, JWC},
title = {Antibiotic resistance patterns and cross-family ARG transfer in families Burkholderiaceae and Sphingomonadaceae: A large-scale genome-wide analysis of over 10 K genomes.},
journal = {Journal of hazardous materials},
volume = {494},
number = {},
pages = {138642},
doi = {10.1016/j.jhazmat.2025.138642},
pmid = {40398027},
issn = {1873-3336},
abstract = {Members of Burkholderiaceae and Sphingomonadaceae play an active role in pollutant degradation, yet their antibiotic resistance risks are frequently overlooked. This study analyzed 9406 Burkholderiaceae and 2343 Sphingomonadaceae genomes to investigate the distribution, horizontal gene transfer (HGT), and co-occurrence patterns of antibiotic resistance genes (ARGs) and metal resistance genes (MRGs). ARGs were prevalent in Burkholderiaceae (93.2 % of genomes), dominated by bacitracin (89.0 %), multidrug (88.1 %), and beta-lactam (40.5 %) resistance, while Sphingomonadaceae exhibited lower ARG prevalence (11.6 %). Notably, Burkholderia and Caballeronia displayed high multidrug resistance (10.1 ARGs per genome) and frequent ARG-MRG co-occurrence (84.4 %). Strong ARG-MRG-MGE correlations were observed in Burkholderiaceae, suggesting MGEs play a key role in resistance dissemination. Additionally, ARGs correlated with metabolic genes, linking metabolic versatility to resistance. Genes like capO (chloramphenicol oxidase) and blaTEM-116 (beta-lactamase) were shared among distantly related genera, while mcr-5.1 (MCR phosphoethanolamine transferase) co-occurred with MRGs across Cupriavidus species, highlighting HGT and co-selection risks. ARG transfer between Burkholderiaceae, Sphingomonadaceae and clinical pathogens was frequent (114-1306 events/10,000 genome pairs), with sulfonamide resistance dominating (51.3 % of HGT). These findings highlight Burkholderiaceae and Sphingomonadaceae as critical reservoirs of resistance genes and emphasize the need for enhanced surveillance and mitigation strategies to curb the spread of multidrug resistance.},
}

@article {pmid40298401,
year = {2025},
author = {Pan, T and Li, Q},
title = {Mobile genetic elements in Klebsiella pneumoniae.},
journal = {Journal of bacteriology},
volume = {207},
number = {5},
pages = {e0001225},
doi = {10.1128/jb.00012-25},
pmid = {40298401},
issn = {1098-5530},
mesh = {*Klebsiella pneumoniae/genetics/pathogenicity/drug effects ; *Interspersed Repetitive Sequences ; Humans ; Virulence/genetics ; Anti-Bacterial Agents/pharmacology ; Gene Transfer, Horizontal ; Plasmids/genetics ; Klebsiella Infections/microbiology ; Genome, Bacterial ; DNA Transposable Elements ; Drug Resistance, Multiple, Bacterial ; },
abstract = {Klebsiella pneumoniae is a clinically important pathogenic bacteria that poses a serious threat to human health. In particular, the emergence of hypervirulent and multidrug-resistant K. pneumoniae has posed great challenges in clinical anti-infective therapy. In the K. pneumoniae genome, mobile genetic elements (MGEs), such as plasmids, prophages, transposons, and insertion sequences, enhance bacterial viability and adaptation by mediating the horizontal transfer of virulence genes, antibiotic resistance genes, and other adaptive genes. This paper reviews the types and characteristics of the main MGEs in K. pneumoniae, focusing on their effects on bacterial virulence and antibiotic resistance, with the aim of providing clues for developing infection control measures and new antibacterial drugs.},
}

*Klebsiella pneumoniae/genetics/pathogenicity/drug effects
*Interspersed Repetitive Sequences
Humans
Virulence/genetics
Anti-Bacterial Agents/pharmacology
Gene Transfer, Horizontal
Plasmids/genetics
Klebsiella Infections/microbiology
Genome, Bacterial
DNA Transposable Elements
Drug Resistance, Multiple, Bacterial

@article {pmid40397871,
year = {2025},
author = {Granato, ET and Palmer, JD and Kirk, C and Sharp, C and Shillcock, G and Foster, KR},
title = {Horizontal gene transfer of molecular weapons can reshape bacterial competition.},
journal = {PLoS biology},
volume = {23},
number = {5},
pages = {e3003095},
doi = {10.1371/journal.pbio.3003095},
pmid = {40397871},
issn = {1545-7885},
mesh = {*Gene Transfer, Horizontal ; *Escherichia coli/genetics ; Plasmids/genetics ; Colicins/genetics ; *Bacteria/genetics ; },
abstract = {Bacteria commonly use molecular weaponry to kill or inhibit competitors. Genes encoding many weapons and their associated immunity mechanisms can be transmitted horizontally. These transfer events are striking because they appear to undermine bacterial weapons when given to competing strains. Here, we develop an ecological model of bacterial warfare to understand the impacts of horizontal gene transfer. Our model predicts that weapon gene transfer from an attacker to a target strain is possible, but will typically occur at a low rate such that transfer has a negligible impact on competition outcomes. We tested the model empirically using a transmissible plasmid encoding colicin E2, a potent antibacterial toxin produced by Escherichia coli. As predicted by the model, we find that toxin plasmid transfer is feasible during warfare, but the resulting transconjugants remain rare. However, exploring the model further reveals realistic conditions where transfer is predicted to have major impacts. Specifically, the model predicts that whenever competing strains have access to unique nutrients, transconjugants can proliferate and reach high abundances. In support of these predictions, short- and long-term experiments show that transconjugants can thrive when nutrient competition is relaxed. Our work shows how horizontal gene transfer can reshape bacterial warfare in a way that benefits a weapon gene and strains that receive it. Interestingly, we also find that there is little cost to a strain that transfers a weapon gene, which is expected to further enable the horizontal gene transfer of molecular weapons.},
}

*Gene Transfer, Horizontal
*Escherichia coli/genetics
Plasmids/genetics
Colicins/genetics
*Bacteria/genetics

@article {pmid40396743,
year = {2025},
author = {Zhang, T and Han, Y and Peng, Y and Deng, Z and Shi, W and Xu, X and Wu, Y and Dong, X},
title = {The risk of pathogenicity and antibiotic resistance in deep-sea cold seep microorganisms.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0157124},
doi = {10.1128/msystems.01571-24},
pmid = {40396743},
issn = {2379-5077},
abstract = {UNLABELLED: Deep-sea cold seeps host high microbial biomass and biodiversity that thrive on hydrocarbon and inorganic compound seepage, exhibiting diverse ecological functions and unique genetic resources. However, potential health risks from pathogenic or antibiotic-resistant microorganisms in these environments remain largely overlooked, especially during resource exploitation and laboratory research. Here, we analyzed 165 metagenomes and 33 metatranscriptomes from 16 global cold seep sites to investigate the diversity and distribution of virulence factors (VFs), antibiotic resistance genes (ARGs), and mobile genetic elements (MGEs). A total of 2,353 VFs are retrieved in 689 metagenome-assembled genomes (MAGs), primarily associated with indirect pathogenesis like adherence. In addition, cold seeps harbor nearly 100,000 ARGs, as important reservoirs, with high-risk ARGs (11.22%) presenting at low abundance. Compared to other environments, microorganisms in cold seeps exhibit substantial differences in VF and ARG counts, with potential horizontal gene transfer facilitating their spread. These virulome and resistome profiles provide valuable insights into the evolutionary and ecological implications of pathogenicity and antibiotic resistance in extreme deep-sea ecosystems. Collectively, these results indicate that cold seep sediments pose minimal public health risks, shedding light on environmental safety in deep-sea resource exploitation and research.

IMPORTANCE: In the "One Health" era, understanding pathogenicity and antibiotic resistance in vast and largely unexplored regions like deep-sea cold seeps is critical for assessing public health risks. These environments serve as critical reservoirs where resistant and virulent bacteria can persist, adapt, and undergo genetic evolution. The increasing scope of human activities, such as deep-sea mining, is disrupting these previously isolated ecosystems, heightening the potential for microbial exchange between deep-sea communities and human or animal populations. This interaction poses a significant risk for the dissemination of resistance and virulence genes, with potential consequences for global public health and ecosystem stability. This study offers the first comprehensive analysis of virulome, resistome, and mobilome profiles in cold seep microbial communities. While cold seeps act as reservoirs for diverse ARGs, high-risk ARGs are rare, and most VFs were low risk that contribute to ecological functions. These results provide a reference for monitoring the spread of pathogenicity and resistance in extreme ecosystems, informing environmental safety assessments during deep-sea resource exploitation.},
}

@article {pmid40390443,
year = {2025},
author = {Xu, M and Gao, P and Chen, HQ and Gao, Y and Xiong, SJ and Wang, XH},
title = {[Effects of Typical Microplastics on Methanogenesis and Antibiotic Resistance Genes in Anaerobic Digestion of Sludge].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {46},
number = {5},
pages = {3189-3199},
doi = {10.13227/j.hjkx.202405273},
pmid = {40390443},
issn = {0250-3301},
mesh = {*Sewage/microbiology/chemistry ; *Methane/metabolism/biosynthesis ; *Drug Resistance, Microbial/genetics ; Anaerobiosis ; *Microplastics ; *Waste Disposal, Fluid/methods ; Bioreactors/microbiology ; Bacteria/genetics ; },
abstract = {Waste sludge is an important carrier of antibiotic resistance genes （ARGs） and an important place for the enrichment of microplastics （MPs）. To explore the impacts of typical MPs on sludge recycling and harmless disposal, the effects of polyamide （PA）, polyethylene （PE）, and polypropylene （PP） MPs on the methanogenesis efficiency of anaerobic digestion were investigated. Meanwhile, based on metagenomic sequencing, the effects of MPs on ARGs, mobile genetic elements （MGEs）, microbial community structure, and host bacteria during anaerobic digestion were analyzed. The results showed that PA-MPs, PE-MPs, and PP-MPs increased the distribution of methane production by 2.2%, 22.3%, and 28.8%, respectively. MPs promoted methanation by improving the dissolution and hydrolysis efficiency of organic matter, and the enrichment of hydrogenotrophic methanogens by PP-MPs further improved the methanogenic efficiency. PA-MPs contributed to the removal of ARGs, while PE-MPs and PP-MPs had adverse effects on the reduction of ARGs. Horizontal gene transfer mediated by integron and insertion sequences was an important factor in the spread of ARGs. Proteobacteria was the key host leading to the diffusion of ARGs. The removal of pathogens from Bacteroidetes by anaerobic digestion contributed to the reduction of ARGs. The selective enrichment or inhibition of Arenimonas, Acinetobacter, Actinobacillus, Nitrospira, and other important host bacteria by MPs was the major cause for the difference in the removal effect of ARGs.},
}

*Sewage/microbiology/chemistry
*Methane/metabolism/biosynthesis
*Drug Resistance, Microbial/genetics
Anaerobiosis
*Microplastics
*Waste Disposal, Fluid/methods
Bioreactors/microbiology
Bacteria/genetics

@article {pmid40382874,
year = {2025},
author = {Miao, S and Zhang, Y and Wu, L and Wang, Y and Zuo, J},
title = {Resistance induction potency assessment of antibiotic production wastewater and associated resistome shaping mechanisms.},
journal = {Water research},
volume = {283},
number = {},
pages = {123811},
doi = {10.1016/j.watres.2025.123811},
pmid = {40382874},
issn = {1879-2448},
abstract = {Antibiotic production wastewater (APW) contains multiple substances known to select for and facilitate horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs); however, whether these substances can induce the evolution of antibiotic resistance in real wastewater environments and the fate of such resistance induction potency during the treatment process are poorly understood, nor are its relationship with wastewater quality parameters and function in shaping the antibiotic resistome. In this study, the impacts of filter-sterilized APW and municipal wastewater on the resistance selection of Escherichia coli and the transfer dynamics of conjugative RP4 plasmid-borne ARGs across indigenous sludge communities were evaluated. The resistance development and transfer processes were accelerated in APW owing to enhanced growth inhibition, oxidative stress, and membrane permeability, with antibiotic concentrations much lower than their minimum inhibition concentrations. The effects were reduced simultaneously with the removal of COD and NH3N, but APW effluents still exhibited significant resistance induction potency with wastewater quality parameters meeting discharge standards. In contrast, municipal wastewater did not result in any detectable changes. Based on the metagenomic assembly and binning, stronger resistance induction potency in the antibiotic production wastewater treatment plant endowed indigenous sludge and effluent with greater accumulation, genetic mobility, and pathogenic accessibility of ARGs than in the municipal wastewater treatment plant. Antibiotic resistome assembly was determined primarily by deterministic processes, driven jointly by resistance induction potency, mobilome variance, and microbiome shifts. These results provide novel insights into the application of bioassays to comprehensively evaluate the antibiotic resistance induction effects of APW and their relationships with the resistome to manage risks during the treatment process.},
}

