@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.},
}

@article {pmid40306109,
year = {2025},
author = {Huang, X and Hou, Y and Zhao, M and Chen, J and Zhu, Z and Liu, H and Wang, M and Hua, L and Chen, H and Wu, B and Peng, Z},
title = {Identification of a broad-spectrum lytic Bordetella phage and assessments of its potential for combating Bordetella infections.},
journal = {Virology},
volume = {608},
number = {},
pages = {110545},
doi = {10.1016/j.virol.2025.110545},
pmid = {40306109},
issn = {1096-0341},
abstract = {Bordetella bronchiseptica (Bb) is a zoonotic respiratory pathogen that frequently causes infections in farming and companion animals, posing threats to agricultural economics and public health. However, Bb strains are intrinsically resistant to several antibiotics commonly used to treat respiratory infections. Phage therapy has been recognized as a promising strategy to combat bacterial infections. In this study, a novel Bordetella phage, designated PY223, was isolated using Bb strains as indicators. Genome network analysis with different phages showed PY223 was related to 15 viral clusters but was not included in any of these clusters. PY223 did not carry any known genes involved in lysogeny and/or horizontal gene transfer. Host range analysis showed that PY223 exhibited the capacity to lyse 70 Bb strains isolated from pigs and/or cats. Measurement of the one-step growth curve showed that PY223 had an incubation period of 10 min and a rapid growth period of 80 min. The burst size was estimated to be approximately 10[9] PFU/cell. In addition, PY223 displayed the capacity to inhibit the growth of Bb for up to 17 h. PY223 was stable under environmental temperatures ranging from 4 °C to 60 °C and/or pH values between 5.0 and 9.0. It remained stable even when exposed to UV light for 30 min. Notably, PY223 effectively eliminated Bb biofilms, inhibited the growth of prophage-harboring Bb strains, and cleared Bb from the environment. In vivo testing in mouse models highlighted its excellent potential for treating respiratory Bordetella infections.},
}

@article {pmid40304893,
year = {2025},
author = {Domingues, S and Lima, T and Escobar, C and Plantade, J and Charpentier, X and da Silva, GJ},
title = {Large DNA fragment ISEc9-mediated transposition during natural transformation allows interspecies dissemination of antimicrobial resistance genes.},
journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology},
volume = {},
number = {},
pages = {},
pmid = {40304893},
issn = {1435-4373},
abstract = {PURPOSE: Antimicrobial resistance poses a significant global health challenge, contributing to a lack of effective therapeutic agents, especially against Gram-negative bacteria. Resistance dissemination is accelerated by horizontal gene transfer (HGT) mechanisms. The extended-spectrum beta lactamases CTX-M confer resistance to several beta-lactams, are usually embedded into plasmids and thought to be mainly disseminated by conjugation. However, an increasing number of isolates carry these enzyme-encoding genes in the chromosome, suggesting that they can spread by other means of HGT. In this study, we aimed to test the involvement of natural transformation in the chromosomal acquisition of a blaCTX-M gene.

METHODS: Natural transformation assays were performed during motility on wet surfaces. Acquisition of foreign DNA by transformants was screened by antimicrobial susceptibility testing, polymerase-chain reaction (PCR) and whole genome sequencing (WGS).

RESULTS: Acinetobacter baumannii A118, a naturally competent clinical strain, was transformed with naked DNA from Salmonella enterica serovar Typhimurium Sal25, which was isolated from swine meat. The transformation occurred at low frequency (2.7 × 10[- 8] ± 2.04 × 10[- 8] transformants per recipient) and blaCTX-M was acquired in one transformant, which was named ACI. WGS of the transformant revealed the acquisition of the blaCTX-M-32 as part of a ca. 36 Kb DNA fragment through an ISEc9-mediated transposition event; various mobile genetic elements and other resistance genes were co-transferred. The blaCTX-M-32 gene was subsequently transferred within A. baumannii at a higher frequency (1.8 × 10[- 6] ± 2.49 × 10[- 6] transformants per recipient).

CONCLUSION: Our results highlight the importance of natural transformation events in the dissemination of antimicrobial resistance genes and mobile genetic elements between and within species.},
}

@article {pmid40304813,
year = {2025},
author = {Qin, S and Wang, H and Wang, M and Shao, B and Ma, C and Yang, B and Jin, X},
title = {Mitochondrial genome evolution in the orchid subfamily Cypripedioideae (Orchidaceae).},
journal = {Functional & integrative genomics},
volume = {25},
number = {1},
pages = {96},
pmid = {40304813},
issn = {1438-7948},
support = {2022YFF1301704)//National Key Research and Development Program of China/ ; },
mesh = {*Orchidaceae/genetics/classification ; *Evolution, Molecular ; *Genome, Mitochondrial ; Phylogeny ; },
abstract = {In this study, the mitogenomes of nine species in the subfamily Cypripedioideae were newly sequenced and assembled using both short and long reads for evolutionary analyses. Complete multi-chromosomal mitogenomes were obtained for Cypripedium subtropicum, C. henryi, Phragmipedium humboldtii, Phr. kovachii, and Paphiopedilum micranthum, and draft assemblies were obtained for four additional Paphiopedilum species. Thirty-nine protein-coding genes were annotated and shared in nine sampled species. sdh4 was discovered in all species of Cypripedioideae, and rpl10 was detected in four species of Paphiopedilum. These two genes might have been horizontally transferred from non-orchid plants at different times. Approximately 101 to 998 repeat sequences were identified with total lengths of 417,136 to 785,960 bp in the mitogenomes of Cypripedioideae. There were 634 and 662 RNA editing sites in C. subtropicum and Pa. gratrixianum, respectively, and C-to-U editing was dominant. The nad and ccm genes exhibited high frequencies of RNA editing. Our study revealed the complexity of orchid mitogenomes, including evidence for the horizontal transfer of rpl10 and sdh4.},
}

*Orchidaceae/genetics/classification
*Evolution, Molecular
*Genome, Mitochondrial
Phylogeny

@article {pmid40303475,
year = {2025},
author = {Lu, J and Zhang, R and Yu, Y and Lou, H and Li, D and Bao, Q and Feng, C},
title = {Identification of a novel chromosome-encoded fosfomycin resistance gene fosC3 in Aeromonas caviae.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1577167},
pmid = {40303475},
issn = {1664-302X},
abstract = {BACKGROUND: Owing to the rapid emerging of multidrug-, even pandrug-resistant pathogens, and lack of new antibiotics, the older antibiotic, fosfomycin, has been reused in recent years in the clinical practice, especially for treatment of uropathogen infections. With the increased use of fosfomycin, bacterial resistance to it has also increased drastically. Elucidating the resistance mechanism to the antimicrobial has become an urgent task.

METHODS: The putative fosfomycin resistance gene fosC3 was cloned, and minimal inhibitory concentrations were determined by the agar dilution method. Enzyme kinetic parameters were measured by high-performance liquid chromatography. Bioinformatics analysis was applied to understand the evolutionary characteristics of FosC3.

RESULTS: The A. caviae strain DW0021 exhibited high level resistance to several antimicrobials including kanamycin, streptomycin, chloramphenicol, florfenicol, tetracycline, and especially higher to fosfomycin (> 1,024 μg/mL), while genome annotation indicated that no function-characterized resistance gene was associated with fosfomycin resistance. A novel functional gene designated fosC3 responsible for fosfomycin resistance was identified in the chromosome of A. caviae DW0021. Among the function-characterized proteins, FosC3 shared the highest amino acid similarity of 58.65% with FosC2. No mobile genetic element (MGE) was found surrounding the fosC3 gene. The recombinant pMD19-fosC3/DH5α displayed a MIC value of 32 μg/mL to fosfomycin, which revealed a 128-fold increase of MIC value to fosfomycin compared to the control pMD19/E. coli DH5α (0.25 μg/mL). FosC3 was phylogenetically close to FosC2 and exhibited a k cat and K m of 82,442 ± 1,475 s[-1], 70.99 ± 4.31 μM, respectively, and a catalytic efficiency of (1.2 ± 0.3) × 10[3] μM[-1]·s[-1].

CONCLUSION: In this work, a novel functional fosfomycin thiol transferase, FosC3, which shared the highest protein sequence similarity with FosC2, was identified in A. caviae. The fosfomycin inactivation enzyme FosC3 could effectively inactivate fosfomycin by chemical modification. It is implied that such mechanism facilitates A. caviae to respond to fosfomycin exposure, thereby enhancing survival. However, fosC3 was not related with any MGE, which differs from many other fosfomycin thiol transferase genes. As a result, fosC3 is not expected to be transmitted to other species through horizontal gene transfer mechanism. Our findings will contribute to the resistance mechanism of the common pathogenic A. caviae.},
}

