@article {pmid40815474,
year = {2025},
author = {Gios, E and Mosley, OE and Takeuchi, N and Handley, KM},
title = {Genetic exchange shapes ultra-small Patescibacteria metabolic capacities in the terrestrial subsurface.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0004625},
doi = {10.1128/msystems.00046-25},
pmid = {40815474},
issn = {2379-5077},
abstract = {UNLABELLED: Bacterial genomes are highly dynamic entities, mostly due to horizontal gene transfer (HGT). HGT is thought to be the main driver of genetic variation and adaptation to the local environment in bacteria. However, little is known about the modalities of HGT within natural microbial communities, especially the implications of genetic exchange for streamlined microorganisms such as Patescibacteria (Candidate Phyla Radiation). We searched for evidence of genetic exchange in 125 Patescibacteria genomes recovered from aquifer environments and detected the presence of hundreds of genomic islands, individually transferred genes, and prophages combined, with up to 13% of genome length attributed to HGT. Results show that most individual gene transfer events occurred between Patescibacteria, although putative donors included phylogenetically diverse groundwater microorganisms. For example, results indicate exchange of a lysR transcriptional regulator gene between Omnitrophota and Patescibacteria taxa with highly similar relative abundance patterns across 16 groundwater samples. Overall, results indicate a wide variety of metabolic functions were introduced into Patescibacteria genomes by HGT, including transcription, translation, and DNA replication, recombination and repair. This study illustrates the evolutionarily dynamic nature of Patescibacteria genomes despite the constraints of streamlining and that HGT in these organisms is also mediated via viral infection.

IMPORTANCE: Genomic fluidity and diversity in bacteria are mainly governed by horizontal gene transfer (HGT), leading to a variety of genome structures and physiological diversity. The predominantly uncultivated Patescibacteria comprise highly diverse bacteria that consistently exhibit small cell and genome sizes. Despite strong pressures to reduce genetic content, we predict that these ultra-small bacteria use HGT to the same extent as other bacteria and that HGT may help facilitate recovery and maintenance of critical metabolic functions, niche exploitation, and putative symbiont-host interactions. Here, we determine the contribution of gene exchange to the evolution and diversification of Patescibacteria, despite the constraints of streamlining. We provide evidence of gene gains in Patescibacteria genomes recovered from aquifer environments and describe the large extent to which ultra-small bacterial genomes are subjected to HGT. Results suggest distinct metabolic functions acquired by Patescibacteria compared to general groundwater communities, suggesting specific evolutionary pressures on gene transfer dynamics occurring in ultra-small prokaryotes.},
}

@article {pmid40815008,
year = {2025},
author = {},
title = {Pathway to Independence - an interview with Sonya Widen.},
journal = {Development (Cambridge, England)},
volume = {152},
number = {16},
pages = {},
doi = {10.1242/dev.205117},
pmid = {40815008},
issn = {1477-9129},
abstract = {Sonya Widen is a Postdoctoral Fellow in Alejandro Burga's lab at the Vienna BioCenter, Austria. She is interested in large DNA transposons called Polintons (or Mavericks) that facilitate horizontal gene transfer across nematodes and how they and other transposons with viral-like properties can influence development and evolution. Sonya is part of the 2025 cohort of Development's Pathway to Independence programme, which aims to support postdocs in their transition towards establishing their own labs and securing independent funding. We spoke to Sonya online to learn about her research interests in genome evolution, hopes for the programme and plans for her future lab.},
}