@article {pmid39988053,
year = {2025},
author = {Monesi, N and Fernandes, GM and Valer, FB and Uliana, JVC and Trinca, V and Azzolini, AECS and Gorab, E and Alberici, LC},
title = {Identification and characterization of a laterally transferred alternative oxidase (AOX) in a terrestrial insect, the dipteran Pseudolycoriella hygida.},
journal = {Biochimie},
volume = {233},
number = {},
pages = {60-74},
doi = {10.1016/j.biochi.2025.02.007},
pmid = {39988053},
issn = {1638-6183},
mesh = {Animals ; *Mitochondrial Proteins/genetics/metabolism/antagonists & inhibitors ; *Oxidoreductases/genetics/metabolism/antagonists & inhibitors ; *Plant Proteins/genetics/metabolism ; *Diptera/enzymology/genetics ; Mitochondria/enzymology/metabolism ; *Gene Transfer, Horizontal ; *Insect Proteins/genetics/metabolism ; Phylogeny ; Salicylamides ; },
abstract = {Alternative oxidase (AOX) (EC 1.10.3.11) is a terminal oxidase in the mitochondrial inner membrane that branches the canonical electron transport system (ETS). AOX is ubiquitous in plants, frequently found in fungi and protists and presents a more sporadic distribution in metazoans. More recently, AOX has gained attention due to its potential application in gene therapy for treatment of mitochondrial diseases. Here we characterized the AOX in the basal Dipteran, Pseudolycoriella hygida using a combination of genomic analyses, molecular, functional and in vivo survival assays. AOX is a single copy gene that encodes three developmental stage specific protein isoforms. AOX localizes to the mitochondria in adult thoracic muscles, which present cyanide-resistant respiration that is sensitive to the AOX inhibitor salicylhydroxamic acid (SHAM). Both the cyanide-resistant respiration and AOX levels gradually increase during aging, but are not influenced by thermal stress. Thoracic mitochondria respire using substrates derived from several metabolic routes, such as pyruvate, proline, acylcarnitine, NADH and glycerol-3P, and present values of oxidative phosphorylation capacity ((P-L)/E = 0.70) and coupling (P/L = 4.35; L/E = 0.21). Adult flies exhibit a high survival resistance for SHAM-sensitive complex III inhibition. Together, our results demonstrate the presence of a functional AOX in a terrestrial arthropod and provide insights regarding AOX function in animals and evolution of respiratory systems in metazoans. Psl. hygida emerges as a natural and valuable model for comprehensive AOX research at the whole-organism level which complements models expressing the heterologous enzyme.},
}

Animals
*Mitochondrial Proteins/genetics/metabolism/antagonists & inhibitors
*Oxidoreductases/genetics/metabolism/antagonists & inhibitors
*Plant Proteins/genetics/metabolism
*Diptera/enzymology/genetics
Mitochondria/enzymology/metabolism
*Gene Transfer, Horizontal
*Insect Proteins/genetics/metabolism
Phylogeny
Salicylamides

@article {pmid40381794,
year = {2025},
author = {Yaikhan, T and Singkhamanan, K and Dechathai, T and Chukamnerd, A and Chusri, S and Pomwised, R and Wonglapsuwan, M and Surachat, K},
title = {Genome-based alert on a clinical Plesiomonas shigelloides PSU59 from Thailand: Resistance and virulence features.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {},
number = {},
pages = {105764},
doi = {10.1016/j.meegid.2025.105764},
pmid = {40381794},
issn = {1567-7257},
abstract = {Plesiomonas shigelloides, an aquatic Gram-negative bacterium, is increasingly recognized as an emerging pathogen with antimicrobial resistance (AMR) potential. This study provides a genome-based alert on P. shigelloides PSU59, isolated from a patient in Thailand. Whole-genome sequencing (WGS) revealed a 3.6 Mb draft genome (38 contigs, 51.9 % GC) encoding 3265 coding sequences and 129 RNA genes. Thirteen AMR genes were identified, including efflux pumps (adeF, tet(A)), target modifiers (dfrA1, sul2), and aminoglycoside-inactivating enzymes. Mobile genetic elements (MGEs) flanking resistance genes suggest horizontal gene transfer (HGT). Virulence analysis revealed 48 factors, notably flagellar genes (fliM, fliN, flhA) linked to motility. Phylogenetic comparison placed PSU59 in Clade 3, closely related to a food-derived strain. These results highlight the pathogenic and drug-resistant potential of P. shigelloides PSU59 and underscore the importance of genomic surveillance in tracking emerging threats among under-recognized pathogens.},
}

@article {pmid40381353,
year = {2025},
author = {Xin, Y and Zhang, J and Tang, Q and Wei, M and Zhu, L and Zhao, Y and Cui, Y and Sun, T and Wei, Y and Richnow, HH},
title = {Virus-host interactions driving the transfer of antibiotic resistance genes in a river-reservoir system under heavy rainfall.},
journal = {Journal of hazardous materials},
volume = {494},
number = {},
pages = {138605},
doi = {10.1016/j.jhazmat.2025.138605},
pmid = {40381353},
issn = {1873-3336},
abstract = {Global river systems are grappling with severe pollution from antibiotic resistance genes (ARGs), with river-reservoir (R-R) systems being a common feature in urban waterways. The intensified extreme rainfall events triggered by global climate change exacerbate the spread of ARGs posed by non-point source pollution and combined sewage overflows. This study employs a metagenomics approach to decipher the profile of ARGs and virus-host interactions driving their transfer under heavy rainfall in North Canal, Beijing, with extensive R-R systems. Results indicated that R-R systems contributed to ARGs reduction despite continuous discharge of treated wastewater into the North Canal. The ARGs assembly is predominantly governed by stochastic process, and heavy rainfall enhances the dispersal capability. Nonetheless, the deterministic process determined the assembly of both microbial and viral community. Heavy rainfall not only significantly increased the abundance and diversity of ARGs within the rivers with minimal change in the reservoir, but also promotes the horizontal gene transfer of ARGs with higher conjugative mobility. Although the species accumulation curves approached saturation, no viruses carrying ARGs were detected among the 23,835 non-redundant viral operational taxonomic units (vOTUs), and lytic phage-ARB interactions drove the ARGs reduction with higher VHRs, highlighting its contribution to the reduction of ARGs in R-R system after heavy rainfall.},
}

@article {pmid40379875,
year = {2025},
author = {Guédon, G and Charron-Bourgoin, F and Lacroix, T and Hamadouche, T and Soler, N and Douzi, B and Chiapello, H and Leblond-Bourget, N},
title = {Massive acquisition of conjugative and mobilizable integrated elements fuels Faecalibacterium plasticity and hints at their adaptation to the gut.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {17013},
pmid = {40379875},
issn = {2045-2322},
mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; Genome, Bacterial ; *Faecalibacterium/genetics/physiology ; *Conjugation, Genetic ; *Adaptation, Physiological/genetics ; Feces/microbiology ; Phylogeny ; },
abstract = {Faecalibacterium is one of the most abundant bacteria of the human gut microbiota of healthy adults and is recognized to have positive effects on health. Here, we precisely and comprehensively analyzed the conjugative mobilome of four complete Faecalibacterium genomes. Despite lacking any plasmid, these bacteria harbor a vast arsenal of 130 elements, including 17 integrative and conjugative elements (ICEs) and 83 integrative and mobilizable elements (IMEs), collectively comprising 14-23% of the genome. Genome comparison of two strains isolated from the same fecal sample (Faecalibacterium and Roseburia strains) revealed almost identical elements indicating that transfer of ICEs and IMEs shape gut microbiome. ICEs and IMEs from Faecalibacterium encode many and diverse predicted functions such as defense and stress response (phages, multidrug, antibiotics, oxidative stress, biliar salts, antimicrobial peptides), nutrient import and metabolisms (Fe[3+], carbohydrates) and riboflavin synthesis. This hints at their important role in the survival and adaptation of Faecalibacterium strains to the gut ecosystem. A rapid survey of 29 additional Faecalibacterium genomes uncovered many putative ICEs and IMEs, reinforcing their role in the rapid and massive evolution of Faecalibacterium genomes.},
}

*Gastrointestinal Microbiome/genetics
Humans
Genome, Bacterial
*Faecalibacterium/genetics/physiology
*Conjugation, Genetic
*Adaptation, Physiological/genetics
Feces/microbiology
Phylogeny

@article {pmid40378740,
year = {2025},
author = {Ding, Y and Dong, S and Ding, D and Chen, X and Xu, F and Niu, H and Xu, J and Fan, Y and Chen, R and Xia, Y and Qiu, X and Feng, H},
title = {Overlooked risk of dissemination and mobility of antibiotic resistance genes in freshwater aquaculture of the Micropterus salmoides in Zhejiang, China.},
journal = {Journal of hazardous materials},
volume = {494},
number = {},
pages = {138604},
doi = {10.1016/j.jhazmat.2025.138604},
pmid = {40378740},
issn = {1873-3336},
abstract = {Residual antibiotics in aquaculture ecosystems can exert selective pressures on bacterial communities, driving bacteria to acquire antibiotic resistance genes (ARGs) through gene mutations or horizontal gene transfer (HGT). This study investigated the antibiotic resistance risk in freshwater aquaculture ecosystems of Micropterus salmoides in Zhejiang Province. The results revealed that oxytetracycline, ciprofloxacin and florfenicol were up to 300 ng/L, and the proportion of multidrug-resistant genes varied from 32.20 % to 50.70 % in the surveyed aquaculture water. Additionally, approximately 9.80 % of all annotated ARGs were identified as possessing plasmid-mediated horizontal transfer risks. The ARGs host prediction revealed that Actinobacteria carried the highest abundance of ARGs, up to 159.38 (coverage, ×/Gb). Furthermore, the abundance of Paer_emrE, ksgA, ompR and golS were positively correlated with Chlorophyll a concentration (p < 0.05), suggesting that algal blooms might facilitate the evolution and transfer of ARGs. Correlations between ARG abundances and total phosphorus, total nitrogen, pH, electrical conductivity indicated that modulating water quality parameters may serve as a viable strategy to mitigate the eco-environmental risk of ARGs in aquaculture water. This study identified antibiotic resistance characteristics in freshwater aquaculture ecosystems of Micropterus salmoides in Zhejiang Province, establishing a foundation on managing antibiotic resistance risks in such aquaculture environments.},
}

@article {pmid40378350,
year = {2025},
author = {Bean, EL and Smith, JL and Grossman, AD},
title = {Identification of insertion sites for the integrative and conjugative element Tn916 in the Bacillus subtilis chromosome.},
journal = {PloS one},
volume = {20},
number = {5},
pages = {e0318964},
pmid = {40378350},
issn = {1932-6203},
mesh = {*Bacillus subtilis/genetics ; *Chromosomes, Bacterial/genetics ; *DNA Transposable Elements/genetics ; *Conjugation, Genetic ; Base Sequence ; Bacterial Proteins/metabolism/genetics ; Gene Transfer, Horizontal ; },
abstract = {Integrative and conjugative elements (ICEs) are found in many bacterial species and are mediators of horizontal gene transfer. Tn916 is an ICE found in several Gram-positive genera, including Enterococcus, Staphylococcus, Streptococcus, and Clostridioides (previously Clostridium). In contrast to the many ICEs that preferentially integrate into a single site, Tn916 can integrate into many sites in the host chromosome. The consensus integration motif for Tn916, based on analyses of approximately 200 independent insertions, is an approximately 16 bp AT-rich sequence. Here, we describe the identification and mapping of approximately 105 independent Tn916 insertions in the Bacillus subtilis chromosome. The insertions were distributed between 1,554 chromosomal sites, and approximately 99% of the insertions were in 303 sites and 65% were in only ten sites. One region, between ykuC and ykyB (kre), was a 'hotspot' for integration with ~22% of the insertions in that single location. In almost all of the top 99% of sites, Tn916 was found with similar frequencies in both orientations relative to the chromosome and relative to the direction of transcription, with a few notable exceptions. Using the sequences of all insertion regions, we determined a consensus motif which is similar to that previously identified for C. difficile. The insertion sites are largely AT-rich, and some sites overlap with regions bound by the nucleoid-associated protein Rok, a functional analog of H-NS of Gram-negative bacteria. Rok functions as a negative regulator of at least some horizontally acquired genes. We found that the presence or absence of Rok had little or no effect on insertion site specificity of Tn916.},
}

*Bacillus subtilis/genetics
*Chromosomes, Bacterial/genetics
*DNA Transposable Elements/genetics
*Conjugation, Genetic
Base Sequence
Bacterial Proteins/metabolism/genetics
Gene Transfer, Horizontal

@article {pmid40378191,
year = {2025},
author = {Policarpo, M and Salzburger, W and Maumus, F and Gilbert, C},
title = {Multiple horizontal transfers of immune genes between distantly related teleost fishes.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msaf107},
pmid = {40378191},
issn = {1537-1719},
abstract = {Horizontal gene transfer (HGT) is less frequent in eukaryotes than in prokaryotes, yet can have strong functional implications and was proposed as causal factor for major adaptations in several eukaryotic lineages. Most cases of eukaryote HGT reported to date are inter-domain transfers and few studies have investigated eukaryote-to-eukaryote HGTs. Here, we performed a large-scale survey of HGT among 242 species of ray-finned fishes. We found multiple lines of evidence supporting 19 teleost-to-teleost HGT events that involve 17 different genes in 11 teleost fish orders. The genes involved in these transfers show lower synonymous divergence than expected under vertical transmission, their phylogeny is inconsistent with that of teleost fishes, and they occur at non syntenic positions in donor and recipient lineages. The distribution of HGT events in the teleost tree is heterogenous, with eight of the 19 transfers occurring between the same two orders (Osmeriformes and Clupeiformes). Though we favor a scenario involving multiple HGT events, future work should evaluate whether hybridization between species belonging to different teleost orders may generate HGT-like patterns. Besides the previously reported transfer of an antifreeze protein, most transferred genes play roles in immunity or are pore forming proteins, suggesting that such genes may be more likely than others to confer strong selective advantage to the recipient species. Overall, our work shows that teleost-to-teleost HGT has occurred on multiple occasions, and it will be worth further quantifying these transfers and evaluating their impact on teleost evolution as more genomes are sequenced.},
}

@article {pmid40374465,
year = {2025},
author = {Toribio-Celestino, L and San Millan, A},
title = {Plasmid-bacteria associations in the clinical context.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2025.04.011},
pmid = {40374465},
issn = {1878-4380},
abstract = {Antimicrobial resistance (AMR) is one of the most pressing global health problems, with plasmids playing a central role in its evolution and dissemination. Over the past decades, many studies have investigated the ecoevolutionary dynamics between plasmids and their bacterial hosts. However, what drives the epidemiological success of certain plasmid-bacterium associations remains unclear. In this opinion article, we review which factors influence these associations and underline that studying plasmid-host interactions of clinical relevance is critical for understanding the evolution and spread of AMR. We also highlight the increasing importance of integrating experimental research with bioinformatics and machine learning tools to study plasmid-bacteria dynamics. This combined approach will assist researchers to dissect the molecular mechanisms underlying successful plasmid-host associations and to design strategies to prevent and predict future high-risk associations.},
}