@article {pmid40303018,
year = {2024},
author = {Jia, Y and Zheng, Z and Yang, B and Zhang, H and Wang, Z and Liu, Y},
title = {A Broad-Spectrum Horizontal Transfer Inhibitor Prevents Transmission of Plasmids Carrying Multiple Antibiotic Resistance Genes.},
journal = {Transboundary and emerging diseases},
volume = {2024},
number = {},
pages = {7063673},
pmid = {40303018},
issn = {1865-1682},
mesh = {*Gene Transfer, Horizontal/drug effects ; *Plasmids/genetics/drug effects ; *Zidovudine/pharmacology ; *Anti-Bacterial Agents/pharmacology ; Animals ; *Bacteria/drug effects/genetics ; *Drug Resistance, Bacterial/genetics ; },
abstract = {The dissemination of antimicrobial resistance (AMR) severely degrades the performance of antibiotics and constantly paralyzes the global health system. In particular, plasmid-mediated transfer of antibiotic resistance genes (ARGs) across bacteria is recognized as the primary driver. Therefore, antiplasmid transfer approaches are urgently warranted to resolve this intractable problem. Herein, we demonstrated the potential of azidothymidine (AZT), an FDA-approved anti-HIV drug, as a broad-spectrum horizontal transfer inhibitor to effectively prevent the transmission of multiple ARGs, including mcr-1, bla NDM-5, and tet(X4), both in vitro and in vivo. It was also noteworthy that the inhibitory effect of AZT was proved to be valid within and across bacterial genera under different mating conditions. Mechanistic studies revealed that AZT dissipated bacterial proton motive force, which was indispensable for ATP synthesis and flagellar motility. In addition, AZT downregulated bacterial secretion systems involving general and type IV secretion systems (T4SS). Furthermore, the thymidine kinase, which is associated with DNA synthesis, turned out to be the potential target of AZT. Collectively, our work demonstrates the broad inhibitory effect of AZT in preventing ARGs transmission, opening new horizons for controlling AMR.},
}

*Gene Transfer, Horizontal/drug effects
*Plasmids/genetics/drug effects
*Zidovudine/pharmacology
*Anti-Bacterial Agents/pharmacology
Animals
*Bacteria/drug effects/genetics
*Drug Resistance, Bacterial/genetics

@article {pmid40302206,
year = {2025},
author = {Drebes Dörr, NC and Lemopoulos, A and Blokesch, M},
title = {Exploring Mobile Genetic Elements in Vibrio cholerae.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evaf079},
pmid = {40302206},
issn = {1759-6653},
abstract = {Members of the bacterial species Vibrio cholerae are known both as prominent constituents of marine environments and as the causative agents of cholera, a severe diarrheal disease. While strains responsible for cholera have been extensively studied over the past century, less is known about their environmental counterparts, despite their contributions to the species' pangenome. This study analyzed the genome compositions of 46 V. cholerae strains, including pandemic and non-pandemic, toxigenic, and environmental variants, to investigate the diversity of mobile genetic elements (MGEs), embedded bacterial defense systems, and phage-associated signatures. Our findings include both conserved and novel MGEs across strains, pointing to shared evolutionary pathways and ecological niches. The defensome analysis revealed a wide array of antiphage/anti-plasmid mechanisms, extending well beyond the traditional CRISPR-Cas and restriction-modification systems. This underscores the dynamic arms race between V. cholerae and MGEs and suggests that non-pandemic strains may act as reservoirs for emerging defense strategies. Moreover, the study showed that MGEs are integrated into genomic hotspots, which may serve as critical platforms for the exchange of defense systems, thereby enhancing V. cholerae's adaptive capabilities against phage attacks and other invading MGEs. Overall, this research offers new insights into V. cholerae's genetic complexity and potential adaptive strategies, offering a better understanding of the differences between environmental strains and their pandemic counterparts, as well as the possible evolutionary pathways that led to the emergence of pandemic strains.},
}

@article {pmid40301684,
year = {2025},
author = {Wagner, TM and Torres-Puig, S and Yimthin, T and Irobalieva, RN and Heller, M and Kaessmeyer, S and Démoulins, T and Jores, J},
title = {Extracellular vesicles of minimalistic Mollicutes as mediators of immune modulation and horizontal gene transfer.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {674},
pmid = {40301684},
issn = {2399-3642},
mesh = {*Extracellular Vesicles/immunology/metabolism ; *Gene Transfer, Horizontal ; Animals ; Cattle ; Plasmids/genetics ; *Tenericutes/genetics/immunology ; Mycoplasma/genetics/immunology ; Proteomics ; Mycoplasma mycoides/genetics/immunology ; *Immunomodulation ; },
abstract = {Extracellular vesicles (EVs) are central components of bacterial secretomes, including the small, cell wall-less Mollicutes. Although EV release in Mollicutes has been reported, EV proteomic composition and function have not been explored yet. We developed a protocol for isolating EVs of the pathogens Mycoplasma mycoides subsp. capri (Mmc) and Mycoplasma (Mycoplasmopsis) bovis and examined their functionality. Proteomic analysis demonstrated that EVs mirror the proteome of the EV-producing bacteria. EVs exhibited nuclease activity, effectively digesting both circular and linear DNA. Notably, M. bovis EVs elicited immune responses in bovine primary blood cells, like those induced by live M. bovis. Our findings reveal that EVs can carry plasmids and enable their horizontal transfer, known as vesiduction. Specifically, the natural plasmid pKMK1, with an unknown transmission route, was detected in EVs of Mmc 152/93 and the tetM-containing pIVB08 plasmid was associated with EVs released by an Mmc GM12 strain carrying this plasmid. pIVB08 could be transferred via homo- and heterologous vesiduction to Mmc, M. capricolum subsp. capricolum and M. leachii. Vesiduction was impeded by membrane disruption but resisted DNase and Proteinase K treatment, suggesting that EVs protect their cargo. These findings enhance our understanding of Mollicutes EVs, particularly in host interactions and horizontal gene transfer.},
}

*Extracellular Vesicles/immunology/metabolism
*Gene Transfer, Horizontal
Animals
Cattle
Plasmids/genetics
*Tenericutes/genetics/immunology
Mycoplasma/genetics/immunology
Proteomics
Mycoplasma mycoides/genetics/immunology
*Immunomodulation

@article {pmid40301564,
year = {2025},
author = {Xue, W and Hong, J and Zhao, R and Yao, H and Zhang, Y and Dai, Z and Wang, T},
title = {Spatial entropy drives the maintenance and dissemination of transferable plasmids.},
journal = {Molecular systems biology},
volume = {},
number = {},
pages = {},
pmid = {40301564},
issn = {1744-4292},
support = {2024YFA0920200//MOST | National Key Research and Development Program of China (NKPs)/ ; 32470701//MOST | National Natural Science Foundation of China (NSFC)/ ; HSE499011086//Shenzhen Institute of Synthetic Biology (iSynBio)/ ; },
abstract = {The dissemination of transferable plasmids, a major type of mobile genetic elements (MGEs), is one main driver of antibiotic resistance outbreaks. While the plasmid persistence condition in well-mixed environments has been extensively studied, most microbiota in nature are spatially heterogeneous. However, our knowledge regarding how spatial landscape shapes plasmid maintenance and dissemination remains limited. Here we establish a theoretical framework describing plasmid spread over a metacommunity of multiple patches. By analyzing the gene flow dynamics on randomly generated landscapes, we show that plasmid survival and dispersal are dictated by a simple feature of the landscape, spatial entropy. Reducing entropy speeds up plasmid range expansion and allows the global maintenance of many plasmids that are predicted to be lost by classic theories. The entropy's effects are experimentally validated in E. coli metacommunities transferring a conjugative plasmid. We further examine a vast collection of prokaryotic genomes and show that prokaryotes from low-entropy environments indeed carry more abundant MGEs and antibiotic resistance genes. Our work provides critical insights into the management and control of antimicrobial resistance.},
}

@article {pmid40301151,
year = {2025},
author = {Kaufmann, H and Salvador, C and Salazar, VW and Cruz, N and Dias, GM and Tschoeke, D and Campos, L and Sawabe, T and Miyazaki, M and Maruyama, F and Thompson, F and Thompson, C},
title = {Genomic Repertoire of Twenty-Two Novel Vibrionaceae Species Isolated from Marine Sediments.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {36},
pmid = {40301151},
issn = {1432-184X},
mesh = {*Geologic Sediments/microbiology ; *Vibrionaceae/genetics/classification/isolation & purification ; *Genome, Bacterial ; Phylogeny ; Japan ; *Seawater/microbiology ; Genetic Variation ; },
abstract = {The genomic repertoire of vibrios has been extensively studied, particularly regarding their metabolic plasticity, symbiotic interactions, and resistance mechanisms to environmental stressors. However, little is known about the genomic diversity and adaptations of vibrios inhabiting deep-sea marine sediments. In this study, we investigated the genomic diversity of vibrios isolated from deep-sea core sediments collected using a manned submersible off Japan. A total of 50 vibrio isolates were obtained and characterized phenotypically, and by genome sequencing. From this total, we disclosed 22 novel species examining genome-to-genome distance, average amino acid identity, and phenotypes (Alivibrio: 1; Enterovibrio: 1; Photobacterium: 8; Vibrio: 12). The novel species have fallen within known clades (e.g., Fisheri, Enterovibrio, Profundum, and Splendidus) and novel clades (JAMM0721, JAMM0388, JAMM0395). The 28 remainder isolates were identified as known species: Aliivibrio sifiae (2), A. salmonicida (1), Enterovibrio baiacu (1), E. norvegicus (1), Photobacterium profundum (3), P. angustum (1), P. chitiniliticum (1), P. frigidiphilum (1), Photobacterium indicum (1), P. sanguinicancri (1). P. swingsii (2), Vibrio alginolyticus (3), V. anguillarum (1), V. campbellii (1), V. fluvialis (1), V. gigantis (1), V. lentus (1), V. splendidus (4), and V. tasmaniensis (1). Genomic analyses revealed that all 50 vibrios harbored genes associated with high-pressure adaptation, including sensor kinases, chaperones, autoinducer-2 (AI-2) signaling, oxidative damage repair, polyunsaturated fatty acid biosynthesis, and stress response mechanisms related to periplasmic and outer membrane protein misfolding under heat shock and osmotic stress. Additionally, alternative sigma factors, trimethylamine oxide (TMAO) respiration, and osmoprotectant acquisition pathways were identified, further supporting their ability to thrive in deep-sea environments. Notably, the genomes exhibited a high prevalence of antibiotic resistance genes, with antibiotic efflux pumps being the most abundant group. The ugd gene expanded in number in some novel species (Photobacterium satsumensis sp. nov. JAMM1754: 4 copies; Vibrio makurazakiensis sp. nov. JAMM1826: 3 copies). This gene may confer antibiotic (polymyxin) resistance to these vibrios.},
}