@article {pmid40811916,
year = {2025},
author = {Chen, Y and Liu, S and Ouyang, T and Jiang, R and Ma, J and Lu, G and Yuan, S and Yan, Z},
title = {Reshaping the antibiotic resistance genes in plastisphere upon deposition in sediment-water interface: Dynamic evolution and propagation mechanism.},
journal = {Journal of hazardous materials},
volume = {496},
number = {},
pages = {139532},
doi = {10.1016/j.jhazmat.2025.139532},
pmid = {40811916},
issn = {1873-3336},
abstract = {Microplastics (MPs) could provide unique niches for microbiota and aggravate their gravity, leading to vertical travel from waters to sediments. Although the plastisphere functions as hotspots for antibiotic resistance genes (ARGs) enrichment, the dynamic evolution and mechanisms of ARGs remain poorly understood when MPs deposited at sediment-water interface (SWI). Herein, this study investigated the dynamic response and reshaping mechanism of ARGs in plastisphere across SWI. It reveals that in deep waters, the ARGs abundance in biodegradable polylactic acid (PLA) plastisphere was higher than non-biodegradable polyethylene terephthalate (PET). However, when plastisphere deposited at SWI from deep waters, the ARGs abundance in PET plastisphere was increased by 45.71-65.10 %, while that decreased by 52.15-53.25 % in PLA. The plastisphere across SWI possessed higher species richness and diversity, more complex interactions, and more key species regulating ARGs compared to deep waters. During sedimentation, the horizontal gene transfer potential was enhanced in PET plastisphere but inhibited PLA. In addition, the function response related to oxidative stress response, cell membrane permeability, and energy metabolism may be underlying mechanisms in regulating ARGs propagation during the travel of plastisphere across SWI. This study highlights the critical roles of SWI in regulating the ARGs propagation in the traveling plastisphere.},
}

@article {pmid40811910,
year = {2025},
author = {Zhang, D and Sun, J and Peng, S and Wang, Y and Lin, X and Wang, S},
title = {Biodegradable microplastics exacerbate the risk of antibiotic resistance genes pollution in agricultural soils.},
journal = {Journal of hazardous materials},
volume = {496},
number = {},
pages = {139490},
doi = {10.1016/j.jhazmat.2025.139490},
pmid = {40811910},
issn = {1873-3336},
abstract = {The widespread emergence of antibiotic resistance genes (ARGs) poses a severe global health threat, exacerbated by agricultural practices such as fertilization and plastic mulch use. While biodegradable plastics are promoted as environmentally friendly alternatives to conventional plastics, their ecological impact on soil ARGs remains poorly understood. This study conducted incubation experiments using soils with distinct long-term fertilization histories (no fertilization CK, chemical fertilizer CF, and pig manure PM) collected from 14-year field experiment sites at Changshu National Agro-Ecosystem Observation and Research Station. The soils were exposed to four types of microplastics (conventional: polyethylene [PE] and polyvinyl chloride [PVC]; biodegradable: polylactic acid [PLA] and polybutylene adipate terephthalate [PBAT]), and the ARGs and mobile genetic elements (MGEs) were quantified using high-throughput quantitative PCR, targeting 329 ARG subtypes and 34 MGEs. Results revealed that PM soil exhibited the highest ARGs abundance, and exposure to biodegradable microplastics (PLA and PBAT) further enriched ARGs by 21.5 % and 47.9 %, respectively. Microplastic exposure enhanced horizontal gene transfer potential by strengthening ARG-MGE co-occurrence, and altered bacterial communities by promoting the proliferation of generalist taxa (e.g., Proteobacteria) identified as key hosts of risk ARGs. These findings challenge the assumption of biodegradable plastics as environmentally friendly, demonstrating their potential to exacerbate ARGs pollution in agricultural soils. This study provides critical insights into the interactive effects of fertilization and microplastic exposure on the soil resistome, with implications for plastic management and ARGs risk control in agroecosystems.},
}

@article {pmid40810119,
year = {2025},
author = {Kumavath, R and Gupta, P and Tatta, ER and Mohan, MS and Salim, SA and Busi, S},
title = {Unraveling the role of mobile genetic elements in antibiotic resistance transmission and defense strategies in bacteria.},
journal = {Frontiers in systems biology},
volume = {5},
number = {},
pages = {1557413},
pmid = {40810119},
issn = {2674-0702},
abstract = {Irrational antibiotic use contributes to the development of antibiotic resistance in bacteria, which is a major cause of healthcare-associated infections globally. Molecular research has shown that multiple resistance frequently develops from the uptake of pre-existing resistance genes, which are subsequently intensified under selective pressures. Resistant genes spread and are acquired through mobile genetic elements which are essential for facilitating horizontal gene transfer. MGEs have been identified as carriers of genetic material and are a significant player in evolutionary processes. These include insertion sequences, transposons, integrative and conjugative elements, plasmids, and genomic islands, all of which can transfer between and within DNA molecules. With an emphasis on pathogenic bacteria, this review highlights the salient features of the MGEs that contribute to the development and spread of antibiotic resistance. MGEs carry non-essential genes, including AMR and virulence genes, which can enhance the adaptability and fitness of their bacterial hosts. These elements employ evolutionary strategies to facilitate their replication and dissemination, thus enabling survival without positive selection for the harboring of beneficial genes.},
}