@article {pmid40373943,
year = {2025},
author = {Bhuiya, S and Kaushik, S and Logheeswaran, J and Karthika, P and Prathiviraj, R and Selvin, J and Kiran, GS},
title = {Emergence of Recurrent Urinary Tract Infection: Dissecting the mechanism of Antimicrobial Resistance, Host-Pathogen Interaction, and Hormonal Imbalance.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {107698},
doi = {10.1016/j.micpath.2025.107698},
pmid = {40373943},
issn = {1096-1208},
abstract = {Urinary tract infection is one of the most common infections worldwide, causing numerous deaths every year. The gut-bladder axis has been recently found to be a key factor in initiating UTI pathogenesis, along with the imbalance in the gut microbiome, which is associated with advanced susceptibility to rUTI. The patients who suffer from UTIs are, more often than not, the ones who have the lowest levels of butyrate-producing gut bacteria. Antibiotics cause dysbiosis in the gut and increase the growth of uropathogenic strains. Moreover, the gut-vagina and vagina-bladder axes are involved in UTIs by transferring microbial species, modulating the immune response, and developing intracellular bacterial reservoirs in the bladder. The rising usage of antibiotics has raised antimicrobial resistance (AMR) worldwide and recently worsened the treatment of UTIs. Resistance mechanisms include enzymatic hydrolysis of antibiotics, efflux systems, biofilm formation, horizontal gene transfer, and a weakened host's immune system, allowing bacteria to escape from the treatments. Besides, in pregnant women and adolescents, the alterations in sex hormone levels increase the risk of rUTIs. Knowledge of microbiota that harbor in the gut-vagina and vagina-bladder axes might lead to the invention of nonantibiotic preventive and therapeutic techniques in the future. In conclusion, this review emphasizes the need for a study to understand the host-microbe interactions, gut health, and AMR to effectively deal with and prevent recurrent UTIs. Also, the review explores a comprehensive analysis of the epigenetic network between host UTIs and marker genes in E. coli.},
}

@article {pmid40373395,
year = {2025},
author = {He, Y and Liu, C and Zhang, J and Wang, G and Liu, H and Peng, C and Liu, X and Wang, J},
title = {Invisible threat: Marine suspended particles mediate delayed decay of antibiotic resistome in coastal effluents.},
journal = {Journal of hazardous materials},
volume = {494},
number = {},
pages = {138610},
doi = {10.1016/j.jhazmat.2025.138610},
pmid = {40373395},
issn = {1873-3336},
abstract = {Suspended particles are recognized as hotspots of antibiotic resistance genes (ARGs) in coastal waters. However, the dynamics of ARGs associated with suspended particles during sewage discharge into coastal environments remain poorly understood. This study simulated sewage influx into coastal waters using microcosms to investigate the decay dynamics of particle-associated (PA) and free-living (FL) ARGs. Results showed that four ARGs, including two sulfonamide resistance genes (sul1 and sul2) and two tetracycline resistance genes (tetB and tetG), exhibited significantly lower decay rates in the PA fraction than in the FL fraction. Specifically, bacterial decay (k = 0.96 day[-1]) and horizontal gene transfer decay (k = 0.62 day[-1]) were both slower in the PA fraction compared to the FL fraction (1.56 day[-1] and 1.98 day[-1], respectively). These results indicated that suspended particles slow down the decay of ARGs. Microbial community analysis revealed approximately 80 % similarity between sewage and seawater at day 0, but a marked increase in unique bacterial genera and unknown-source taxa was observed at day 15. These results suggest that sewage discharge rapidly alters the composition of native seawater communities. Furthermore, suspended particles harbored higher abundances of unknown-source bacteria and displayed stronger bacterial community interactions than the surrounding water. These findings advance our understanding of ARG persistence and microbial community dynamics, offering critical insights for understanding ARGs dissemination from wastewater discharge.},
}

@article {pmid40372033,
year = {2025},
author = {Kiiru, S and Kasiano, P and Maina, J and Mwaniki, JN and Songoro, E and Kariuki, S},
title = {Molecular characterization of multidrug-resistant E. coli recovered from diarrheagenic children under 5 years from Mukuru Informal Settlement, Nairobi, Kenya, based on whole-genome sequencing analysis.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0142024},
doi = {10.1128/spectrum.01420-24},
pmid = {40372033},
issn = {2165-0497},
abstract = {UNLABELLED: High genomic plasticity within Escherichia coli enables it to acquire and accumulate genetic material through horizontal gene transfer. In this study, we sought to investigate the virulence genes, phylogroups, antibiotic resistance genes, plasmid replicons, multilocus sequence types (MLST), and core genome MLST of multidrug-resistant E. coli recovered from diarrheagenic children under 5 years from Mukuru Informal Settlement in Nairobi, Kenya. A total of 39 multidrug-resistant (MDR) strains had their DNA extracted, and whole-genome sequencing was done using the Illumina HiSeq 2000 platform. Twenty-six E. coli assemblies were analyzed using web-based bioinformatics tools available at the Centre for Genomic Epidemiology and EnteroBase. The isolates were categorized into four main phylogroups, where 10/26 (38.5%) belonged to the B2 phylogroup, 4/26 (15.4%) belonged to D, 3/26 (11.5%) belonged to A, 1/26 (3.8%) belonged to B1, while 8/26 (30.8%) were not determined. FimH30 was predominantly found in the most frequent phylogroup B2 and sequence type (ST) 131. The most common beta-lactam resistance genes were bla TEM-1B and blaCTXM 15, followed by three fluoroquinolone resistance genes [qnrS1 6/26 (23.1%), qnrB4 2/26 (7.7%), and aac(6')-Ib-cr, 8/26 (30.8%)]. Of 26 isolates, 15 had at least one amino acid substitution in the housekeeping genes gyrA (p.S83L), gyrA (p.D87N), parC (p.S80I), parC (p.E84V), parC (p.S57T), and parE (p.I529L), associated with resistance to fluoroquinolones. A total of 40 diverse virulence genes were detected among the isolates. Thirteen different STs were isolated from the E. coli genomes, which included ST 131, ST 3036, ST 38, ST 10, ST 12569, ST 15271, ST 2076, ST 311, ST 3572, ST 394, ST 453, ST 46, and ST 1722. Only two isolates (2/26, 7.7%) from the Municipal City Council clinic were genetically related. Additionally, the most abundant plasmid replicon identified belonged to the IncF family, IncFII(pRSB107), in particular, followed by the Col family. The study highlighted the first E. coli ST46 to harbor the bla NDM5 gene encoded in Col(BS512), IncFII(pRSB107), and IncFIB(AP001918) plasmid replicons in Kenya. We further demonstrated the diversity of MDR E. coli associated with diarrhea in an endemic setting in Kenya.

IMPORTANCE: This study investigated the molecular characterization of multidrug-resistant Escherichia coli isolated from diarrheagenic children under 5 years of age in Mukuru Informal Settlement in Nairobi, Kenya. This is an important addition to the genomic analysis data of multi-drug resistant diarrheal Escherichia coli in Kenya. The use of whole-genome sequencing to identify and characterize these isolates is valuable and provides valuable insights into the molecular epidemiology of E. coli in the region.},
}

@article {pmid40370256,
year = {2025},
author = {Wachino, JI},
title = {Horizontal Gene Transfer Systems for Spread of Antibiotic Resistance in Gram-Negative Bacteria.},
journal = {Microbiology and immunology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1348-0421.13222},
pmid = {40370256},
issn = {1348-0421},
abstract = {Antibiotic-resistant bacteria have become a significant global threat to public health due to the increasing difficulty in treatment. These bacteria acquire resistance by incorporating various antibiotic resistance genes (ARGs) through specialized gene transfer mechanisms, allowing them to evade antibiotic attacks. Conjugation, transformation, and transduction are well-established mechanisms that drive the acquisition and dissemination of ARGs in Gram-negative bacteria. In particular, the horizontal transfer of plasmids carrying multiple ARGs is highly problematic, as it can instantly convert susceptible bacteria into multidrug-resistant ones. Transduction, mediated by bacteriophages that package ARG-containing chromosomal DNA from host cells, also plays a crucial role in ARG spread without requiring direct cell-to-cell contact. Recently, a novel horizontal gene transfer (HGT) mechanism involving outer membrane vesicles (OMVs) has been identified as a key player in ARG dissemination. OMVs-nanoscale, spherical structures produced by bacteria during growth-have been found to carry small plasmids and chromosomal DNA fragments containing ARGs from their host bacteria. This newly discovered transfer process, termed "vesiduction," enables intercellular DNA exchange and further contributes to the spread of antibiotic resistance. Additionally, mobile genetic elements such as transposons, insertion sequences, and site-specific recombination systems like integrons facilitate rearrangement of ARGs, including their translocation between chromosomes and plasmids. This review explores the molecular mechanisms underlying the HGT of ARGs, with a particular focus on clinically isolated antibiotic-resistant Gram-negative bacteria.},
}

@article {pmid40368010,
year = {2025},
author = {Liu, H and Wang, L and Dong, Z and Wen, S and Liu, C and Wang, J and Wang, J and Zhu, L and Kim, YM and Wang, J},
title = {Insights into the drivers of antibiotic resistance gene migration in soil-lettuce system with manure application from different sources.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {126444},
doi = {10.1016/j.envpol.2025.126444},
pmid = {40368010},
issn = {1873-6424},
abstract = {The application of livestock manure serves as a significant source of ARGs in soils. To study the impact of manure application on the migration of ARGs in the soil-plant system, we set different application ratios (1%, 3%, 8%) of chicken and cow manure for treatment. The study's results demonstrated that the application of organic fertilizers increased the quantity of resistance genes in soil, root, and leaf zones. This change was influenced by the type and proportion of the organic fertilizers used. ARGs and MGEs exhibited the highest absolute enrichment levels in leaf tissues (2.53 and 2.01 times, respectively) with the 3% cow manure treatment. In contrast, chicken manure exhibited the highest enrichment levels after the 1% addition (2.51 and 1.81 times, respectively). The applied manure exhibited a high degree of similarity in bacterial community composition with the soil-lettuce system, indicating that ARGs may spread through microorganisms in this system. This study demonstrated that the evolution of bacterial community structure plays a pivotal role in mediating and driving the migration of ARGs within manure-amended soil-plant ecosystems, providing a theoretical basis for understanding the transmission of ARGs in soils and plants due to agricultural production activities.},
}

@article {pmid40366029,
year = {2025},
author = {Rojas-Villalobos, C and Ossandon, FJ and Castillo-Vilcahuaman, C and Sepúlveda-Rebolledo, P and Castro-Salinas, D and Zapata-Araya, A and Arisan, D and Perez-Acle, T and Issotta, F and Quatrini, R and Moya-Beltrán, A},
title = {MOBHunter: a data integration platform for identification and classification of mobile genetic elements in microbial genomes.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkaf396},
pmid = {40366029},
issn = {1362-4962},
support = {1221035//ANID/ ; ANID/BASAL/FB210008//ANID/ ; 32300527//PROYECTO FONDECYT POSTDOCTORADO/ ; 3140005//PROYECTO FONDECYT POSTDOCTORADO/ ; 21241467//ANID/BECAS/DOCTORADO NACIONAL/ ; USS-FIN-24-CNGD-26//Fondo VRID apoyo a congresos/ ; //VRID-Universidad San Sebastián PROYECTO/USS-FIN-23-PDOC-03USS/ ; //Vicerrectoría de Investigación y Postgrado - Escuela de Postgrado - Universidad Tecnológica Metropolitana/ ; USS-FIN-25-APCS-20//Vicerrectoría de Investigación y Doctorados de la Universidad San Sebastián - Fondo/ ; },
abstract = {Horizontal gene transfer plays a critical role in microbial genome evolution and adaptation. Integrated foreign DNA fragments encompass various types of mobile genetic elements (MGEs), ranging from small transposons to conspicuous integrative and conjugative elements. These regions often confer advantageous traits, including antibiotic resistance or novel metabolic capabilities, and contain foreign sequence signatures and hallmark genes such as transposases, integrases, etc. While bioinformatic tools target specific MGE subsets using alignments, compositional signatures, or diagnostic gene mapping, no single platform offers a unified framework for comprehensive, evidence-based, MGE identification and classification. To address this challenge, we developed MOBHunter, an advanced bioinformatic pipeline that consolidates standalone tools and in-house algorithms. Unlike basic tool concatenation, MOBHunter yields consensus identifications, score-supported classifications, and enhanced web visualizations. The platform reduces end user analysis time by integrating data collection, processing, and interpretation into a unified workflow. It delivers robust classifications of MGEs into distinct families and provides a comprehensive overview of the flexible regions of any given input genome. URL: https://informatica.utem.cl/mobhunter/.},
}