*Geologic Sediments/microbiology
*Vibrionaceae/genetics/classification/isolation & purification
*Genome, Bacterial
Phylogeny
Japan
*Seawater/microbiology
Genetic Variation

@article {pmid40300599,
year = {2025},
author = {Ba, F and Zhang, Y and Wang, L and Ji, X and Liu, WQ and Ling, S and Li, J},
title = {Integrase enables synthetic intercellular logic via bacterial conjugation.},
journal = {Cell systems},
volume = {},
number = {},
pages = {101268},
doi = {10.1016/j.cels.2025.101268},
pmid = {40300599},
issn = {2405-4720},
abstract = {Integrases have been widely used in synthetic biology for genome engineering and genetic circuit design. They mediate DNA recombination to alter the genotypes of single cell lines in vivo, with these changes being permanently recorded and inherited via vertical gene transfer. However, integrase-based intercellular DNA messaging and its regulation via horizontal gene transfer remain underexplored. Here, we introduce a versatile strategy to design, build, and test integrase-based intercellular DNA messaging through bacterial conjugation. First, we screened conjugative plasmids and recipient cells for efficient conjugation. Then, we established a layered framework to describe the interactions among hierarchical E. coli strains and implemented dual-layer Boolean logic gates to demonstrate intercellular DNA messaging and management. Finally, we expanded the design to include four-layer single-processing pathways and dual-layer multi-processing systems. This strategy advances intercellular DNA messaging, hierarchical signal processing, and the application of integrase in systems and synthetic biology.},
}

@article {pmid40298586,
year = {2025},
author = {Niño-Vega, GA and Ortiz-Ramírez, JA and López-Romero, E},
title = {Novel Antibacterial Approaches and Therapeutic Strategies.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {4},
pages = {},
pmid = {40298586},
issn = {2079-6382},
abstract = {The increase in multidrug-resistant organisms worldwide is a major public health threat driven by antibiotic overuse, horizontal gene transfer (HGT), environmental drivers, and deficient infection control in hospitals. In this article, we discuss these factors and summarize the new drugs and treatment strategies suggested to combat the increasing challenges of multidrug-resistant (MDR) bacteria. New treatments recently developed involve targeting key processes involved in bacterial growth, such as riboswitches and proteolysis, and combination therapies to improve efficacy and minimize adverse effects. It also tackles the challenges of the Gram-negative bacterial outer membrane, stressing that novel strategies are needed to evade permeability barriers, efflux pumps, and resistance mechanisms. Other approaches, including phage therapy, AMPs, and AI in drug discovery, are also discussed as potential alternatives. Finally, this review points out the urgency for continued research and development (R&D), industry-academic partnerships, and financial engines to ensure that MDR microbes do not exceed the value of antibacterial therapies.},
}

@article {pmid40298491,
year = {2025},
author = {Karampatakis, T and Tsergouli, K and Behzadi, P},
title = {Carbapenem-Resistant Pseudomonas aeruginosa's Resistome: Pan-Genomic Plasticity, the Impact of Transposable Elements and Jumping Genes.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {4},
pages = {},
pmid = {40298491},
issn = {2079-6382},
abstract = {Pseudomonas aeruginosa, a Gram-negative, motile bacterium, may cause significant infections in both community and hospital settings, leading to substantial morbidity and mortality. This opportunistic pathogen can thrive in various environments, making it a public health concern worldwide. P. aeruginosa's genomic pool is highly dynamic and diverse, with a pan-genome size ranging from 5.5 to 7.76 Mbp. This versatility arises from its ability to acquire genes through horizontal gene transfer (HGT) via different genetic elements (GEs), such as mobile genetic elements (MGEs). These MGEs, collectively known as the mobilome, facilitate the spread of genes encoding resistance to antimicrobials (ARGs), resistance to heavy metals (HMRGs), virulence (VGs), and metabolic functions (MGs). Of particular concern are the acquired carbapenemase genes (ACGs) and other β-lactamase genes, such as classes A, B [metallo-β-lactamases (MBLs)], and D carbapenemases, which can lead to increased antimicrobial resistance. This review emphasizes the importance of the mobilome in understanding antimicrobial resistance in P. aeruginosa.},
}

@article {pmid40298490,
year = {2025},
author = {Garcia-Torné, M and Falcó, I and Borrell, X and Bautista, A and Mazigh, R and Aznar, R and Sánchez, G and Farré, M and Llorca, M},
title = {Comprehensive Study of Antibiotics and Antibiotic Resistance Genes in Wastewater and Impacted Mediterranean Water Environments.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {4},
pages = {},
pmid = {40298490},
issn = {2079-6382},
support = {869178-Aquatic Pollutants//Water JPI/ ; ON-HEALTH 2021 SGR 01150//Government of Catalonia/ ; CEX2021-001189-S//Spanish Ministry of Science and Innovation/ ; PRE2021-099409//Spanish Ministry of Science and Innovation/ ; MS21-006//Ministry of Universities of the Government of Spain, financed by the European Union (NextGeneration EU)/ ; },
abstract = {Background: The spread of antimicrobial resistance is a central public health problem. Wastewater treatment plants and impacted environments are well-known hotspots for antibiotic resistance. However, there is still limited knowledge regarding where antibiotic resistance genes (ARGs) acquire mobility. Method: In this study, we aimed to gather evidence on the seasonal patterns of ARG spread in two Mediterranean areas from NE and E of Spain (Ebro River and Ebro Delta, and Xúquer River and Albufera de València), correlating ARG presence, with special focus on the faecal bacteria Escherichia coli, with antibiotic residues and environmental conditions. The analytical methodology employed was based on a suspect screening approach, while a novel prioritisation approach for antibiotics was proposed to identify those areas more susceptible to the spread of ARG. Results: Our findings demonstrate that ARG levels in wastewater were similar across different seasons, although a greater diversity of ARGs was recorded in summer. We hypothesise that horizontal gene transfer among aquatic bacterial populations during the northeastern Mediterranean summer, when temperatures reach approximately 35~40 °C, could be a key driver of ARG dissemination. By contrast, the highest concentrations of antibiotics in winter samples, with temperatures around 5~10 °C, may promote the spread of microbial resistance. Conclusions: Our key findings highlight that water temperature and sunlight irradiation are crucial factors influencing antibiotic levels and microbial abundance, requiring further investigation in future studies.},
}

@article {pmid40294085,
year = {2025},
author = {Bellotti, G and Cortimiglia, C and Antinori, ME and Cocconcelli, PS and Puglisi, E},
title = {Comprehensive genome-wide analysis for the safety assessment of microbial biostimulants in agricultural applications.},
journal = {Microbial genomics},
volume = {11},
number = {4},
pages = {},
pmid = {40294085},
issn = {2057-5858},
mesh = {*Agriculture/methods ; Whole Genome Sequencing ; *Genome, Bacterial ; *Bacteria/genetics/drug effects ; Virulence Factors/genetics ; *Fertilizers/microbiology ; Interspersed Repetitive Sequences ; },
abstract = {Microbial biostimulants (MBs) offer a sustainable approach to agriculture by helping to reduce reliance on synthetic fertilizers. However, as MBs are intentionally released into the environment, their safety should be rigorously assessed. While taxa with qualified presumption of safety (QPS) benefit from established safety indications, non-QPS taxa lack such guidance. To address this gap, we propose a pipeline combining whole genome sequencing (WGS) and extensive literature search (ELS) data to evaluate microbial safety. We analysed public genomes of three QPS species (Rhodopseudomonas palustris, Bacillus velezensis, Priestia megaterium) and four non-QPS genera (Arthrobacter, Azotobacter, Azospirillum, Herbaspirillum), screening them for virulence factors (VFs), antimicrobial resistance (AMR) genes and mobile genetic elements (MGEs). Results confirmed the safety of QPS taxa, revealing no VFs and only a few intrinsic and non-clinically relevant AMRs. Among non-QPS taxa, VF hits were more prevalent in Azotobacter and Azospirillum spp., though they were mostly related to beneficial plant interactions rather than pathogenicity. AMR genes in non-QPS taxa were primarily associated with efflux pumps or were sporadically distributed. Notably, the only genus-wide pattern observed was that most Azospirillum and Herbaspirillum genomes harboured chromosomally encoded β-lactamases sharing similar genetic structures; however, the detected β-lactamase (bla) genes were distantly related to clinically relevant bla variants, and the absence of MGEs suggests a low risk of horizontal gene transfer, indicating the overall safety of these genera. In general, this WGS-ELS framework provides a robust tool for assessing the safety of non-QPS MBs, supporting regulatory decision-making and ensuring their safe use in sustainable agriculture while safeguarding public health.},
}

*Agriculture/methods
Whole Genome Sequencing
*Genome, Bacterial
*Bacteria/genetics/drug effects
Virulence Factors/genetics
*Fertilizers/microbiology
Interspersed Repetitive Sequences

@article {pmid40289079,
year = {2025},
author = {Tsiklauri, R and Kobakhidze, S and Tsereteli, M and Jimsherishvili, L and Kakabadze, N and Koulouris, S and Kotetishvili, M},
title = {Genome data cross-contamination versus interdomain recombination: Equus caballus and Mus musculus genetic loci in the insertion sequence-rich genomes of two clonally related methicillin-resistant Staphylococcus aureus strains from China.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {251},
pmid = {40289079},
issn = {1471-2180},
mesh = {*Methicillin-Resistant Staphylococcus aureus/genetics/classification/isolation & purification ; China ; *Genome, Bacterial ; Animals ; *Recombination, Genetic ; Staphylococcal Infections/microbiology/veterinary ; Horses/microbiology ; *DNA Transposable Elements ; DNA, Bacterial/genetics ; },
abstract = {BACKGROUND: Methicillin-resistant Staphylococcus aureus (MRSA) represents a significant global health threat, responsible for infections in both humans and animals. Determining genetic patterns associated with the genome plasticity of MRSA is critical for predicting the evolutionary trajectories of its emerging pathogenic clones.