@article {pmid40362661,
year = {2025},
author = {Rybak, B and Werbowy, O and Debowski, K and Plotka, M and Kocot, AM},
title = {Coagulase-Negative Staphylococci Determined as Blood Culture Contamination Have High Virulence Characteristic Including Transfer of Antibiotic Resistance Determinants to Staphylococcus aureus and Escherichia coli.},
journal = {International journal of molecular sciences},
volume = {26},
number = {9},
pages = {},
doi = {10.3390/ijms26094424},
pmid = {40362661},
issn = {1422-0067},
mesh = {Biofilms/drug effects/growth & development ; Humans ; *Escherichia coli/genetics/drug effects/pathogenicity ; *Staphylococcus aureus/drug effects/pathogenicity/genetics/isolation & purification ; Coagulase/metabolism ; Anti-Bacterial Agents/pharmacology ; *Blood Culture ; *Drug Resistance, Bacterial/genetics ; Virulence/genetics ; Microbial Sensitivity Tests ; *Staphylococcus/drug effects/pathogenicity/genetics/isolation & purification ; Staphylococcal Infections/microbiology ; Gene Transfer, Horizontal ; },
abstract = {This study aimed to evaluate the virulence of 36 clinical isolates estimated as blood culture contaminants (BCCs). MALDI-TOF MS classified all isolates as coagulase-negative staphylococci (CoNS) with the highest percentage of S. epidermidis (77.78%). All tested strains formed biofilms with greater ability at room temperature than 37 °C. CoNS were sensitive to vancomycin (0% resistance) and had relatively low resistance to linezolid and rifampicin (8.33 and 22.22% resistance). The highest resistance was observed for penicillin (94.44%). Moreover, we observed the transfer of antibiotic resistance genes from the tested CoNS to S. aureus and even to E. coli, although with lower efficiency. CoNS in planktonic form were completely combated by antiseptics after 10 and 60 s exposition, and activity against biofilms was time-dependent. The complete elimination of biofilms was observed after a 180 s exposure to Kodan and CITROclorex, and this exposure to Rivanol and Octenidyne showed still viable cells (>0.9 log CFU/mL). Our findings showed that a careful selection of antiseptics and extending the exposure time before blood collection can reduce the occurrence of blood culture contamination. However, our most important finding is the indication that CoNS naturally occurring on human skin and mucous membranes exhibit antibiotic resistance, and what is more, determinants of antibiotic resistance are transferred to both closely related Gram-positive bacteria and phylogenetically distant Gram-negative bacteria. Thus, our findings shed new light on CoNS-they indicate the necessity of their control due to the effective transfer of mobile genetic elements harboring antibiotic resistance genes, which may contribute to the spread of resistance genes and deepening the antibiotic crisis.},
}

Biofilms/drug effects/growth & development
Humans
*Escherichia coli/genetics/drug effects/pathogenicity
*Staphylococcus aureus/drug effects/pathogenicity/genetics/isolation & purification
Coagulase/metabolism
Anti-Bacterial Agents/pharmacology
*Blood Culture
*Drug Resistance, Bacterial/genetics
Virulence/genetics
Microbial Sensitivity Tests
*Staphylococcus/drug effects/pathogenicity/genetics/isolation & purification
Staphylococcal Infections/microbiology
Gene Transfer, Horizontal

@article {pmid40359552,
year = {2025},
author = {Otten, L and Liu, H and Meeprom, N and Linan, A and Puglisi, C and Chen, K},
title = {Accumulation of numerous cellular T-DNA sequences in the genus Diospyros by multiple rounds of natural transformation.},
journal = {The Plant journal : for cell and molecular biology},
volume = {122},
number = {3},
pages = {e70202},
doi = {10.1111/tpj.70202},
pmid = {40359552},
issn = {1365-313X},
support = {32370382//National Natural Science Foundation of China/ ; (G242406 to KC)//Shanghai landscaping and city appearance administrative bureau/ ; },
mesh = {*Diospyros/genetics ; *DNA, Bacterial/genetics ; *Gene Transfer, Horizontal/genetics ; *Transformation, Genetic ; Genome, Plant/genetics ; Phylogeny ; Agrobacterium/genetics ; },
abstract = {Horizontal gene transfer (HGT) is an important phenomenon in the evolutionary history of plants. Natural transformation by Agrobacterium is a special case of HGT and leads to the insertion of cellular T-DNA (cT-DNA) sequences, for example, in Diospyros lotus. The genus Diospyros contains about 795 species with economically important members, like different types of persimmon (D. kaki, D. lotus, and D. virginiana) and ebony (e.g., D. ebenum). Whole genome sequences (WGS) from D. kaki, D. oleifera, D. lotus, and D. virginiana were investigated for cT-DNAs. These four species belong to one clade and contain 15 different cT-DNAs (DiTA to DiTO). The hexaploid species D. kaki cv. "Xiaoguo-tianshi" contains seven types of cT-DNA (DiTA to DiTG) on 27 of 42 homeologs, adding up to 628 kb of cT-DNA. Five of these seven cT-DNAs are non-fixed, as shown by empty chromosomal insertion sites. The evolutionary history of the Diospyros cT-DNAs was reconstructed using the divergence of their inverted repeats. Insert age varied from 3 to 12 million years. Partial cT-DNA sequences were detected in 35 additional species from five Diospyros clades. Our data highlight the unexpectedly large scale of natural Agrobacterium transformation in Diospyros and demonstrate the necessity of whole genome approaches for studies on the origin and evolution of cT-DNAs.},
}

*Diospyros/genetics
*DNA, Bacterial/genetics
*Gene Transfer, Horizontal/genetics
*Transformation, Genetic
Genome, Plant/genetics
Phylogeny
Agrobacterium/genetics

@article {pmid40359213,
year = {2025},
author = {Zhai, K and Yin, K and Lin, Y and Chen, S and Bi, Y and Xing, R and Ren, C and Chen, Z and Yu, Z and Chen, Z and Zhou, S},
title = {Free Radicals on Aging Microplastics Regulated the Prevalence of Antibiotic Resistance Genes in the Aquatic Environment: New Insight into the Effect of Microplastics on the Spreading of Biofilm Resistomes.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c12699},
pmid = {40359213},
issn = {1520-5851},
abstract = {The spread of antibiotic resistance genes (ARGs) by microplastics has received a great concern in coexisting "hotspots". Despite most microplastics suffering from natural aging, little is known about the effect of aging microplastics (A-MPs) on ARGs dissemination. Here, we demonstrated significant suppression of A-MPs on ARGs dissemination in natural rivers. Although ARGs and mobile genetic elements (MGEs) were effectively enriched on A-MPs, the relative abundance of ARGs and MGEs on A-MPs as well as in receiving water decreased by approximately 21.4% to 42.3% during a period of 30 days of dissemination. Further investigation revealed that [•]OH was consistently generated on A-MPs with a maximum value of 0.2 μmol/g. Importantly, scavenging of [•]OH significantly increased the relative abundance of ARGs and MGEs both on A-MPs and in receiving water 1.4-29.1 times, indicating the vital role of [•]OH in suppressing ARGs dissemination. Microbial analysis revealed that [•]OH inhibited the potential antibiotic-resistant bacteria in surface biofilms, such as Pseudomonas and Acinetobacter (with a decrease of 68.8% and 89.3%). These results demonstrated that [•]OH was extensively produced on A-MPs, which greatly reduced both the vertical and horizontal gene transfer of ARGs. This study provided new insights into the dissemination of ARGs through microplastics in natural systems.},
}

@article {pmid40358144,
year = {2025},
author = {Mukherjee, SD and Suryavanshi, M and Knight, J and Lange, D and Miller, AW},
title = {Metagenomic and phylogenetic analyses reveal gene-level selection constrained by bacterial phylogeny, surrounding oxalate metabolism in the gut microbiota.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0091324},
doi = {10.1128/msphere.00913-24},
pmid = {40358144},
issn = {2379-5042},
abstract = {The gut microbiota is critical for neutralizing dietary toxins. Oxalate is a toxin commonly produced by plants to deter herbivory and is widely consumed in the human diet. Excess levels of systemic or urinary oxalate increase risk of multiple urologic and cardiometabolic diseases. The current study employed multiple amplicon-based and shotgun metagenomic methodologies, alongside comparative phylogenetic analyses, to interrogate evolutionary radiation surrounding microbial oxalate degradation within the human gut microbiome. In conservative genome-based estimates, over 30% of gut microbial species harbored at least one oxalate-handling gene, with the specific pathways used dependent on bacterial phylum. Co-occurrence analyses revealed interactions between specialist genes that can metabolize oxalate or its by-products, but not multi-functional genes that can act in more than one oxalate-related pathway. Specialization was rare at the genome level. Amplicon-based metagenomic sequencing of the oxalate-degrading gene, formyl-CoA transferase (frc), coupled with molecular clock phylogenetic analyses are indicative of rapid evolutionary divergence, constrained by phylum. This was corroborated by paired analyses of non-synonymous to synonymous substitutions (dN/dS ratios), which pointed toward neutral to positive selection. Sequence similarity network analyses of frc sequences suggest extensive horizontal gene transferring has occurred with the frc gene, which may have facilitated rapid divergence. The frc gene was primarily allocated to the Pseudomonodota phylum, particularly the Bradyrhizobium genus, which is a species capable of utilizing oxalate as a sole carbon and energy source. Collectively evidence provides strong support that, for oxalate metabolism, evolutionary selection occurs at the gene level, through horizontal gene transfer, rather than at the species level.IMPORTANCEA critical function of the gut microbiota is to neutralize dietary toxins, such as oxalate, which is highly prevalent in plant-based foods and is not degraded by host enzymes. However, little is known about the co-evolutionary patterns of plant toxins and the mammalian gut microbiota, which are expected to exhibit features of an evolutionary arms race. In the current work, we present molecular evidence that microbial genes for oxalate degradation are highly prevalent in humans, potentially driven by extensive horizontal gene transfer events. Phylogenetic analyses reveal that oxalate-degrading genes are under a positive selection pressure and have historically undergone rapid diversification events, which has led to diverse ecological strategies for handling oxalate by gut bacteria. Collectively, data shed light on potential evolutionary relationships between the diet and the gut microbiota that occur relatively independently of the mammalian host.},
}

@article {pmid40118050,
year = {2025},
author = {Berridge, MV and Zobalova, R and Boukalova, S and Caicedo, A and Rushworth, SA and Neuzil, J},
title = {Horizontal mitochondrial transfer in cancer biology: Potential clinical relevance.},
journal = {Cancer cell},
volume = {43},
number = {5},
pages = {803-807},
doi = {10.1016/j.ccell.2025.03.002},
pmid = {40118050},
issn = {1878-3686},
mesh = {Humans ; *Neoplasms/genetics/pathology/metabolism ; *Mitochondria/genetics/metabolism ; *Gene Transfer, Horizontal ; Animals ; DNA, Mitochondrial/genetics ; Clinical Relevance ; },
abstract = {Recent research highlights horizontal mitochondrial transfer as a key biological phenomenon linked to cancer onset and progression. The transfer of mitochondria and their genomes between cancer and non-cancer cells shifts our understanding of intercellular gene trafficking, increasing the metabolic fitness of cancer cells and modulating antitumor immune responses. This process not only facilitates tumor progression but also presents potential therapeutic opportunities.},
}

Humans
*Neoplasms/genetics/pathology/metabolism
*Mitochondria/genetics/metabolism
*Gene Transfer, Horizontal
Animals
DNA, Mitochondrial/genetics
Clinical Relevance

@article {pmid40356790,
year = {2025},
author = {, and Casacuberta, J and Barro, F and Braeuning, A and de Maagd, R and Epstein, MM and Frenzel, T and Gallois, JL and Koning, F and Messéan, A and Moreno, FJ and Nogué, F and Savoini, G and Schulman, AH and Tebbe, C and Veromann, E and Ardizzone, M and De Sanctis, G and Dumont, AF and Ferrari, A and Gennaro, A and Gómez Ruiz, JÁ and Goumperis, T and Kagkli, DM and Lewandowska, A and Camargo, AM and Franco, MN and Piffanelli, P and Raffaello, T and Rodrigues, M and Sánchez-Brunete, E},
title = {Assessment of genetically modified sugar beet KWS20-1 (application GMFF-2023-14732).},
journal = {EFSA journal. European Food Safety Authority},
volume = {23},
number = {5},
pages = {e9381},
doi = {10.2903/j.efsa.2025.9381},
pmid = {40356790},
issn = {1831-4732},
abstract = {Genetically modified sugar beet KWS20-1 was developed to confer tolerance to glyphosate-, dicamba- and glufosinate-ammonium-based herbicides. These properties were achieved by introducing the cp4 epsps, dmo and pat expression cassettes. The molecular characterisation data and bioinformatic analyses do not identify issues requiring further safety assessment. None of the identified differences in the agronomic/phenotypic and compositional characteristics tested between sugar beet KWS20-1 and its conventional counterpart need further assessment, except for pectin in roots, which underwent additional evaluation and was found not to raise any safety or nutritional concerns. The GMO Panel does not identify safety concerns regarding the potential toxicity and allergenicity of the CP4 EPSPS, DMO and PAT proteins as expressed in sugar beet KWS20-1, and finds no evidence that the genetic modification would change the overall safety of sugar beet KWS20-1 as food and feed. In the context of this application, the consumption of food and feed from sugar beet KWS20-1 does not represent a nutritional concern in humans and animals. The GMO Panel concludes that sugar beet KWS20-1 is as safe as the conventional counterpart and non-GM sugar beet reference varieties tested, and no post-market monitoring of food/feed is considered necessary. The scope of the application does not include cultivation and import of viable materials in the EU and the products would be expected to only contain residual amounts of DNA and protein. The environmental risk assessment was limited to the possible plant-to-bacteria horizontal gene transfer and the evaluation of potential interactions of KWS20-1 sugar beet products with biogeochemical cycles, and neither of them indicates a safety concern. The GMO Panel concludes that the sugar beet KWS20-1 is as safe as its conventional counterpart and the tested non-GM reference sugar beet varieties with respect to potential effects on human and animal health and the environment.},
}

@article {pmid40356278,
year = {2025},
author = {Watanabe, Y and Kunishi, K and Matsui, H and Sakata, N and Noutoshi, Y and Toyoda, K and Ichinose, Y},
title = {Genomic Islands of Pseudomonas syringae pv. tabaci 6605: Identification of PtaGI-1 as a Pathogenicity Island With Effector Genes and a Tabtoxin Cluster.},
journal = {Molecular plant pathology},
volume = {26},
number = {5},
pages = {e70087},
doi = {10.1111/mpp.70087},
pmid = {40356278},
issn = {1364-3703},
support = {22H0234814//Japan Society for the Promotion of Science/ ; },
mesh = {*Genomic Islands/genetics ; *Pseudomonas syringae/genetics/pathogenicity ; *Multigene Family/genetics ; Virulence/genetics ; Nicotiana/microbiology ; *Bacterial Toxins/genetics ; Plant Diseases/microbiology ; Genes, Bacterial ; Mutation/genetics ; },
abstract = {Genomic islands (GIs) are 20-500 kb DNA regions that are thought to be acquired by horizontal gene transfer. GIs that confer pathogenicity and environmental adaptation have been reported in Pseudomonas species; however, GIs that enhance bacterial virulence have not. Here, we identified 110 kb and 103 kb GIs in P. syringae pv. tabaci 6605 (Pta6605), the causative agent of tobacco wildfire disease, which has the ability to produce tabtoxin as a phytotoxin. These GIs are partially homologous to known genomic islands in Pseudomonas aeruginosa and P. syringae pv. phaseolicola and were designated PtaGI-1 and PtaGI-2. Both PtaGIs conserve core genes, whereas each GI possesses different accessory genes. PtaGI-1 contains a tabtoxin biosynthetic gene cluster and three type III effector genes among its accessory genes, whereas PtaGI-2 also contains homologous genes to hsvABC, pathogenicity-related genes in Erwinia amylovora. Inoculation revealed that the PtaGI-1 mutant, but not the PtaGI-2 mutant, lost the ability to biosynthesise tabtoxin and to cause disease. Therefore, PtaGI-1 is thought to be a pathogenicity island. Both PtaGI-1 and PtaGI-2 have a pseudogene of tRNA[Lys] on the left border and an intact tRNA[Lys] gene on the right border. In a colony of Pta6605, both GIs can be excised at tRNA[Lys], and PtaGI-1 and PtaGI-2 exist in a circular form. These results indicate that tabtoxin biosynthesis genes in PtaGI-1 are required for disease development, and PtaGI-1 is necessary for Pta6605 virulence.},
}

*Genomic Islands/genetics
*Pseudomonas syringae/genetics/pathogenicity
*Multigene Family/genetics
Virulence/genetics
Nicotiana/microbiology
*Bacterial Toxins/genetics
Plant Diseases/microbiology
Genes, Bacterial
Mutation/genetics

@article {pmid40351943,
year = {2025},
author = {Kumar, A and Sharma, A and Mehrishi, P and Solanki, S and Faujdar, SS and Khatun, A},
title = {Detection of the blaNDM-1 Gene in Carbapenem-Resistant Enterobacterales Causing Urinary Tract Infections in Patients at a Rural Teaching Hospital.},
journal = {Cureus},
volume = {17},
number = {4},
pages = {e81811},
pmid = {40351943},
issn = {2168-8184},
abstract = {BACKGROUND: Carbapenem-resistant Enterobacterales (CRE) pose a significant public health threat due to their resistance to last-line antibiotics. Urinary tract infections (UTIs) caused by multidrug-resistant organisms have become a major challenge in clinical settings. The spread of CRE is largely attributed to the acquisition of carbapenemase-encoding genes, horizontal gene transfer, and overuse of broad-spectrum antibiotics.

METHODOLOGY: A total of 9235 urine samples were analyzed, and more than 10[5] CFU/mL bacterial count was considered positive for UTI. These bacteria were identified and further screened for CRE and blaNDM-1 genes.

RESULTS: A total of 9235 urine samples were analyzed, out of which 555 were identified as Enterobacterales. Among these, 47 were confirmed as CRE, accounting for 8.5% of the Enterobacterales isolates. Out of 47 CRE, 28 were positive for the blaNDM-1 gene.

CONCLUSIONS: The study highlights the increasing burden of CRE and the urgent need for stringent antimicrobial stewardship, effective infection control measures, and the development of new therapeutic strategies to combat MDR infections. Additionally, risk factors associated with CRE infections, their implications on public health, and potential future therapeutic approaches are discussed.},
}

@article {pmid40350664,
year = {2025},
author = {Sarink, MJ and Grassi, L and Tielens, AGM and Verbon, A and Vos, MC and Goessens, W and Strepis, N and Klaassen, CHW and van Hellemond, JJ},
title = {Acanthamoeba castellanii Can Facilitate Plasmid Transfer Between Environmental Pseudomonas spp.},
journal = {Journal of basic microbiology},
volume = {},
number = {},
pages = {e70051},
doi = {10.1002/jobm.70051},
pmid = {40350664},
issn = {1521-4028},
support = {//This work was funded by the Erasmus MC and the Netherlands Centre for One Health./ ; },
abstract = {The conditions in which antimicrobial resistance (AMR) genes are transferred in natural environments are poorly understood. Acanthamoeba castellanii (a cosmopolitan environmental amoeba) feeds on bacteria by phagocytosis, which places the consumed bacteria closely together in a food vacuole (phagosome) of the amoeba. This way, amoebae can facilitate genetic exchanges between intra-amoebal bacteria. We studied this phenomenon in the clinically relevant bacteria Pseudomonas oleovorans and Pseudomonas aeruginosa (strain 957). The internalization of both the plasmid donor and recipient bacteria was shown by confocal microscopy. In seven independent experiments, an on average 12-fold increase in transfer of the blaVIM-2 gene between these two Pseudomonas strains was observed in the presence of A. castellanii compared to its absence. Negligible or no plasmid transfer was observed from P. oleovorans to 18 other investigated strains of P. aeruginosa. AMR gene transfer via plasmids between Pseudomonas species is highly strain-dependent and A. castellanii can substantially enhance plasmid transfer. This process of plasmid transfer might also occur between other bacteria and predatory protozoa, such as amoebae that reside in the gut of humans and animals.},
}

@article {pmid40346915,
year = {2025},
author = {Chen, SY and Huang, K and He, ZH and Zhao, FJ},
title = {Ampicillin Exposure and Glutathione Deficiency Synergistically Promote Conjugative Transfer of Plasmid-Borne Antibiotic Resistance Genes.},
journal = {Environmental microbiology},
volume = {27},
number = {5},
pages = {e70106},
doi = {10.1111/1462-2920.70106},
pmid = {40346915},
issn = {1462-2920},
support = {42090062//National Natural Science Foundation of China/ ; 336168//Research Council of Norway/ ; },
mesh = {*Glutathione/deficiency/metabolism ; *Ampicillin/pharmacology ; *Plasmids/genetics ; *Anti-Bacterial Agents/pharmacology ; *Conjugation, Genetic/drug effects ; Escherichia coli/genetics/drug effects ; Enterobacter/genetics/drug effects ; Oxidative Stress ; *Drug Resistance, Bacterial/genetics ; *Gene Transfer, Horizontal ; Soil Microbiology ; *Drug Resistance, Microbial/genetics ; },
abstract = {Plasmid-mediated conjugation is an important pathway for the spread of antibiotic resistance genes (ARGs), posing a significant risk to global public health. It has been reported that the conjugative transfer of ARGs could be enhanced by oxidative stress. Whether endogenous glutathione (GSH), a major non-protein thiol compound involved in cellular redox homeostasis, influences conjugative transfer is unknown. In this study, we show that the deletion of the GSH biosynthesis gene gshA and ampicillin exposure synergistically promoted the conjugative transfer of plasmid RP4 bearing multiple ARGs from the soil bacterium Enterobacter sp. CZ-1 to Escherichia coli S17-1λπ in co-culture experiments and to diverse soil bacteria belonging to eight phyla, including some potential human pathogens, in a soil incubation experiment. The deletion of gshA increased ROS generation and cell membrane permeability, and upregulated the expression of the genes involved in intracellular oxidative stress regulation, membrane permeability, plasmid replication, and the SOS response process, especially under ampicillin exposure. These results suggest that endogenous GSH is an important factor affecting the spread of plasmid-borne ARGs. Exposure to antibiotics and environmental stresses that cause a depletion of endogenous GSH in vivo are likely to increase the risk of ARG dissemination in the environment.},
}

*Glutathione/deficiency/metabolism
*Ampicillin/pharmacology
*Plasmids/genetics
*Anti-Bacterial Agents/pharmacology
*Conjugation, Genetic/drug effects
Escherichia coli/genetics/drug effects
Enterobacter/genetics/drug effects
Oxidative Stress
*Drug Resistance, Bacterial/genetics
*Gene Transfer, Horizontal
Soil Microbiology
*Drug Resistance, Microbial/genetics

@article {pmid40036506,
year = {2025},
author = {Lin, J and Ni, S and Li, B and Guo, Y and Gao, X and Liu, Y and Yi, L and Wang, P and Chen, R and Yao, J and Wood, TK and Wang, X},
title = {A noncanonical intrinsic terminator in the HicAB toxin-antitoxin operon promotes the transmission of conjugative antibiotic resistance plasmids.},
journal = {Nucleic acids research},
volume = {53},
number = {5},
pages = {},
pmid = {40036506},
issn = {1362-4962},
support = {42188102//National Science Foundation of China/ ; 2022FY100600//Science & Technology Fundamental Resources Investigation Program/ ; 2022RC1169//Science and Technology Innovation Program of Hunan Province/ ; 2019BT02Y262//Local Innovative and Research Teams Project of Guangdong Pearl River Talents Program/ ; SCSIO2023QY03//South China Sea Institute of Oceanology, Chinese Academy of Sciences/ ; //Ocean Negative Carbon Emissions Program/ ; },
mesh = {*Toxin-Antitoxin Systems/genetics ; *Operon ; *Plasmids/genetics ; *Conjugation, Genetic ; *Escherichia coli Proteins/genetics ; *Terminator Regions, Genetic ; Escherichia coli/genetics/drug effects ; *Drug Resistance, Bacterial/genetics ; Promoter Regions, Genetic ; *Bacterial Toxins/genetics ; Anti-Bacterial Agents/pharmacology ; Gene Transfer, Horizontal ; },
abstract = {Conjugative plasmids, major vehicles for the spread of antibiotic resistance genes, often contain multiple toxin-antitoxin (TA) systems. However, the physiological functions of TA systems remain obscure. By studying two TA families commonly found on colistin-resistant IncI2 mcr-1-bearing plasmids, we discovered that the HicAB TA, rather than the StbDE TA, acts as a crucial addiction module to increase horizontal plasmid-plasmid competition. In contrast to the canonical type II TA systems in which the TA genes are cotranscribed and/or the antitoxin gene has an additional promoter to allow for an increased antitoxin/toxin ratio, the HicAB TA system with the toxin gene preceding the antitoxin gene employs internal transcription termination to allow for a higher toxin production. This intrinsic terminator, featuring a G/C-rich hairpin with a UUU tract, lies upstream of the antitoxin gene, introducing a unique mechanism for the enhancing toxin/antitoxin ratio. Critically, the hicAB TA significantly contributes to plasmid competition and plasmid persistence in the absence of antibiotic selection, and deleting this intrinsic terminator alone diminishes this function. These findings align with the observed high occurrence of hicAB in IncI2 plasmids and the persistence of these plasmids after banning colistin as a feed additive. This study reveals how reprogramming the regulatory circuits of TA operons impacts plasmid occupancy in the microbial community and provides critical targets for combating antibiotic resistance.},
}

*Toxin-Antitoxin Systems/genetics
*Operon
*Plasmids/genetics
*Conjugation, Genetic
*Escherichia coli Proteins/genetics
*Terminator Regions, Genetic
Escherichia coli/genetics/drug effects
*Drug Resistance, Bacterial/genetics
Promoter Regions, Genetic
*Bacterial Toxins/genetics
Anti-Bacterial Agents/pharmacology
Gene Transfer, Horizontal

@article {pmid40345346,
year = {2025},
author = {Zhang, Q and Yan, D and Chen, L},
title = {virK and mig-14 Constitute a PhoP-dependent Operon and Contribute to the Intracellular Survival and Polymyxin B Resistance of Salmonella Typhi.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {107668},
doi = {10.1016/j.micpath.2025.107668},
pmid = {40345346},
issn = {1096-1208},
abstract = {In bacteria, adjacent and functionally similar genes are typically transcribed as operons. The virulence genes virK and mig-14 are acquired through horizontal gene transfer in Salmonella. Previous studies have reported that these two genes have similar functions in terms of bacterial survival within macrophages and resistance to antimicrobial peptides. Nevertheless, the specific expression characteristics of the two genes remain unclear. This study revealed that virK and mig-14 were transcribed as a single operon in Salmonella Typhi. The virK-mig-14 operon was found to be activated under conditions of early hyperosmotic stress and polymyxin B stimulation, and its activation was dependent on the presence of the regulator PhoP. The luminescence assay demonstrated that the activity of the virK promoter was markedly elevated in an environment conducive to operon activation, whereas the mig-14 promoter exhibited no discernible change. This suggests that mig-14 is predominantly transcribed as a component of the operon. In the PhoP activation environment, which has a mildly acidic pH, low Mg[2+] levels, and intracellular macrophages, the virK-mig-14 operon exhibited significant activation. The absence of virK or mig-14 resulted in the impaired survival of Salmonella Typhi within macrophages and decreased its tolerance to polymyxin B. Collectively, this study shows that virK and mig-14 constitute an operon whose activation depends on PhoP and that it promotes S. Typhi's survival in macrophages and resistance to polymyxin B.},
}

@article {pmid39988070,
year = {2025},
author = {Zhang, Y and Yang, C and Yao, J and Zhou, L and Zhang, X and Wang, H and Liu, L and Tu, Y and Li, X},
title = {Spread of the Fosfomycin resistance fosA3 gene via the IS26 mobile element between plasmids and the chromosome of carbapenem-resistant Escherichia coli in China.},
journal = {Journal of global antimicrobial resistance},
volume = {42},
number = {},
pages = {80-87},
doi = {10.1016/j.jgar.2025.02.011},
pmid = {39988070},
issn = {2213-7173},
mesh = {*Fosfomycin/pharmacology ; *Plasmids/genetics ; China ; *Escherichia coli/genetics/drug effects ; *Escherichia coli Proteins/genetics ; *Anti-Bacterial Agents/pharmacology ; Phylogeny ; Humans ; Whole Genome Sequencing ; Escherichia coli Infections/microbiology ; *Carbapenem-Resistant Enterobacteriaceae/genetics/drug effects ; Microbial Sensitivity Tests ; *Chromosomes, Bacterial/genetics ; *Interspersed Repetitive Sequences ; Carbapenems/pharmacology ; *Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; },
abstract = {OBJECTIVE: This study investigated fosA3-positive strains selected from carbapenem-resistant Escherichia coli (CREC) and further characterized them through genomic and phenotypic analyses.