RESULTS: The specific genetic loci of the MRSA strains WH3018 and WH9628 from Wuhan, China, ranging in size from 399 to 3,622 base pairs, were determined to be highly homologous (DNA identity: 90.95-100%) to corresponding chromosomal regions from Equus caballus and Mus musculus in the GenBank database. These eukaryotic-associated loci included the microsatellite DNAs or Y chromosome-specific regions from E. caballus, or 45 S-28 S ribosomal RNA/H19 loci from M. musculus, all exhibiting recurrent patterns across the genomes of both MRSA strains. The SplitsTree and RDP4 analyses did not reveal significant recombination signals for the eukaryotic-associated loci that had mimicked interdomain recombination events in the MRSA strains WH3018 and WH9628. The G + C content of these loci (47.6-65.0%) was notably higher than that of the S. aureus reference genome (32.5%). Furthermore, the MRSA genomes showed a significantly larger number and greater diversity of insertion sequences (ISs) (38 ISs per genome) compared to the S. aureus reference genome (16 ISs). Additionally, these genomes also exhibited an extensive decay of prophages and the accumulation of pseudo-transposases.

CONCLUSIONS: The recurring patterns of the eukaryotic-associated loci strongly suggested genome data contamination across the genomes of the MRSA strains WH3018 and WH9628. These MRSA genomes likely underwent extensive prophage decay and an increased proliferation of pseudo-transposases.},
}

*Methicillin-Resistant Staphylococcus aureus/genetics/classification/isolation & purification
China
*Genome, Bacterial
Animals
*Recombination, Genetic
Staphylococcal Infections/microbiology/veterinary
Horses/microbiology
*DNA Transposable Elements
DNA, Bacterial/genetics

@article {pmid40288735,
year = {2025},
author = {Wang, M and Masoudi, A and Wang, C and Feng, J and Yu, Z and Liu, J},
title = {Urban afforestation converges soil resistome and mitigates the abundance of human pathogenic bacteria.},
journal = {Environmental research},
volume = {278},
number = {},
pages = {121693},
doi = {10.1016/j.envres.2025.121693},
pmid = {40288735},
issn = {1096-0953},
abstract = {Afforestation has emerged as a nature-based strategy for climate mitigation and urban sustainability, yet its effects on antibiotic resistance genes (ARGs) in soils remain underexplored. This study investigates how the conversion of croplands into plantation forests affects the soil resistome, bacterial communities, and physicochemical properties in an urban environment. Using high-throughput metagenomic and 16S rRNA amplicon sequencing, we analyzed soil samples from croplands and afforested plots with Chinese pine (Pinus tabulaeformis) and Chinese scholar (Sophora japonica) trees, across two-time points post-afforestation. Our results show that afforestation promotes the convergence of both bacterial and ARG communities over time, accompanied by a significant reduction in the relative abundance of human pathogenic bacteria. Afforested soils exhibited a lower prevalence of high-risk ARGs (e.g., qnrA, qnrB from the quinolone class) and reduced co-occurrence between ARGs and mobile genetic elements (MGEs), particularly transposases and recombinases, suggesting diminished horizontal gene transfer. Additionally, afforestation-induced changes in soil pH and nutrient dynamics emerged as key ecological factors shaping ARG profiles. Differences between afforestation types were also observed, with Pinus plantations presenting lower ARG-derived risks than Sophora forests. This study supports afforestation as a nature-based solution for enhancing urban sustainability, reducing public health risks, and achieving resilient ecosystems under anthropogenic influence.},
}

@article {pmid40288673,
year = {2025},
author = {Kabeya, N and Ramos-Llorens, M and Nakano, Y and Gomes-Dos-Santos, A and Teixeira, A and Fujibayashi, M and Haro, JG and Navarro, JC and Castro, LFC and Haga, Y and Monroig, Ó},
title = {Methyl-end desaturases determine the capability for de novo biosynthesis of polyunsaturated fatty acids in bivalves.},
journal = {Biochimica et biophysica acta. Molecular and cell biology of lipids},
volume = {1870},
number = {5},
pages = {159617},
doi = {10.1016/j.bbalip.2025.159617},
pmid = {40288673},
issn = {1879-2618},
abstract = {Recent studies have shown that many invertebrate species possess methyl-end desaturases (herein referred to as 'ωx'), enabling biosynthesis of polyunsaturated fatty acids (PUFA). However, the phylogenetic distribution of these enzymes across the animal kingdom remains puzzling, possibly due to horizontal gene transfer (HGT) and/or independent large-scale gene loss in certain invertebrate lineages. In molluscs, ωx genes have been identified in various cephalopods and gastropods but remain barely explored in bivalves. The increasing availability of genomic and transcriptomic resources enables a comprehensive exploration of the ωx gene repertoire in bivalves. To elucidate the distribution of ωx in bivalves, we conducted a broad homology search across existing genome and transcriptome assemblies, followed by functional characterisation of ωx in lineage representative species. Our results revealed no ωx-like sequences in any of the 65 Pteriomorphia species, suggesting gene loss in this clade. However, ωx-like sequences were found in Protobranchia, Palaeoheterodonta and Imparidentia. We analysed ωx from Solemya pusilla (Protobranchia), Lanceolaria oxyrhyncha and Margaritifera margaritifera (Palaeoheterodonta), and Ruditapes philippinarum and Tridacna crocea (Imparidentia). Except for M. margaritifera, which had two ωx genes, each species had a single ωx gene. Functional analysis showed Δ15Δ17Δ19 desaturase activity in the R. philippinarum and T. crocea ωx, while the L. oxyrhyncha ωx exhibited Δ15Δ17 activity but not Δ19. Both ωx from M. margaritifera showed no detectable activity in yeast. Interestingly, the S. pusilla ωx exhibited Δ12 desaturase activity. These findings highlight the diversity of ωx desaturation capabilities in bivalves, with significant gene loss in Pteriomorphia.},
}

@article {pmid40284824,
year = {2025},
author = {Silva, V and Caniça, M and de la Rivière, R and Barros, P and Cabral, JA and Poeta, P and Igrejas, G},
title = {Bats as Hosts of Antimicrobial-Resistant Mammaliicoccus lentus and Staphylococcus epidermidis with Zoonotic Relevance.},
journal = {Veterinary sciences},
volume = {12},
number = {4},
pages = {},
pmid = {40284824},
issn = {2306-7381},
abstract = {Bats are increasingly recognized as reservoirs for antimicrobial-resistant bacteria, playing a potential role in the dissemination of resistance genes across species and regions. In this study, 105 bats from 19 species in Portugal were sampled to investigate the presence, antimicrobial resistance, and genetic characteristics of Mammaliicoccus and Staphylococcus isolates. Thirteen Mammaliicoccus lentus and Staphylococcus epidermidis were recovered. Antimicrobial susceptibility testing revealed multidrug resistance in three isolates, with S. epidermidis carrying mph(C), msr(A), and dfrC genes, and M. lentus harboring salB, tet(K), and str. Notably, qacA was detected in S. epidermidis, highlighting its plasmid-associated potential for horizontal gene transfer to more pathogenic bacteria. Heavy metal resistance genes (arsB and cadD) were also identified, suggesting the role of environmental factors in co-selecting antimicrobial resistance. Molecular typing revealed the S. epidermidis strain as ST297, a clone associated with both healthy humans and invasive infections. These findings emphasize the need for monitoring bats as reservoirs of resistance determinants, particularly in the context of zoonotic and environmental health. The presence of mobile genetic elements and plasmids further underscores the potential for the dissemination of resistance. This study reinforces the importance of adopting a One Health approach to mitigate the risks associated with antimicrobial resistance.},
}

@article {pmid40284646,
year = {2025},
author = {Alglave, L and Faure, K and Mullié, C},
title = {Plasmid Dissemination in Multispecies Carbapenemase-Producing Enterobacterales Outbreaks Involving Clinical and Environmental Strains: A Narrative Review.},
journal = {Microorganisms},
volume = {13},
number = {4},
pages = {},
pmid = {40284646},
issn = {2076-2607},
abstract = {Outbreaks involving carbapenemase-producing enterobacteria (CPE) have become a common occurrence in healthcare settings. While clonal dissemination is firmly established as a cause for these outbreaks, horizontal gene transfers (HGTs) between different species of Enterobacterales found in clinical and environmental isolates are less so. To gather evidence backing up this hypothesis, a review covering the 2013-2024 period was performed. HGTs between different species of clinical and environmental Enterobacterales were identified in thirteen papers, half of those published within the last three years. A combination of short- and long-read whole genome sequencing (WGS) was predominantly used to identify mobile genetic elements and plasmids. The more frequently reported carbapenemases were KPCs, followed by NDMs and IMPs. Predictably, broad-host-range plasmids were responsible for over 50% of HGTs, with the IncA/C group being in the lead. Klebsiella pneumoniae and Enterobacter cloacae complexes were the most frequent species identified in clinical samples, while Citrobacter freundii dominated environmental ones. Drains and pipework frequently constituted CPE reservoirs in protracted outbreaks, alternating epidemic outbursts with silent phases. Including WGS in a systematic environmental surveillance would help in swiftly identifying those CPE reservoirs and possibly help better control plasmid outbursts by allowing the implementation of adequate infection prevention and control measures.},
}

@article {pmid40284645,
year = {2025},
author = {González-Sánchez, A and Lozano-Aguirre, L and Jiménez-Flores, G and López-Sámano, M and García-de Los Santos, A and Cevallos, MA and Le Borgne, S},
title = {Physiology, Heavy Metal Resistance, and Genome Analysis of Two Cupriavidus gilardii Strains Isolated from the Naica Mine (Mexico).},
journal = {Microorganisms},
volume = {13},
number = {4},
pages = {},
pmid = {40284645},
issn = {2076-2607},
abstract = {Here, we report the characterization of two Cupriavidus strains, NOV2-1 and OV2-1, isolated from an iron-oxide deposit in an underground tunnel of the Naica mine in Mexico. This unique biotope, characterized by its high temperature (≈50 °C) and the presence of heavy metals, is no longer available for sampling at this time. The genomes of NOV2-1 and OV2-1 comprised two replicons: a chromosome of 3.58 and 3.53 Mb, respectively, and a chromid of 2.1 Mb in both strains. No plasmids were found. The average nucleotide identity and the core genome phylogeny showed that NOV2-1 and OV2-1 belonged to the Cupriavidus gilardii species. NOV2-1 and OV2-1 grew up to 48 °C, with an optimal temperature of 42 °C. Discrete differences were observed between C. gilardii CCUG38401[T], NOV2-1, and OV2-1 in the biochemical tests. NOV2-1 and OV2-1 presented resistance to zinc, lead, copper, cadmium, nickel, and cobalt. Several complete and incomplete gene clusters related to the resistance to these heavy metals (ars, czc, cop 1, sil-cop 2, cup, mmf, and mer) were detected in the genome of these strains. Although further studies are needed to determine the origin and role of the detected gene clusters, it is suggested that the czc system may have been mobilized by horizontal gene transfer. This study expands the extreme biotopes where Cupriavidus strains can be retrieved.},
}

@article {pmid40283102,
year = {2025},
author = {Zhao, Y and Wang, Y and Lu, J and Zhu, B and Li, AD},
title = {Exploring the Ecological Impacts of Herbicides on Antibiotic Resistance Genes and Microbial Communities.},
journal = {Life (Basel, Switzerland)},
volume = {15},
number = {4},
pages = {},
pmid = {40283102},
issn = {2075-1729},
support = {BK20230742//the Natural Science Foundation of Jiangsu Province/ ; GWJJ2024100202//2024 Annual Project of the National Health Commission (NHC) Capacity Building and Continuing Education Center/ ; M2022083//Scientific Research Project of Jiangsu Health Committee/ ; ZDXK202249//Jiangsu Provincial Medical Key Discipline/ ; 2024ZB315//Jiangsu Funding Program for Excellent Postdoctor/ ; },
abstract = {The widespread application of herbicides has profound ecological consequences, particularly regarding the distribution of antibiotic resistance genes (ARGs) and microbial communities. In this study, we analyzed herbicide-related metagenomic data to assess the impact of herbicide exposure on ARGs and microbial populations. Our results demonstrate that herbicide application significantly increased the abundance of ARGs, particularly those associated with multidrug resistance, sulfonamides, and bacitracin, with notable increases in subtypes such as bacA and sul1. Microbial community analyses revealed a dominance of Pseudomonadota and Actinomycetota, along with a significant down-regulation of genera like Fibrisoma, Gilsonvirus, Limnobacter, and Wilnyevirus in the experimental group. Additionally, herbicide exposure led to a marked reduction in biodiversity. When threshold values were relaxed, correlation analyses revealed a co-occurrence pattern between multiple genes and sul1, suggesting that horizontal gene transfer plays a pivotal role in the spread of antibiotic resistance in herbicide-contaminated soils. Moreover, environmental factors were found to significantly influence both microbial community composition and ARG distribution. These findings highlight the complex ecological effects of herbicides on microbial diversity and the dissemination of resistance genes, emphasizing the need for further research into the long-term environmental and public health implications of herbicide use.},
}

@article {pmid40280885,
year = {2025},
author = {Kaur, A and Sunny, A and Jones, JB and Goss, EM},
title = {Investigating Plasmids Diversity in X. euvesicatoria pv. perforans Population.},
journal = {Phytopathology},
volume = {},
number = {},
pages = {},
doi = {10.1094/PHYTO-02-25-0042-FI},
pmid = {40280885},
issn = {0031-949X},
abstract = {Plasmids are key drivers of horizontal gene transfer. These genetic elements promote diversification and rapid adaptation of bacterial populations to changing environments by transferring beneficial traits within and between bacterial species. Xanthomonas euvesicatoria pv. perforans is a devastating plant pathogen that causes bacterial spot disease in tomato and pepper. The pathogen population in Florida contains several distinct genetic lineages that differ in relative frequency. The objective of this study was to characterize plasmid diversity and gene content, and plasmid distribution in relation to chromosomal phylogeny. Our in silico-based plasmid prediction revealed the presence of diverse plasmids ranging from ~16 kb to ~235 kb. A network approach based on shared k-mer content uncovered ten distinct plasmid groups with high genetic similarity (cliques). Interestingly, these plasmid cliques were confined to specific phylogenetic clusters suggesting potential incompatibility or restricted plasmid movement between clusters. Some of the predicted plasmids carry virulence genes coding for type III secretion effectors (T3SEs), including transcriptional activator-like effectors (TALEs) and genes related to biocide resistance, such as copper. We also identified gene reshuffling between the plasmids, likely carried out by transposons present within them. Overall, these results provide foundational insights into plasmid diversity in Xanthomonas euvesicatoria pv. perforans with implications for the role of these mobile genetic elements in genome dynamics and pathogen adaptation.},
}

@article {pmid40279390,
year = {2025},
author = {Djermoun, S and Rode, DKH and Jiménez-Siebert, E and Netter, N and Lesterlin, C and Drescher, K and Bigot, S},
title = {Biofilm architecture determines the dissemination of conjugative plasmids.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {17},
pages = {e2417452122},
doi = {10.1073/pnas.2417452122},
pmid = {40279390},
issn = {1091-6490},
support = {ANR-19-ARMB-0006-01//Agence Nationale de la Recherche (ANR)/ ; 16GW0245//Bundesministerium für Bildung und Forschung (BMBF)/ ; RF20200502684//Association Vaincre la Mucoviscidose (French CF Association)/ ; 955910//EC | H2020 | PRIORITY 'Excellent science' | H2020 Marie Skłodowska-Curie Actions (MSCA)/ ; TMCG-3 _ 213801/SNSF_/Swiss National Science Foundation/Switzerland ; DR 982/6-1 part of SPP 2389//Deutsche Forschungsgemeinschaft (DFG)/ ; 57552336//Deutscher Akademischer Austauschdienst France (DAAD France)/ ; 47902YJ//Germaine de Stael swiss Academy of Engineering Sciences/ ; },
mesh = {*Biofilms/growth & development ; *Plasmids/genetics ; *Escherichia coli/genetics/physiology ; *Conjugation, Genetic ; Gene Transfer, Horizontal ; Microscopy, Fluorescence ; },
abstract = {Plasmid conjugation is a contact-dependent horizontal gene transfer mechanism that significantly contributes to the dissemination of antibiotic resistance among bacteria. While the molecular mechanisms of conjugation have been extensively studied, our understanding of plasmid transfer dynamics within spatially structured bacterial communities and the influence of community architecture on plasmid dissemination remains limited. In this study, we use live-cell fluorescence microscopy to investigate the propagation of the broad host range RP4 conjugative plasmid in Escherichia coli populations exhibiting varying levels of spatial organization. In high-density, two-dimensional cell monolayers, direct and tight contact between donors and recipients is not only necessary but also sufficient to trigger RP4 plasmid transfer, ensuring optimal plasmid propagation. In three-dimensional mature biofilms, the emergent community architecture limits the ability of donor cells to enter regions with high cell density, which hinders the establishment of direct contacts with recipients and impedes plasmid transfer in biofilms. In contrast, microcolonies, early-stage biofilms, and biofilms with a lower surface coverage leave open access points for donor cells in regions that later emerge as high-cell-density regions in mature biofilms, which facilitates plasmid transfer. These findings reveal the crucial role of bacterial community architecture in determining the efficiency of plasmid dissemination.},
}

*Biofilms/growth & development
*Plasmids/genetics
*Escherichia coli/genetics/physiology
*Conjugation, Genetic
Gene Transfer, Horizontal
Microscopy, Fluorescence

@article {pmid40278619,
year = {2025},
author = {Pei, Y and Hamar, P and Pei, DS},
title = {Deciphering Multidrug-Resistant Pseudomonas aeruginosa: Mechanistic Insights and Environmental Risks.},
journal = {Toxics},
volume = {13},
number = {4},
pages = {},
pmid = {40278619},
issn = {2305-6304},
support = {CSTB2024TIAD-CYKJCXX0017//Sichuan-Chongqing Special Key Project/ ; },
abstract = {The rise of multidrug-resistant (MDR) Pseudomonas aeruginosa (P. aeruginosa) presents a significant challenge to clinical treatment and environmental risks. This review delves into the complex mechanisms underlying MDR development in P. aeruginosa, such as genetic mutations, horizontal gene transfer (HGT), and the interaction between virulence factors and resistance genes. It evaluates current detection methods, from traditional bacteriology to advanced molecular techniques, emphasizing the need for rapid and accurate diagnostics. This review also examines therapeutic strategies, including broad-spectrum antibiotics, novel drug candidates, combination therapies, and innovative approaches like RNA interference, CRISPR-Cas9 gene editing, and bridge RNA-guided gene editing. Importantly, this review highlights the distribution, migration, and environmental risks of MDR P. aeruginosa, underscoring its adaptability to diverse environments. It concludes by stressing the necessity for continued research and development in antimicrobial resistance, advocating for an integrated approach that combines genomics, clinical practice, and environmental considerations to devise innovative solutions and preserve antibiotic efficacy.},
}