METHODS: fosA3-positive CREC strains were subjected to agar dilution. Whole-genome sequencing (WGS) was used to identify molecular mechanisms of fosfomycin resistance and to investigate plasmid structure characteristics through comparative analysis. Conjugative transfer experiments were used to evaluate plasmid transfer ability, followed by plasmid stability assessment. Growth rate analysis evaluated the fitness costs of transconjugants. Phylogenetic analysis was performed on fosA3-positive CREC strains. Furthermore, analysis of fos genes carrying E. coli sequence types (STs) from the NCBI database explored the evolution and spread of fosfomycin resistance.

RESULTS: Between 2016 and 2023, a total of 11.23% CREC strains (10/89) carrying fosA3 were collected from a hospital for further analysis. These ten fosA3-positive strains were also resistant to fluoroquinolones and ceftazidime-avibactam. The fosA3 gene was located within a similar genetic background (IS26-fosA3-1811bp-IS26) on plasmids or chromosomes. The fosA3-carrying IncFII(pHN7A8)-IncX3 cointegrate plasmid pEC00-2-145k was transferable, with fitness cost of 20% to host. Furthermore, three of ten fosA3-positive CREC strains belonged to ST156. Analysis of fos genes carrying E. coli strains from China in the NCBI database identified ST156 (5.39%, 147/2,725) and ST167 (5.21%, 142/2,725) as predominant STs.

CONCLUSIONS: This study revealed fosA3 in CREC strains was associated with IS26 and spreads fosfomycin resistance through horizontal transfer, occurring both on chromosomes and plasmids. The first fosA3-carrying cointegrate plasmid pHN7A8-IncX3-type in E. coli isolates was reported, highlighting a new route of fosfomycin resistance spread. Additionally, notable diversity of ST among fosA3-carrying E. coli strains highlights complexity of fosfomycin resistance dissemination and the importance of surveillance and control measures.},
}

*Fosfomycin/pharmacology
*Plasmids/genetics
China
*Escherichia coli/genetics/drug effects
*Escherichia coli Proteins/genetics
*Anti-Bacterial Agents/pharmacology
Phylogeny
Humans
Whole Genome Sequencing
Escherichia coli Infections/microbiology
*Carbapenem-Resistant Enterobacteriaceae/genetics/drug effects
Microbial Sensitivity Tests
*Chromosomes, Bacterial/genetics
*Interspersed Repetitive Sequences
Carbapenems/pharmacology
*Drug Resistance, Bacterial/genetics
Gene Transfer, Horizontal

@article {pmid39909367,
year = {2025},
author = {Zhang, G and Li, C and Li, X and Li, Y and Li, Y and Zeng, X and Xu, C and Wu, S and Dong, N},
title = {Ibuprofen prevents the conjugative transfer of plasmid-mediated antimicrobial resistance genes.},
journal = {Journal of global antimicrobial resistance},
volume = {42},
number = {},
pages = {10-14},
doi = {10.1016/j.jgar.2025.01.012},
pmid = {39909367},
issn = {2213-7173},
mesh = {*Plasmids/genetics ; *Conjugation, Genetic/drug effects ; *Ibuprofen/pharmacology ; *Drug Resistance, Multiple, Bacterial/genetics/drug effects ; *Anti-Bacterial Agents/pharmacology ; Humans ; Microbial Sensitivity Tests ; Escherichia coli/genetics/drug effects ; *Gene Transfer, Horizontal/drug effects ; },
abstract = {Refractory infections caused by multidrug-resistant bacteria pose a significant threat to public health. Here we report that ibuprofen inhibits conjugation of the RP4 plasmid and plasmids from clinical strains carrying different resistance genes including mcr-1, blaNDM, blaKPC, tet(X4), and tmexCD1-toprJ1. Mechanistic studies suggest that ibuprofen reduces ATP production and inhibits conjugation-related genes. The inhibitory effect of ibuprofen on conjugation has significant clinical implications for preventing the spread of multidrug resistance, opening new therapeutic avenues to combat multidrug-resistant bacteria.},
}

*Plasmids/genetics
*Conjugation, Genetic/drug effects
*Ibuprofen/pharmacology
*Drug Resistance, Multiple, Bacterial/genetics/drug effects
*Anti-Bacterial Agents/pharmacology
Humans
Microbial Sensitivity Tests
Escherichia coli/genetics/drug effects
*Gene Transfer, Horizontal/drug effects

@article {pmid40343121,
year = {2025},
author = {Liang, H and Qi, H and Wang, C and Wang, Y and Liu, M and Chen, J and Sun, X and Xia, T and Feng, S and Chen, C and Zheng, D},
title = {Analysis of the complete mitogenomes of three high economic value tea plants (Tea-oil Camellia) provide insights into evolution and phylogeny relationship.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1549185},
doi = {10.3389/fpls.2025.1549185},
pmid = {40343121},
issn = {1664-462X},
abstract = {INTRODUCTION: Tea-oil Camellia species play a crucial economic and ecological role worldwide, yet their mitochondrial genomes remain largely unexplored.

METHODS: In this study, we assembled and analyzed the complete mitochondrial genomes of Camellia oleifera and C. meiocarpa, revealing multi-branch structures that deviate from the typical circular mitochondrial genome observed in most plants. The assembled mitogenomes span 953,690 bp (C. oleifera) and 923,117 bp (C. meiocarpa), containing 74 and 76 annotated mitochondrial genes, respectively.

RESULTS: Comparative genomic analyses indicated that C. oleifera and C. meiocarpa share a closer genetic relationship, whereas C. drupifera is more distantly related. Codon usage analysis revealed that natural selection plays a dominant role in shaping codon bias in these mitochondrial genomes. Additionally, extensive gene transfer events were detected among the three species, highlighting the dynamic nature of mitochondrial genome evolution in Tea-oil Camellia. Phylogenetic reconstruction based on mitochondrial genes exhibited incongruence with chloroplast phylogenies, suggesting potential discordance due to hybridization events, incomplete lineage sorting (ILS), or horizontal gene transfer (HGT). Furthermore, we identified species-specific mitochondrial markers, which provide valuable molecular tools for distinguishing Tea-oil Camellia species.

DISCUSSION: Our findings enhance the understanding of mitochondrial genome evolution and genetic diversity in Tea-oil Camellia, offering essential genomic resources for phylogenetics, species identification, and evolutionary research in woody plants.},
}

@article {pmid40343117,
year = {2025},
author = {Meng, D and Lu, T and He, M and Ren, Y and Fu, M and Zhang, Y and Yang, P and Lin, X and Yang, Y and Zhang, Y and Yang, Y and Jin, X},
title = {Organelle genomes of two Scaevola species, S. taccada and S. hainanensis, provide new insights into evolutionary divergence between Scaevola and its related species.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1587750},
doi = {10.3389/fpls.2025.1587750},
pmid = {40343117},
issn = {1664-462X},
abstract = {Chloroplast and mitochondrial genomes harbor crucial information that can be utilized for elucidating plant evolution and environmental adaptation. The organellar genomic characteristics of Goodeniaceae, a sister family to Asteraceae, remain unexplored. Here, using a combination of short-read and long-read sequencing technologies, we successfully assembled the complete organellar genomes of two Goodeniaceae species native to China, Scaevola taccada and S. hainanensis. Chloroplast genome collinearity analysis revealed that Scaevola expanded its genome length through inverted repeat expansion and large single copy fragment duplication, resulting in 181,022 bp (S. taccada) and 182,726 bp (S. hainanensis), ~30 kb increase compared to its related species. Mitochondrial genomes of two Scaevola species exhibit multi-ring topology, forming dual mitochondrial chromosomes of 314,251 bp (S. taccada) and 276,175 bp (S. hainanensis). Sequence variation analysis demonstrated substantial chloroplast sequence divergence (Pi = 0.45) and an increase in gene copy number within the genus. Relative synonymous codon usage (RSCU) analysis revealed that Scaevola chloroplast has a higher bias for A/U-ending codons than mitochondria, with chloroplasts RSCU values ranging from 0.32 to 1.94, whereas mitochondrial RSCU values ranging from 0.38 to 1.62. Phylogenetic analyses support the monophyly of the Asteraceae-Goodeniaceae sister group, whereas the extended evolutionary branches of Scaevola, coupled with mitochondrial collinearity analysis, indicate rapid organellar genome evolution of Scaevola. Organellar-nuclear horizontal gene transfer analysis identified specific increased in the copy numbers of photosynthesis-related genes and chloroplast-nuclear transfer events in S. taccada. Our study not only provides insights for understanding environmental adaptation mechanisms of coastal plants, but also contributes to elucidating organellar genome evolution in Scaevola and Goodeniaceae.},
}

@article {pmid40341387,
year = {2025},
author = {Marin, MG and Quinones-Olvera, N and Wippel, C and Behruznia, M and Jeffrey, BM and Harris, M and Mann, BC and Rosenthal, A and Jacobson, KR and Warren, RM and Li, H and Meehan, CJ and Farhat, MR},
title = {Pitfalls of bacterial pan-genome analysis approaches: a case study of M. tuberculosis and two less clonal bacterial species.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btaf219},
pmid = {40341387},
issn = {1367-4811},
abstract = {UNLABELLED: Pan-genome analysis is a fundamental tool for studying bacterial genome evolution; however, the variety of methods used to define and measure the pan-genome poses challenges to the interpretation and reliability of results. Using Mycobacterium tuberculosis (Mtb)-characterized by clonal evolution, absence of horizontal gene transfer, and a small accessory genome-as a model system, we systematically evaluated sources of variability in pan-genome estimates. Our analysis revealed that differences in assembly type (short-read vs. hybrid), annotation pipeline, and pan-genome software, significantly impact predictions of core and accessory genome size. Extending our analysis to two additional bacterial species, Escherichia coli and Staphylococcus aureus, we observed consistent tool-dependent biases but species-specific patterns in pan-genome variability. Our findings highlight the need for robust quality control and careful methodological selection to accurately capture genome diversity and evolution. This work underscores the importance of integrating nucleotide- and protein-level analyses to improve the reliability and reproducibility of pan-genome studies across diverse bacterial populations.

AVAILABILITY: Panqc is freely available under an MIT license at https://github.com/maxgmarin/panqc.

CONTACT: maha_farhat@hms.harvard.edu.

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

@article {pmid40339917,
year = {2025},
author = {Schuster, HJ and van Mansfeld, R and van der Reijden, WA and van Houdt, R and Matamoros, S},
title = {VanB transposon analysis detects horizontal gene transfer in vancomycin resistant Enterococcus faecium: description of two outbreaks.},
journal = {The Journal of hospital infection},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jhin.2025.04.021},
pmid = {40339917},
issn = {1532-2939},
abstract = {BACKGROUND: Outbreaks with vancomycin resistant Enterococcus faecium (VRE) are common in hospitals worldwide. Whole genome MLST (wgMLST) is often used to identify outbreak strains, but VRE typing can still be challenging due to their limited genomic variation.

AIM: Developing a method for sequence analysis of vancomycin resistance genes in parallel to wgMLST and application of this new method for real-time investigation of two parallel VRE outbreaks.

METHODS: We developed a bioinformatics pipeline to compare the sequences of transposons containing vanB resistance genes. We used this pipeline in addition to wgMLST to investigate two separate ongoing VRE outbreaks. We also sequenced five separate colonies from 15 different samples and 10 vancomycin sensitive isolates.

FINDINGS: Of 46 strains collected during two outbreaks, we identified 26 and 9 strains to be part of the two outbreaks based on wgMLST clustering. In 6 strains we identified an identical vanB transposon but a different wgMLST cluster, indicating horizontal gene transfer. This potential outbreak spread would have been missed without transposon analysis. We found no variability in vanB transposon sequence or wgMLST profiles within different colonies from the same sample. We identified 1 vancomycin sensitive E. faecium in blood culture with a similar wgST as one of the outbreak strains.