@article {pmid40278556,
year = {2025},
author = {Zeng, Y and Feng, R and Huang, C and Liu, J and Yang, F},
title = {Antibiotic Resistance Genes in Agricultural Soils: A Comprehensive Review of the Hidden Crisis and Exploring Control Strategies.},
journal = {Toxics},
volume = {13},
number = {4},
pages = {},
pmid = {40278556},
issn = {2305-6304},
support = {42277033//the National Natural Science Foundation of China/ ; 202401AT070304//Basic Research Foundation of Yunnan Province of China/ ; Y2024QC28//Central Public-interest Scientific Institution Basal Research Fund/ ; 23JCYBJC00250//Tianjin Municipal Natural Science Foundation/ ; },
abstract = {This paper aims to review the sources, occurrence patterns, and potential risks of antibiotic resistance genes (ARGs) in agricultural soils and discuss strategies for their reduction. The pervasive utilization of antibiotics has led to the accumulation of ARGs in the soil. ARGs can be transferred among microorganisms via horizontal gene transfer, thereby increasing the likelihood of resistance dissemination and heightening the threat to public health. In this study, we propose that physical, chemical, and bioremediation approaches, namely electrokinetic remediation, advanced oxidation, and biochar application, can effectively decrease the abundance of ARGs in the soil. This study also highlights the significance of various control measures, such as establishing a strict regulatory mechanism for veterinary drugs, setting standards for the control of ARGs in organic fertilizers, and conducting technical guidance and on-farm soil monitoring to reduce the environmental spread of ARGs and protect public health.},
}

@article {pmid40275408,
year = {2025},
author = {Pérez-Carrascal, OM and Pratama, AA and Sullivan, MB and Küsel, K},
title = {Unveiling plasmid diversity and functionality in pristine groundwater.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {42},
pmid = {40275408},
issn = {2524-6372},
abstract = {BACKGROUND: Plasmids are key in creating a dynamic reservoir of genetic diversity, yet their impact on Earth's continental subsurface-an important microbial reservoir-remains unresolved. We analyzed 32 metagenomic samples from six groundwater wells within a hillslope aquifer system to assess the genetic and functional diversity of plasmids and to evaluate the role of these plasmids in horizontal gene transfer (HGT).

RESULTS: Our results revealed 4,609 non-redundant mobile genetic elements (MGEs), with 14% (664) confidently classified as plasmids. These plasmids displayed well-specific populations, with fewer than 15% shared across wells. Plasmids were linked to diverse microbial phyla, including Pseudomonadota (42.17%), Nitrospirota (3.31%), Candidate Phyla Radiation (CPR) bacteria (2.56%), and Omnitrophota (2.11%). The presence of plasmids in the dominant CPR bacteria is significant, as this group remains underexplored in this context. Plasmid composition strongly correlated with well-specific microbial communities, suggesting local selection pressures. Functional analyses highlighted that conjugative plasmids carry genes crucial for metabolic processes, such as cobalamin biosynthesis and hydrocarbon degradation. Importantly, we found no evidence of high confidence emerging antibiotic resistance genes, contrasting with findings from sewage and polluted groundwater.

CONCLUSIONS: Overall, our study emphasizes the diversity, composition, and eco-evolutionary role of plasmids in the groundwater microbiome. The absence of known antibiotic resistance genes highlights the need to preserve groundwater in its pristine state to safeguard its unique genetic and functional landscape.},
}

@article {pmid40275130,
year = {2025},
author = {Medina-Chávez, NO and Rodriguez-Cruz, UE and Souza, V and De la Torre-Zavala, S and Travisano, M},
title = {Salty secrets of Halobacterium salinarum AD88: a new archaeal ecotype isolated from Cuatro Cienegas Basin.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {399},
pmid = {40275130},
issn = {1471-2164},
support = {IG200319,IN204822//PAPIIT-DGAPA, UNAM/ ; NASA IDEAS16002//NASA IDEAS/ ; },
mesh = {*Halobacterium salinarum/genetics/isolation & purification/classification/metabolism ; Phylogeny ; Genome, Archaeal ; Mexico ; Genomics ; },
abstract = {The Cuatro Cienegas Basin (CCB) in Mexico, represents a unique ecological habitat, characterized by extreme and fluctuating conditions, providing a window into ancient evolutionary processes. This basin, characterized by hypersalinity and phosphorus scarcity, harbors diverse microbial communities that exhibit remarkable adaptations to oligotrophic conditions. Among these, Halobacterium salinarum, a halophilic archaeon known for its polyploid genome and metabolic versatility, has been extensively studied as a model for extremophile survival. However, only a limited number of H. salinarum strains have been successfully cultured and characterized to date. Here, we report the isolation and genomic analysis of a novel Halobacterium salinarum strain, AD88, from microbial mats at the Archaean Domes site in the CCB. This strain displays unique genomic features, including smaller plasmid sizes and distinctive metabolic pathways for phosphorus and sulfur utilization. Comparative analyses with other Halobacterium strains revealed genetic innovations, such as genes involved in sulfolipid biosynthesis, enabling membrane stability in phosphorus-depleted environments, and adaptations for horizontal gene transfer, which facilitate genomic flexibility in response to environmental pressures. This study reveals that H. salinarum AD88 is the first recorded diploid strain of Halobacterium, a feature previously undocumented in this genus. Phylogenomic reconstruction positioned AD88 tightly within the Halobacterium clade, reflecting its evolutionary history within the genus. Pangenome analysis further highlighted the open nature of the Halobacterium genus, with AD88 contributing novel accessory genes linked to ecological specialization. These findings emphasize the evolutionary significance of the CCB as a natural laboratory for studying microbial adaptation and expand our understanding of archaeal genomic diversity and functional innovation under extreme conditions.},
}

*Halobacterium salinarum/genetics/isolation & purification/classification/metabolism
Phylogeny
Genome, Archaeal
Mexico
Genomics

@article {pmid40274494,
year = {2025},
author = {Good, BH and Bhatt, AS and McDonald, MJ},
title = {Unraveling the tempo and mode of horizontal gene transfer in bacteria.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2025.03.009},
pmid = {40274494},
issn = {1878-4380},
abstract = {Research on horizontal gene transfer (HGT) has surged over the past two decades, revealing its critical role in accelerating evolutionary rates, facilitating adaptive innovations, and shaping pangenomes. Recent experimental and theoretical results have shown how HGT shapes the flow of genetic information within and between populations, expanding the range of possibilities for microbial evolution. These advances set the stage for a new wave of research seeking to predict how HGT shapes microbial evolution within natural communities, especially during rapid ecological shifts. In this article, we highlight these developments and outline promising research directions, emphasizing the necessity of quantifying the rates of HGT within diverse ecological contexts.},
}

@article {pmid40273693,
year = {2025},
author = {Yan, X and Xin, Y and Zhu, L and Tang, Q and Chen, M and Wei, Y and Zhang, J and Richnow, HH},
title = {Neglected role of virus-host interactions driving antibiotic resistance genes reduction in an urban river receiving treated wastewater.},
journal = {Water research},
volume = {282},
number = {},
pages = {123627},
doi = {10.1016/j.watres.2025.123627},
pmid = {40273693},
issn = {1879-2448},
abstract = {Treated wastewater from wastewater treatment plants (WWTPs) is a major contributor to the transfer of antibiotic resistance genes (ARGs) into urban rivers. However, the role of viral communities in this process remains poorly understood. This study focused on North Canal in Beijing, China, which receives over 80 % of its water from treated wastewater, to investigate the impact of viral communities on ARGs transfer. Results showed significant seasonal variation in the abundance and composition of ARGs, with 30 high-risk ARGs detected, accounting for 1.50 % ± 1.28 % of total ARGs. The assembly of ARGs in North Canal followed a stochastic process of homogenizing dispersal, with conjugative mobility playing a key role in horizontal gene transfer with Pseudomonas as primary host for HGT. The potential conjugative mobility of ARGs is significantly higher in wet season (69.4 % ± 17.3 %) compared to dry season (42.9 % ± 17.1 %), with conjugation frequencies ranging from 1.18 × 10[-6] to 2.26 × 10[-4]. Viral species accumulation curves approaching saturation indicated the well captured viral diversity, and no phages carrying ARGs were found among 27,523 non-redundant viral operational taxonomic units. Most of the phages (89.2 % ± 3.8 %) were lytic in North Canal, which were observed to contribute to ARGs reduction by lysing their host bacteria, reflected by higher virus-host ratio and demonstrated by the phage lysis assays in treated wastewater and receiving river. We provided compelling evidence that phage-host interactions can reduce ARGs through host lysis, highlighting their potential role in mitigating ARG transmission in urban rivers receiving treated wastewater.},
}

@article {pmid40273218,
year = {2025},
author = {Urriza, M and Dimaria, G and de Oliveira, LO and Catara, V and Murillo, J},
title = {Comparative genomics of native plasmids from plant pathogenic Gammaproteobacteria.},
journal = {DNA research : an international journal for rapid publication of reports on genes and genomes},
volume = {},
number = {},
pages = {},
doi = {10.1093/dnares/dsaf009},
pmid = {40273218},
issn = {1756-1663},
abstract = {Plasmids are key in the evolution and adaptation of plant pathogenic Gammaproteobacteria (PPG), yet their diversity and functional contributions remain underexplored. Here, comparative genomics revealed extensive variation in plasmid size, replicon types, mobility, and genetic content across PPG. Most plasmids are small (<200 kb), except in Pantoea, exhibiting high coding densities (76-78%). Five ancestral replicon types were identified across multiple orders, indicating vertical descent yet efficient horizontal transfer across taxa, although with limited genetic conservation. Virulence plasmids are widespread (56-68%) but differ in virulence gene content across orders: type III effector (T3E) genes are common in Pseudomonas and Xanthomonas, but rare in Enterobacterales and Xylella, aligning with their smaller effector repertoires. Plasmids frequently carry regulatory genes, highlighting their role in bacterial phenotype modulation. Distinct patterns were observed among orders: Enterobacterales plasmids often harbor thiamine biosynthesis operons and transcriptional regulators but lack post-transcriptional regulators, while Pseudomonas and Xanthomonas plasmids are highly mobile, enriched in T3E genes, and exhibit high insertion sequence densities, fostering DNA mobility. Resistance to ultraviolet light is common, but not to antimicrobial compounds. These findings highlight the dynamic role of plasmids in spreading adaptive traits, shaping virulence, and driving the evolution of plant pathogenic bacteria.},
}

@article {pmid40269132,
year = {2025},
author = {Kumar, T and Rekhi, A and Lee, Y and Tran, J and Nagtalon, AGD and Rohatgi, S and Cyphert, EL},
title = {Leveraging the microbiome to combat antibiotic resistant gynecological infections.},
journal = {npj antimicrobials and resistance},
volume = {3},
number = {1},
pages = {32},
pmid = {40269132},
issn = {2731-8745},
abstract = {The vaginal resistome can be considered a collection of the resistant determinants in the vaginal microbiome. Here we review the vaginal resistome including the microbes and resistant genes harbored in common gynecological infections, vaginal microbes that participate in horizontal gene transfer, host factors that contribute to the resistome, and common therapies. Finally, we provide perspective on technologies that can be leveraged to study the vaginal resistome and remaining challenges.},
}

@article {pmid40268300,
year = {2025},
author = {Goyal, A and Chure, G},
title = {Paradox of the Sub-Plankton: Plausible Mechanisms and Open Problems Underlying Strain-Level Diversity in Microbial Communities.},
journal = {Environmental microbiology},
volume = {27},
number = {4},
pages = {e70094},
pmid = {40268300},
issn = {1462-2920},
mesh = {*Biodiversity ; *Microbiota ; *Bacteria/genetics/classification ; Gene Transfer, Horizontal ; Genetic Variation ; Ecosystem ; Biological Evolution ; },
abstract = {Microbial communities are often complex and highly diverse, typically with dozens of species sharing spatially-restricted environments. Within these species, genetic and ecological variation often exists at a much finer scale, with closely related strains coexisting and competing. While the coexistence of strains in communities has been heavily explored over the past two decades, we have no self-consistent theory of how this diversity is maintained. This question challenges our conventional understanding of ecological coexistence, typically framed around species with clear phenotypic and ecological differences. In this review, we synthesise plausible mechanisms underlying strain-level diversity (termed microdiversity), focusing on niche-based mechanisms such as nutrient competition, neutral mechanisms such as migration, and evolutionary mechanisms such as horizontal gene transfer. We critically assess the strengths and caveats of these mechanisms, acknowledging key gaps that persist in linking genetic similarity to ecological divergence. Finally, we highlight how the origin and maintenance of microdiversity could pose a major challenge to conventional ecological thinking. We articulate a call-to-arms for a dialogue between well-designed experiments and new theoretical frameworks to address this grand conceptual challenge in understanding microbial biodiversity.},
}

*Biodiversity
*Microbiota
*Bacteria/genetics/classification
Gene Transfer, Horizontal
Genetic Variation
Ecosystem
Biological Evolution

@article {pmid40267282,
year = {2025},
author = {Yang, Z and Chen, H and Zhong, GH and Liu, J},
title = {cAMP-Mediated Biofilm eDNA Transfer Facilitates the Resilience of Soil Microbiome to Agrochemical Stress.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c00961},
pmid = {40267282},
issn = {1520-5118},
abstract = {Soil microorganisms utilize extracellular DNA (eDNA)-based biofilms as a defense against xenobiotics. However, the specific effects and transfer pathways of eDNA under persistent agrochemical exposure remain unclear. This study examined the transfer dynamics of carbofuran-hydrolase gene pchA from Pseudomonas stutzeri PS21. During biofilm formation, pchA was released from eDNA, leading to an enrichment of beneficial microorganisms such as Acidobacteria and Elusimicrobia, which enhanced organic compound metabolism and improved soil microbiome resilience. An increase in the pchA-associated mobile genetic elements and the colocalization of pchA with other bacterial species indicated the potential horizontal gene transfer (HGT) under carbofuran exposure. Additionally, carbofuran triggered a cAMP-dependent apoptotic pathway, leading to a 59.6% increase in pchA copy number, which suggested that cAMP played a role in initiating HGT. In conclusion, the cAMP-mediated interspecific transfer of pchA could enhance microbial coadaptation to carbofuran contamination, thereby strengthening the collective defense of soil microbiome against agrochemical stress.},
}

@article {pmid40262895,
year = {2025},
author = {Lind, AL and McDonald, NA and Gerrick, ER and Bhatt, AS and Pollard, K},
title = {Contiguous and complete assemblies of Blastocystis gut microbiome-associated protists reveal evolutionary diversification to host ecology.},
journal = {Genome research},
volume = {},
number = {},
pages = {},
doi = {10.1101/gr.279080.124},
pmid = {40262895},
issn = {1549-5469},
abstract = {Blastocystis, an obligate host-associated protist, is the most common microbial eukaryote in the human gut and is widely distributed across vertebrate hosts. The evolutionary transition of Blastocystis from its free-living stramenopile ancestors to a radiation of host-associated organisms is poorly understood. To explore this, we cultured and sequenced eight strains representing the significant phylogenetic diversity of the genus using long-read, short-read, and Hi-C DNA sequencing, alongside gene annotation and RNA sequencing. Comparative genomic analyses revealed significant variation in gene content and genome structure across Blastocystis Notably, three strains from herbivorous tortoises, phylogenetically distant from human subtypes, have markedly larger genomes with longer introns and intergenic regions, and retain canonical stop codons absent in the human-associated strains. Despite these genetic differences, all eight isolates exhibit gene losses linked to the reduced cellular complexity of Blastocystis, including losses of cilia and flagella genes, microtubule motor genes, and signal transduction genes. Isolates from herbivorous tortoises contained higher numbers of plant carbohydrate-metabolizing enzymes, suggesting that like gut bacteria, these protists ferment plant material in the host gut. We find evidence that some of these carbohydrate-metabolizing enzymes were horizontally acquired from bacteria, indicating that horizontal gene transfer is an ongoing process in Blastocystis that has contributed to host-related adaptation. Together, these results highlight substantial genetic and metabolic diversity within the Blastocystis genus, indicating different lineages of Blastocystis have varied ecological roles in the host gut.},
}

@article {pmid40262702,
year = {2025},
author = {Zhang, S and Sun, C},
title = {Ecological divergence of marine bacteria Alteromonas mediterranea.},
journal = {Molecular phylogenetics and evolution},
volume = {208},
number = {},
pages = {108359},
doi = {10.1016/j.ympev.2025.108359},
pmid = {40262702},
issn = {1095-9513},
abstract = {Alteromonas mediterranea, originally designated as A. macleodii, is a deep-sea ecotype that plays an important ecological role in the ocean. However, a comprehensive understanding of their biogeographic distribution and evolutionary histories remains limited. In this study, our analysis indicated that A. mediterranea members could adapt contrasting marine ecosystems and flourish in nutrient-rich habitats such as feces and coral reefs. No significant correlations between the relative abundance of A. mediterranea members and the environmental variables were identified. Phylogenetic analysis and geographic patterns of A. mediterranea strains suggested that they could be clustered into two clades (clade Ⅰ and clade Ⅱ). In contrast, many distinct genomic traits exist between these clades, such as the complete genes encoding cytochrome o ubiquinol oxidase only involved in clade Ⅱ. Genes were more likely to be lost in the evolutionary history of A. mediterranea relatives. Gene loss might be a major force in all phylogenetic groups driving the distinct clades. Adaptation to different biotopes resulted in the functional differentiation of A. mediterranea members, with the loss of genes encoding carbohydrate-active enzymes. Genes acquired horizontally from unclassified bacteria, and Proteobacteria represented by Gammaproteobacteria played key roles in the functional diversification of A. mediterranea in marine habitats. Given these data, these results are useful for information supplementation of A. mediterranea strains, particularly for making significant advances in understanding marine microbial ecology within different clonal frames using genome-wide recruitments.},
}