CONCLUSIONS: Real-time analysis of transposons containing vancomycin resistance genes provides additional information for analysis of vanB-VRE outbreaks. It detects possible horizontal gene transfer which would not be detected using conventional methods. Transposon analysis is a valuable addition to whole genome sequence analysis during vanB-VRE outbreaks.},
}

@article {pmid40337914,
year = {2025},
author = {Robertson, HM and Walker, JF and Moyroud, E},
title = {CAnDI: a new tool to investigate conflict in homologous gene trees and explain convergent trait evolution.},
journal = {Systematic biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/sysbio/syaf028},
pmid = {40337914},
issn = {1076-836X},
abstract = {Phenotypic convergence is found across the tree of life, and morphological similarities in distantly related species are often presumed to have evolved independently. However, clarifying the origins of traits has recently highlighted the complex nature of evolution, as apparent convergent features often share similar genetic foundations. Hence, the tree topology of genes that underlie such traits frequently conflicts with the overall history of species relationships. This conflict, which usually results from incomplete lineage sorting, introgression or horizontal gene transfer, creates both a challenge for systematists and an exciting opportunity to investigate the rich, complex network of information that connects molecular trajectories with trait evolution. Here we present a novel conflict identification program named CAnDI (Conflict And Duplication Identifier), which enables the analysis of conflict in homologous gene trees rather than inferred orthologs. We demonstrate that the analysis of conflicts in homologous trees using CAnDI yields more comparisons than in ortholog trees in six datasets from across the eukaryotic tree of life. Using the carnivorous trap of Caryophyllales, a charismatic group of flowering plants, as a case study we demonstrate that analysing conflict on entire homolog trees can aid in inferring the contribution of standing genetic variation to trait evolution: by dissecting all gene relationships within homolog trees, we find genomic evidence that the molecular basis of the pleisiomorphic mucilaginous sticky trap was likely present in the ancestor of all carnivorous Caryophyllales. We also show that many genes whose evolutionary trajectories group species with similar trap devices code for proteins contributing to plant carnivory and identify a LATERAL ORGAN BOUNDARY DOMAIN transcription factor as a possible candidate for regulating sticky trap development.},
}

@article {pmid40332509,
year = {2025},
author = {Ye, T and Li, H and Hai, D and Zhaxi, Z and Duan, J and Lin, Y and Xie, J and Cheng, J and Li, B and Chen, T and Yu, X and Lyu, X and Xiao, X and Fu, Y and Jiang, D},
title = {A Hypovirulence-Associated Partitivirus and Re-Examination of Horizontal Gene Transfer Between Partitiviruses and Cellular Organisms.},
journal = {International journal of molecular sciences},
volume = {26},
number = {8},
pages = {},
doi = {10.3390/ijms26083853},
pmid = {40332509},
issn = {1422-0067},
support = {31861143043//ISF-NSFC/ ; AML2023A02//the funds of the National Key Laboratory of Agricultural Microbiology/ ; },
mesh = {*Gene Transfer, Horizontal ; *Ascomycota/virology/genetics ; Phylogeny ; *Fungal Viruses/genetics/pathogenicity ; *RNA Viruses/genetics ; RNA-Dependent RNA Polymerase/genetics ; Capsid Proteins/genetics ; Genome, Viral ; Virulence/genetics ; Animals ; },
abstract = {Previous research has unearthed the integration of the coat protein (CP) gene from alphapartitivirus into plant genomes. Nevertheless, the prevalence of this horizontal gene transfer (HGT) between partitiviruses and cellular organisms remains an enigma. In our investigation, we discovered a novel partitivirus, designated Sclerotinia sclerotiorum alphapartitivirus 1 (SsAPV1), from a hypovirulent strain of Sclerotinia sclerotiorum. Intriguingly, we traced homologs of the SsAPV1 CP to plant genomes, including Helianthus annuus. To delve deeper, we employed the CP and RNA-dependent RNA polymerase (RdRP) sequences of partitiviruses as "bait" to search the NCBI database for similar sequences. Our search unveiled a widespread occurrence of HGT between viruses from all five genera within the family Partitiviridae and other cellular organisms. Notably, numerous CP-like and RdRP-like genes were identified in the genomes of plants, protozoa, animals, fungi, and even, for the first time, in an archaeon. The majority of CP and RdRP genes were integrated into plant and insect genomes, respectively. Furthermore, we detected DNA fragments originating from the SsAPV1 RNA genome in some subcultures of virus-infected strains. It suggested that SsAPV1 RdRP may possesses reverse transcriptase activity, facilitating the integration of viral genes into cellular organism genomes, and this function requires further confirmation. Our study not only offers a hypovirulence-associated partitivirus with implications for fungal disease control but also sheds light on the extensive integration events between partitiviruses and cellular organisms and enhances our comprehension of the origins, evolution, and ecology of partitiviruses, as well as the genome evolution of cellular organisms.},
}

*Gene Transfer, Horizontal
*Ascomycota/virology/genetics
Phylogeny
*Fungal Viruses/genetics/pathogenicity
*RNA Viruses/genetics
RNA-Dependent RNA Polymerase/genetics
Capsid Proteins/genetics
Genome, Viral
Virulence/genetics
Animals

@article {pmid40328220,
year = {2025},
author = {Doremus, MR and Hunter, MS},
title = {Symbiosis: An escalating arms race between a butterfly and bacterium.},
journal = {Current biology : CB},
volume = {35},
number = {9},
pages = {R339-R341},
doi = {10.1016/j.cub.2025.03.061},
pmid = {40328220},
issn = {1879-0445},
abstract = {Symbiotic bacteria such as Wolbachia can dramatically affect the reproduction of their arthropod hosts, in some instances causing male progeny to die as embryos. A recent paper describes an escalating arms race over Wolbachia-mediated male-killing in a tropical butterfly, with butterfly suppression of male-killing being overcome by acquisition of an additional male-killing gene via phage-mediated horizontal gene transfer.},
}

@article {pmid40328153,
year = {2025},
author = {Chu, Y and Dong, X and Fang, S and Gan, L and Lee, X and Zhou, L},
title = {Viruses in human-impacted estuarine ecotones: Distribution, metabolic potential, and environmental risks.},
journal = {Water research},
volume = {282},
number = {},
pages = {123750},
doi = {10.1016/j.watres.2025.123750},
pmid = {40328153},
issn = {1879-2448},
abstract = {Estuaries, as dynamic ecological interfaces between marine and terrestrial systems, are characterized by high productivity and intricate microbial communities. Viruses exert critical regulatory effects on microbial processes, influencing ecological functions and contributing to environmental dynamics in estuarine ecosystems. Despite their significance, the diversity and ecological roles of estuarine viruses remain insufficiently understood. This study explored the viral biogeographic patterns, metabolic potential, and influencing factors in 30 subtropical estuaries in China. Few estuarine viruses (< 22 %) exhibited homology with known viruses, and the low overlap of virus clusters with other environments highlights their novelty and habitat specificity. Mantel tests and random forest analysis identified salinity, temperature, nutrients, and pollutants as key factors influencing viral composition and functional profiles. In addition, correlation analysis between virus and host confirmed significant virus-host interactions, while functional analyses highlighted the role of environmental conditions and horizontal gene transfer in shaping auxiliary metabolic genes linked to elemental biogeochemical cycles, particularly phosphorus, sulfur, and nitrogen. The detection of antibiotic resistance genes (ARGs) and virulence factors (VFs) within viral genomes underscores the role of viruses as reservoirs of ARGs and VFs in these ecosystems. These results demonstrate the profound influence of abiotic and host factors on viral community structures in subtropical estuarine ecotones and underscore the ecological significance of metabolic genes in biogeochemical cycling. By clarifying these interactions, this study advances the understanding of viral contributions to ecosystem functioning and biogeochemical dynamics in estuarine environments.},
}

@article {pmid40326718,
year = {2025},
author = {Naseef Pathoor, N and Valsa, V and Ganesh, PS and Gopal, RK},
title = {From resistance to treatment: the ongoing struggle with Acinetobacter baumannii.},
journal = {Critical reviews in microbiology},
volume = {},
number = {},
pages = {1-22},
doi = {10.1080/1040841X.2025.2497791},
pmid = {40326718},
issn = {1549-7828},
abstract = {Acinetobacter baumannii (A. baumannii) has become a major hospital-acquired pathogen, well-known for its rapid development of resistance to multiple antibiotics. The rising incidence of antibiotic-resistant A. baumannii presents a significant global public health challenge. Gaining a deep understanding of the mechanisms behind this resistance is essential for creating effective treatment options. This comprehensive review explores the understanding of various antibiotic resistance mechanisms in A. baumannii. It covers intrinsic resistance, acquired resistance genes, efflux pumps, changes in outer membrane permeability, alterations in drug targets, biofilm formation, and horizontal gene transfer. Additionally, the review investigates the role of mobile genetic elements and the clinical implications of antibiotic resistance in A. baumannii infections. The insights provided may inform the development of new antimicrobial agents and the design of effective infection control strategies to curb the spread of multidrug-resistant (MDR) A. baumannii strains in healthcare environments. Unlike previous reviews, this study offers a more integrative perspective by also addressing the pathogen's environmental resilience, with particular emphasis on its resistance to desiccation and the formation of robust biofilms. It further evaluates both established and emerging therapeutic strategies, thereby expanding the current understanding of A. baumannii persistence and treatment.},
}

@article {pmid40325439,
year = {2025},
author = {Urban, JM and Gerbi, SA and Spradling, AC},
title = {Chromosome-scale scaffolds of the fungus gnat genome reveal multi-Mb-scale chromosome-folding interactions, centromeric enrichments of retrotransposons, and candidate telomere sequences.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {443},
pmid = {40325439},
issn = {1471-2164},
support = {NIH/GM121455/NH/NIH HHS/United States ; },
abstract = {BACKGROUND: The lower Dipteran fungus gnat, Bradysia (aka Sciara) coprophila, has compelling chromosome biology. Paternal chromosomes are eliminated during male meiosis I and both maternal X sister chromatids are retained in male meiosis II. Embryos start with three copies of the X chromosome, but 1-2 copies are eliminated from somatic cells as part of sex determination, and one is eliminated in the germline to restore diploidy. In addition, there is gene amplification in larval polytene chromosomes, and the X polytene chromosome folds back on itself mediated by extremely long-range interactions between three loci. These developmentally normal events present opportunities to study chromosome behaviors that are unusual in other systems. Moreover, little is known about the centromeric and telomeric sequences of lower Dipterans in general, and there are recent claims of horizontally-transferred genes in fungus gnats. Overall, there is a pressing need to learn more about the fungus gnat chromosome sequences.

RESULTS: We produced the first chromosome-scale models of the X and autosomal chromosomes where each somatic chromosome is represented by a single scaffold. Extensive analysis supports the chromosome identity and structural accuracy of the scaffolds, demonstrating they are co-linear with historical polytene maps, consistent with evolutionary expectations, and have accurate centromere positions, chromosome lengths, and copy numbers. The positions of alleged horizontally-transferred genes in the nuclear chromosomes were broadly confirmed by genomic analyses of the chromosome scaffolds using Hi-C and single-molecule long-read datasets. The chromosomal context of repeats shows family-specific biases, such as retrotransposons correlated with the centromeres. Moreover, scaffold termini were enriched with arrays of retrotransposon-related sequence as well as nucleosome-length (~ 175 bp) satellite repeats. Finally, the Hi-C data captured Mb-scale physical interactions on the X chromosome that are seen in polytene spreads, and we characterize these interesting "fold-back regions" at the sequence level for the first time.

CONCLUSIONS: The chromosome scaffolds were shown to be of exceptional quality, including loci harboring horizontally-transferred genes. Repeat analyses demonstrate family-specific biases and telomere repeat candidates. Hi-C analyses revealed the sequences of ultra-long-range interactions on the X chromosome. The chromosome-scale scaffolds pave the way for further studies of the unusual chromosome movements in Bradysia coprophila.},
}

@article {pmid40127991,
year = {2025},
author = {Barretto, LAF and Fowler, CC},
title = {Multifaceted Evolution of the PhoPQ Two-Component System in Salmonella enterica Enhanced the Expression of Horizontally Acquired Virulence Genes.},
journal = {Molecular microbiology},
volume = {123},
number = {5},
pages = {464-478},
doi = {10.1111/mmi.15355},
pmid = {40127991},
issn = {1365-2958},
support = {RGPIN-2020-03964//Natural Sciences and Engineering Research Council of Canada/ ; //NSREC CGS-M Scholarship/ ; //University of Alberta Faculty of Science/ ; },
mesh = {*Bacterial Proteins/genetics/metabolism ; Gene Expression Regulation, Bacterial ; Virulence/genetics ; *Salmonella enterica/genetics/pathogenicity/metabolism ; Escherichia coli/genetics/metabolism ; Escherichia coli Proteins/genetics/metabolism ; Evolution, Molecular ; *Virulence Factors/genetics ; Gene Transfer, Horizontal ; },
abstract = {For a bacterium to adapt to a new environmental niche, its regulatory networks must evolve to effectively sense and respond to cues within that niche. For bacterial pathogens, which encounter harsh and dynamic host niches that require efficient coordination between detecting host cues and regulating virulence genes, this process is a key aspect of how virulence properties evolve. Here, we investigate how a widely conserved two-component regulatory system (TCS), PhoP/PhoQ (PhoPQ), evolved in Salmonella enterica to adopt a new role as a master regulator of gene expression within its species-specific intracellular niche: the Salmonella-containing vacuole (SCV). By comparing Salmonella PhoPQ with the closely related Escherichia coli PhoPQ ortholog, we demonstrate that optimizing virulence gene expression in Salmonella required a multifaceted evolution of several PhoPQ functional domains and establish that distinct genetic differences and mechanisms enhance virulence gene expression for different inducing cues. Interestingly, we find that the increased activity of the Salmonella PhoPQ system has a much more profound impact on the expression of H-NS-repressed, horizontally acquired virulence genes than on the ancestral members of the PhoP regulon. We observe that the PhoPQ systems of other related bacteria exhibit activity levels similar to the E. coli system, suggesting that the differences we observe are the result of Salmonella-specific adaptations that produced a more active PhoPQ system when encountering SCV conditions. Collectively, this study offers a window into the evolutionary adaptations of a TCS that enable it to assume an expanded regulatory role in a unique environment.},
}

*Bacterial Proteins/genetics/metabolism
Gene Expression Regulation, Bacterial
Virulence/genetics
*Salmonella enterica/genetics/pathogenicity/metabolism
Escherichia coli/genetics/metabolism
Escherichia coli Proteins/genetics/metabolism
Evolution, Molecular
*Virulence Factors/genetics
Gene Transfer, Horizontal