@article {pmid40261943,
year = {2025},
author = {Gori, K and Baez-Ortega, A and Strakova, A and Stammnitz, MR and Wang, J and Chan, J and Hughes, K and Belkhir, S and Hammel, M and Moralli, D and Bancroft, J and Drydale, E and Allum, KM and Brignone, MV and Corrigan, AM and de Castro, KF and Donelan, EM and Faramade, IA and Hayes, A and Ignatenko, N and Karmacharya, R and Koenig, D and Lanza-Perea, M and Lopez Quintana, AM and Meyer, M and Neunzig, W and Pedraza-Ordoñez, F and Phuentshok, Y and Phuntsho, K and Ramirez-Ante, JC and Reece, JF and Schmeling, SK and Singh, S and Tapia Martinez, LJ and Taulescu, M and Thapa, S and Thapa, S and van der Wel, MG and Wehrle-Martinez, AS and Stratton, MR and Murchison, EP},
title = {Horizontal transfer of nuclear DNA in transmissible cancer.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {18},
pages = {e2424634122},
doi = {10.1073/pnas.2424634122},
pmid = {40261943},
issn = {1091-6490},
support = {102942/Z/13/A 222551/Z/21/Z//Wellcome Trust (WT)/ ; BB/Y514299/1//UKRI | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; },
mesh = {Animals ; *Gene Transfer, Horizontal ; Dogs ; *Dog Diseases/genetics ; *Venereal Tumors, Veterinary/genetics ; *Cell Nucleus/genetics ; Marsupialia/genetics ; *DNA/genetics ; },
abstract = {Horizontal transfer of nuclear DNA between cells of host and cancer is a potential source of adaptive variation in cancer cells. An understanding of the frequency and significance of this process in naturally occurring tumors is, however, lacking. We screened for this phenomenon in the transmissible cancers of dogs and Tasmanian devils and found an instance in the canine transmissible venereal tumor (CTVT). This involved introduction of a 15-megabase dicentric genetic element, composed of 11 fragments of six chromosomes, to a CTVT sublineage occurring in Asia around 2,000 y ago. The element forms the short arm of a small submetacentric chromosome and derives from a dog with ancestry associated with the ancient Middle East. The introduced DNA fragment is transcriptionally active and has adopted the expression profile of CTVT. Its features suggest that it may derive from an engulfed apoptotic body. Our findings indicate that nuclear horizontal gene transfer, although likely a rare event in tumor evolution, provides a viable mechanism for the acquisition of genetic material in naturally occurring cancer genomes.},
}

Animals
*Gene Transfer, Horizontal
Dogs
*Dog Diseases/genetics
*Venereal Tumors, Veterinary/genetics
*Cell Nucleus/genetics
Marsupialia/genetics
*DNA/genetics

@article {pmid40261018,
year = {2025},
author = {Chi, W and Zhang, H and Li, X and Zhou, Y and Meng, Q and He, L and Yang, Y and Liu, S and Shi, K},
title = {Comparative genomic analysis of 255 Oenococcus oeni isolates from China: unveiling strain diversity and genotype-phenotype associations of acid resistance.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0326524},
doi = {10.1128/spectrum.03265-24},
pmid = {40261018},
issn = {2165-0497},
abstract = {Oenococcus oeni, the only species of lactic acid bacteria capable of fully completing malolactic fermentation under challenging wine conditions, continues to intrigue researchers owing to its remarkable adaptability, particularly in combating acid stress. However, the mechanism underlying its superior adaptation to wine stresses still remains elusive due to the lack of viable genetic manipulation tools for this species. In this study, we conducted genomic sequencing and acid resistance phenotype analysis of 255 O. oeni isolates derived from diverse wine regions across China, aiming to elucidate their strain diversity and genotype-phenotype associations of acid resistance through comparative genomics. A significant correlation between phenotypes and evolutionary relationships was observed. Notably, phylogroup B predominantly consisted of acid-resistant isolates, primarily originating from Shandong and Shaanxi wine regions. Furthermore, we uncovered a noteworthy linkage between prophage genomic islands and acid resistance phenotype. Using genome-wide association studies, we identified key genes correlated with acid resistance, primarily involved in carbohydrates and amino acid metabolism processes. This study offers profound insights into the genetic diversity and genetic basis underlying adaptation mechanisms to acid stress in O. oeni.IMPORTANCEThis study provides valuable insights into the genetic basis of acid resistance in Oenococcus oeni, a key lactic acid bacterium in winemaking. By analyzing 255 isolates from diverse wine regions in China, we identified significant correlations between strain diversity, genomic islands, and acid resistance phenotypes. Our findings reveal that certain prophage-related genomic islands and specific genes are closely linked to acid resistance, offering a deeper understanding of how O. oeni adapts to acidic environments. These discoveries not only advance our knowledge of microbial stress responses but also pave the way for selecting and engineering acid-resistant strains, enhancing malolactic fermentation efficiency and wine quality. This research underscores the importance of genomics in improving winemaking practices and addressing challenges posed by high-acidity wines.},
}

@article {pmid40259521,
year = {2025},
author = {Gatica-Soria, LM and Roulet, ME and Tulle, WD and Sato, HA and Barrandeguy, ME and Sanchez-Puerta, MV},
title = {Highly variable mitochondrial chromosome content in a holoparasitic plant due to recurrent gains of foreign circular DNA.},
journal = {Physiologia plantarum},
volume = {177},
number = {2},
pages = {e70231},
doi = {10.1111/ppl.70231},
pmid = {40259521},
issn = {1399-3054},
support = {06/A092-T1//Secretaría de Investigación, Internacionales y Posgrado, Universidad Nacional de Cuyo/ ; PICT2020-01018//Fondo para la Investigación Científica y Tecnológica/ ; PICT2021 -GTR_TI-00435//Fondo para la Investigación Científica y Tecnológica/ ; },
mesh = {Gene Transfer, Horizontal/genetics ; DNA, Mitochondrial/genetics ; *Chromosomes, Plant/genetics ; *DNA, Circular/genetics ; *Genome, Mitochondrial/genetics ; Evolution, Molecular ; Phylogeny ; },
abstract = {Multichromosomal mitochondrial genomes (mtDNAs) in eukaryotes exhibit remarkable structural diversity, yet intraspecific variability and the origin of the individual chromosomes remain poorly understood. We focus on a holoparasitic angiosperm with an mtDNA consisting of 65 chromosomes largely composed of foreign DNA acquired by horizontal gene transfer (HGT) from its mimosoid hosts. The frequency, timing and population dynamics of these HGT events have not been examined. Here, we sampled different individuals of the holoparasite Lophophytum mirabile, along with their host plants, to assess mtDNA intraspecific variability and capture recent events that may bring insights into the HGT process. We also gathered mitochondrial data from 43 mimosoids to identify older and recent HGT events and assess precisely the proportion of foreign DNA. Through comparative genomic and evolutionary analyses, we uncovered great intraspecific variability in chromosome content and defined the mitochondrial pangenome of L. mirabile with 105 distinct chromosomes. The estimated foreign content reaches 93.5% of the mtDNA, including 73 fully foreign chromosomes that support the circle-mediated HGT model as a key mechanism for their acquisition. We inferred recurrent DNA transfers from the host plants, leading to new mitochondrial chromosomes that replicate autonomously. Our results emphasize the importance of adopting a pangenomic approach to fully capture the genetic diversity and evolution of multichromosomal mitochondrial genomes. This study shows that HGT can strongly influence the mtDNA content and generate enormous intraspecific variability even in geographically close individuals.},
}

Gene Transfer, Horizontal/genetics
DNA, Mitochondrial/genetics
*Chromosomes, Plant/genetics
*DNA, Circular/genetics
*Genome, Mitochondrial/genetics
Evolution, Molecular
Phylogeny

@article {pmid40258067,
year = {2025},
author = {Christman, ND and Dalia, AB},
title = {The molecular basis for DNA-binding by competence T4P is distinct in a representative Gram-positive and Gram-negative species.},
journal = {PLoS pathogens},
volume = {21},
number = {4},
pages = {e1013128},
pmid = {40258067},
issn = {1553-7374},
support = {R35 GM128674/GM/NIGMS NIH HHS/United States ; },
mesh = {*Streptococcus pneumoniae/genetics/metabolism ; *Fimbriae, Bacterial/metabolism/genetics ; *DNA, Bacterial/metabolism/genetics ; *Fimbriae Proteins/metabolism/genetics ; *DNA-Binding Proteins/metabolism/genetics ; *Gram-Negative Bacteria/metabolism/genetics ; *DNA Transformation Competence ; Bacterial Proteins/metabolism/genetics ; *Gram-Positive Bacteria/metabolism/genetics ; Protein Binding ; },
abstract = {Competence type IV pili (T4P) are bacterial surface appendages that facilitate DNA uptake during horizontal gene transfer by natural transformation. These dynamic structures actively extend from the cell surface, bind to DNA in the environment, and then retract to import bound DNA into the cell. Competence T4P are found in diverse Gram-negative (diderm) and Gram-positive (monoderm) bacterial species. While the mechanism of DNA-binding by diderm competence T4P has been the recent focus of intensive study, relatively little is known about DNA-binding by monoderm competence T4P. Here, we use Streptococcus pneumoniae as a model system to address this question. Competence T4P likely bind to DNA via a tip-associated complex of proteins called minor pilins, and recent work highlights a high degree of structural conservation between the minor pilin tip complexes of monoderm and diderm competence T4P. In diderms, positively charged residues in one minor pilin, FimT, are critical for DNA-binding. We show that while these residues are conserved in ComGD, the FimT homolog of monoderms, they only play a minor role in DNA uptake for natural transformation. Instead, we find that two-positively charged residues in the neighboring minor pilin, ComGF (the PilW homolog of monoderms), play the dominant role in DNA uptake for natural transformation. Furthermore, we find that these residues are conserved in other monoderms, but not diderms. Together, these results suggest that the molecular basis for DNA-binding has either diverged or evolved independently in monoderm and diderm competence T4P.},
}

*Streptococcus pneumoniae/genetics/metabolism
*Fimbriae, Bacterial/metabolism/genetics
*DNA, Bacterial/metabolism/genetics
*Fimbriae Proteins/metabolism/genetics
*DNA-Binding Proteins/metabolism/genetics
*Gram-Negative Bacteria/metabolism/genetics
*DNA Transformation Competence
Bacterial Proteins/metabolism/genetics
*Gram-Positive Bacteria/metabolism/genetics
Protein Binding