@article {pmid40319560,
year = {2025},
author = {Gross, N and Brodard, I and Overesch, G and Kittl, S},
title = {Genetic basis of β-lactam resistance in Corynebacterium auriscanis and association with otitis externa in dogs and cats.},
journal = {Veterinary microbiology},
volume = {305},
number = {},
pages = {110526},
doi = {10.1016/j.vetmic.2025.110526},
pmid = {40319560},
issn = {1873-2542},
abstract = {Corynebacterium (C.) auriscanis is an opportunistic pathogen regularly isolated from canine otitis externa, an important condition often hard to treat. We found a surprisingly high prevalence of β-lactam resistant isolates of C. auriscanis (47 %), even though β-lactams are not routinely used for otitis externa treatment in Switzerland. To determine the genetic base of this phenotype, a selection of isolates of C. auriscanis with high and low minimal inhibitory concentration values were subjected to whole genome sequencing. Comparative analysis revealed a gene cassette containing three genes (hdfR encoding a LysR-family transcriptional regulator, blaB encoding a β-lactamase related protein and pbp2c encoding a D,D-transpeptidase) as the likely resistance-encoding determinant in the isolates from otitis externa. This locus had previously been described in C. jeikeium as well as C. diphtheriae and was associated with mobile genetic elements. In our six C. auriscanis isolates the pbp2c locus was always associated with the same IS3 family transposase, an association also found on C. diphtheriae plasmid CP091096, indicating horizontal gene transfer between species. To elucidate the function of the three genes in the pbp2c locus, we constructed plasmids with different combinations of these genes, transformed β-lactam sensitive isolates with the plasmids and tested resistance in the mutants phenotypically. By doing so we confirmed Pbp2c to be the primary factor conferring β-lactam resistance and HdfR and BlaB being important for expression and regulation. Interestingly, resistance to all β-lactams including carbapenems was constitutive in one C. auriscanis transformant while an induction effect was visible for the other transformed C. auriscanis strain, C. glutamicum and C. rouxii as previously described for C. jeikeium. Therefore, testing of β-lactam resistance should be done in combination including induction in Corynebacterium spp.},
}

@article {pmid40318462,
year = {2025},
author = {Zhang, T and Fan, L and Zhang, YN},
title = {Antibiotic resistance genes in aquatic systems: Sources, transmission, and risks.},
journal = {Aquatic toxicology (Amsterdam, Netherlands)},
volume = {284},
number = {},
pages = {107392},
doi = {10.1016/j.aquatox.2025.107392},
pmid = {40318462},
issn = {1879-1514},
abstract = {The widespread use of antibiotics has significantly contributed to the spread of antibiotic resistance genes (ARGs), which have become a major challenge to global ecological and public health. Antibiotic resistance not only proliferates in clinical settings but also persists in aquatic systems, where its residues and cross-domain spread pose a dual threat to both ecosystems and human health. ARGs spread rapidly within microbial communities through horizontal gene transfer (HGT) and vertical gene transfer (VGT). Aquatic systems are the key transmission medium. This review summarizes recent studies on the Source-Transport-Sink dynamics of ARGs in aquatic environments, along with their environmental and health risk assessments, with a particular focus on the potential ecotoxicity of ARGs transmission. It also examines the distribution characteristics of ARGs across different regions and the ecological risk assessment methods employed, highlighting the limitations of existing models when addressing the complex behaviors of ARGs. By analyzing the potential hazards of ARGs to aquatic ecosystems and public health, this article aims to provide a scientific foundation for future research and the development of public policies.},
}

@article {pmid40314822,
year = {2025},
author = {Bell I, PJ and Muniyan, R},
title = {Synergistic pathogenesis: exploring biofilms, efflux pumps and secretion systems in Acinetobacter baumannii and Staphylococcus aureus.},
journal = {Archives of microbiology},
volume = {207},
number = {6},
pages = {134},
pmid = {40314822},
issn = {1432-072X},
mesh = {*Biofilms/growth & development ; *Acinetobacter baumannii/pathogenicity/drug effects/physiology/genetics ; Humans ; *Staphylococcus aureus/pathogenicity/drug effects/physiology/genetics/metabolism ; Anti-Bacterial Agents/pharmacology ; Virulence Factors/metabolism/genetics ; Staphylococcal Infections/microbiology/drug therapy ; Drug Resistance, Multiple, Bacterial ; Cross Infection/microbiology ; *Membrane Transport Proteins/metabolism/genetics ; Bacterial Proteins/metabolism/genetics ; Acinetobacter Infections/microbiology ; },
abstract = {Antimicrobial resistance (AMR) is a growing global health crisis, particularly among ESKAPE pathogens: Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species. Among them, A. baumannii and S. aureus are major contributors to nosocomial infections, with high prevalence in intensive care units and immunocompromised patients. Their ability to resist multiple antibiotic classes complicates treatment strategies, leading to increased morbidity and mortality. Key resistance mechanisms, including biofilm formation, efflux pump activity, and horizontal gene transfer, enhance their survival and persistence. Furthermore, interactions during polymicrobial infections intensify disease severity through synergistic effects that promote both virulence and resistance. The epidemiological burden of these pathogens highlights the urgent need for novel antimicrobial strategies and targeted interventions. This review explores their virulence factors, resistance mechanisms, pathogenic interactions, and clinical implications, emphasizing the necessity of innovative therapeutic approaches to combat their growing threat.},
}

*Biofilms/growth & development
*Acinetobacter baumannii/pathogenicity/drug effects/physiology/genetics
Humans
*Staphylococcus aureus/pathogenicity/drug effects/physiology/genetics/metabolism
Anti-Bacterial Agents/pharmacology
Virulence Factors/metabolism/genetics
Staphylococcal Infections/microbiology/drug therapy
Drug Resistance, Multiple, Bacterial
Cross Infection/microbiology
*Membrane Transport Proteins/metabolism/genetics
Bacterial Proteins/metabolism/genetics
Acinetobacter Infections/microbiology

@article {pmid40311358,
year = {2025},
author = {Gómez-Brandón, M and Aira, M and Probst, M and Liu, N and Zhang, Z and Zhu, YG and Domínguez, J},
title = {Earthworms attenuate antibiotic resistance genes and mobile genetic elements during vermicomposting of sewage sludge.},
journal = {Journal of environmental management},
volume = {384},
number = {},
pages = {125562},
doi = {10.1016/j.jenvman.2025.125562},
pmid = {40311358},
issn = {1095-8630},
abstract = {Sewage sludge is among the richest reservoirs of antibiotic resistance genes (ARGs) that may spread to urban environment. Further investigation is warranted for removal of sludge-borne ARGs in large-scale vermicomposting systems. Under this scenario, there is the necessity to unveil the role of the widely-used earthworm species Eisenia andrei, since the current body of literature mostly focuses on E. fetida. The present study sought to evaluate the changes in sludge-borne ARGs and mobile genetic elements in a pilot-scale vermireactor in the presence of E. andrei in response to both gut- and cast-associated processes (GAPs and CAPs, respectively), by coupling high-throughput quantitative PCR and Illumina sequencing. After gut transit, large decreases in the relative abundances and number of the genes conferring resistance to major antibiotic classes, including some specific genes classified as of potentially high risk to human health, were recorded in the fresh casts. Likewise, genes encoding resistance to heavy metals were about nine-times lower in the egested materials than in the initial sludge. Genes coding for integrases or insertional sequences also exhibited reduced abundance as a result of GAP and CAP processes, suggesting that vermicompost appears to be less prone to horizontal gene transfer than untreated sludge. These findings provide evidence about the capacity of the earthworm E. andrei to diminish the risk of ARG spread during vermicomposting, reinforcing its potential for bioremediation purposes by transforming large quantities of waste into an improved fertiliser. This is crucial to propel vermicomposting technology forward and achieve transition toward net zero-waste process.},
}

@article {pmid40310292,
year = {2025},
author = {Alejandre-Sixtos, JE and Aguirre-Martínez, K and Cruz-López, J and Mares-Rivera, A and Álvarez-Martínez, SM and Zamorano-Sánchez, D},
title = {Insights on the regulation and function of the CRISPR/Cas transposition system located in the pathogenicity island VpaI-7 from Vibrio parahaemolyticus RIMD2210633.},
journal = {Infection and immunity},
volume = {},
number = {},
pages = {e0016925},
doi = {10.1128/iai.00169-25},
pmid = {40310292},
issn = {1098-5522},
abstract = {CRISPR/Cas-mediated transposition is a recently recognized strategy for horizontal gene transfer in a variety of bacterial species. However, our understanding of the factors that control their function in their natural hosts is still limited. In this work, we report our initial genetic characterization of the elements associated with the CRISPR/Cas-transposition machinery (CASTm) from Vibrio parahaemolyticus (VpaCASTm), which are encoded within the pathogenicity island VpaI-7. Our results revealed that the components of the VpaCASTm and their associated CRISPR arrays (VpaCAST system) are transcriptionally active in their native genetic context. Furthermore, we were able to detect the presence of polycistrons and several internal promoters within the loci that compose the VpaCAST system. Our results also suggest that the activity of the promoter of the atypical CRISPR array is not repressed by the baseline activity of its known regulator VPA1391 in V. parahaemolyticus. In addition, we found that the activity of the promoter of tniQ was modulated by a regulatory cascade involving ToxR, LeuO, and H-NS. Since it was previously reported that the activity of the VpaCAST system was less efficient than that of the VchCAST system at promoting transposition of a miniaturized CRISPR-associated transposon (mini-CAST) in Escherichia coli, we analyzed if the transposition efficiency mediated by the VpaCAST system could be enhanced inside its natural host V. parahaemolyticus. We provide evidence that this might be the case, suggesting that there could be host induction factors in V. parahaemolyticus that could enable more efficient transposition of CASTs.IMPORTANCEMobile genetic elements such as transposons play important roles in the evolutionary trajectories of bacterial genomes. The success of transposon dissemination depends on their ability to carry selectable markers that improve the fitness of the host cell or loci with addictive traits such as the toxin-antitoxin systems. Here we aimed to characterize a transposon from Vibrio parahaemolyticus that carries and could disseminate multiple virulence factors. This transposon belongs to a recently discovered family of transposons whose transposition is guided by crRNA. We showed that the transposition machinery of this transposon is transcribed in V. parahaemolyticus and that there are likely host-associated factors that favor transposition in the natural host V. parahaemolyticus over transposition in Escherichia coli.},
}

@article {pmid40307209,
year = {2025},
author = {Song, X and Wang, Y and Wang, Y and Zhao, K and Tong, D and Gao, R and Lv, X and Kong, D and Ruan, Y and Wang, M and Tang, X and Li, F and Luo, Y and Zhu, Y and Xu, J and Ma, B},
title = {Rhizosphere-triggered viral lysogeny mediates microbial metabolic reprogramming to enhance arsenic oxidation.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {4048},
pmid = {40307209},
issn = {2041-1723},
support = {42277283//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42090060//National Natural Science Foundation of China (National Science Foundation of China)/ ; 41991334//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Rhizosphere ; *Arsenic/metabolism ; Oxidation-Reduction ; *Oryza/microbiology/virology/metabolism ; Soil Microbiology ; *Lysogeny/genetics ; Microbiota/genetics ; Gene Transfer, Horizontal ; Metagenome ; Plant Roots/microbiology/virology ; Oxidoreductases/genetics/metabolism ; Metabolic Reprogramming ; },
abstract = {The rhizosphere is a critical hotspot for metabolic activities involving arsenic (As). While recent studies indicate many functions for soil viruses, much remains overlooked regarding their quantitative impact on rhizosphere processes. Here, we analyze time-series metagenomes of rice (Oryza sativa L.)rhizosphere and bulk soil to explore how viruses mediate rhizosphere As biogeochemistry. We observe the rhizosphere favors lysogeny in viruses associated with As-oxidizing microbes, with a positive correlation between As oxidation and the prevalence of these microbial hosts. Moreover, results demonstrate these lysogenic viruses enrich both As oxidation and phosphorus co-metabolism genes and mediated horizontal gene transfers (HGTs) of As oxidases. In silico simulation with genome-scale metabolic models (GEMs) and in vitro validation with experiments estimate that rhizosphere lysogenic viruses contribute up to 25% of microbial As oxidation. These findings enhance our comprehension of the plant-microbiome-virome interplay and highlight the potential of rhizosphere viruses for improving soil health in sustainable agriculture.},
}

*Rhizosphere
*Arsenic/metabolism
Oxidation-Reduction
*Oryza/microbiology/virology/metabolism
Soil Microbiology
*Lysogeny/genetics
Microbiota/genetics
Gene Transfer, Horizontal
Metagenome
Plant Roots/microbiology/virology
Oxidoreductases/genetics/metabolism
Metabolic Reprogramming

@article {pmid40306591,
year = {2025},
author = {Sam-On, MFS and Mustafa, S and Mohd Hashim, A and Abdul Malek, AZ},
title = {Probiogenomic insights into Bacillus velezensis MFSS1 for controlling aquaculture pathogens.},
journal = {Microbial pathogenesis},
volume = {205},
number = {},
pages = {107645},
doi = {10.1016/j.micpath.2025.107645},
pmid = {40306591},
issn = {1096-1208},
abstract = {Bacillus velezensis MFSS1 (previously known as B. subtilis FS6) was reported to have good probiotic criteria and antibacterial activity against Vibrio spp. and Aeromonas spp., through phenotypic analysis. However, whole genome sequencing is required for commercialising a new probiotic, especially due to reports on probiotics that can cause horizontal gene transfer towards the host microbiome. Therefore, this study aims to investigate the comprehensive genomic characteristics of B. velezensis MFSS1, focusing on its antimicrobial genes against aquaculture pathogens, its probiotic traits, and safety assessment. The bacterial genome was sequenced using Oxford Nanopore sequencing, resulting in 7 contigs with a total length of 3,914,361 base pairs and an average G + C content of 46.58 %. The analysis using ContEst16S and average nucleotide identity revealed that the bacterium previously reported as B. subtilis is actually B. velezensis. Additionally, secondary metabolites against pathogens were predicted using the antiSMASH website, which identified eight secondary metabolites: Bacillibactin, Bacilysin, Surfactin, Difficidin, Fengycin, Bacillaene, Macrolactin H, and Plantazolicin. Furthermore, several probiotic markers were detected, functioning in acid tolerance, bile salt tolerance, adhesion, osmotic stress, and intestinal persistence during the delivery of the bacteria to the host. Interestingly, the in silico safety assessment of the bacterium revealed a lack of 96 antibiotic resistance genes and confirmed it as non-pathogenic to humans, compared with genomic bacteria from ATCC. The study indicates that B. velezensis MFSS1 is a good probiotic through genomic analysis and can be commercialised to control aquaculture pathogens and reduce reliance on antibiotics.},
}