@article {pmid40802478,
year = {2025},
author = {Vesel, N and Stare, E and Štefanič, P and Floccari, VA and Mulec, IM and Dragoš, A},
title = {Naturally competent bacteria and their genetic parasites - A battle for control over horizontal gene transfer?.},
journal = {FEMS microbiology reviews},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsre/fuaf035},
pmid = {40802478},
issn = {1574-6976},
abstract = {Host-mediated natural competence for transformation of DNA and mobile genetic element (MGE)-driven conjugation and transduction are key modes of horizontal gene transfer. While these mechanisms are traditionally believed to shape bacterial evolution by enabling the acquisition of new genetic traits, numerous studies have elucidated an antagonistic relationship between natural transformation and MGEs. A new role of natural transformation as a chromosome curing mechanism has now been proposed. Experimental data, along with mathematical models, suggest that transformation can eliminate deleterious MGEs. Supporting this hypothesis, MGEs have been shown to use various mechanisms to decrease or block transformability, such as disrupting competence genes, regulating the development of competence, hindering DNA uptake machinery, producing DNases that target the exogenous (transforming) DNA, and causing lysis of competent cells. A few examples of synergistic relationships between natural transformation and MGEs have also been reported, with natural transformation facilitating MGE transfer and phages enhancing transformation by supplying extracellular DNA through lysis and promoting competence via kin discrimination. Given the complexity of the relationships between natural transformation and MGEs, the balance between antagonism and synergy likely depends on specific selection pressures in a given context. The evidence collected here indicates a continuous conflict over horizontal gene transfer in bacteria, with semiautonomous MGEs attempting to disrupt host-controlled DNA acquisition, while host competence mechanisms work to resist MGE interference.},
}

@article {pmid40801289,
year = {2025},
author = {Mougin, J and Labreuche, Y and Boulo, V and Goudenège, D and Saad, J and Courtay, G and Le Grand, J and Chevalier, O and Pouzadoux, J and Montagnani, C and Travers, MA and Petton, B and Destoumieux-Garzón, D},
title = {Antibiotic Use in Oyster Hatcheries Promotes Rapid Spread of a Highly Transferable and Modular Resistance Plasmid in Vibrio.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf163},
pmid = {40801289},
issn = {1751-7370},
abstract = {Plasmids play a key role in the horizontal gene transfer of antibiotic resistance genes, particularly in aquaculture where ARG-carrying Vibrio bacteria are frequently detected. Given the expansion of global aquaculture and its reliance on antibiotics, we investigated how these practices influence the emergence, dynamics, and spread of ARGs, focusing on Magallana gigas hatcheries - the world's most widely farmed shellfish. Among the three antibiotics tested, only chloramphenicol led to a pronounced selection and dissemination of chloramphenicol-resistant Vibrio isolates. Resistance was mediated by catA2, located in a highly modular, insertion sequence- and transposase-rich region of a conjugative plasmid, alongside tet(B). This plasmid was closely related to emerging pAQU-type plasmids unreported in Europe. pAQU-MAN, derived from Marine ANtimicrobial resistance, is a low-copy, highly transferable plasmid that rapidly spread throughout the hatchery following CHL treatment. Though naturally found in commensal Vibrio, it exhibited a broad host range, transferring efficiently to both oyster- and human-pathogenic Vibrio strains, as well as to E. coli, with high conjugation rates. Additionally, it remained stable in Vibrio hosts and was transmitted from oyster parents to progenies, even in the absence of antibiotic. It eventually disappeared from the microbial community associated to adults. Our findings highlight that antibiotic use in oyster hatcheries can select for highly modular and transferable multidrug-resistant plasmids, posing a risk of environmental dissemination, although their limited persistence in juvenile oyster reduces the likelihood of transmission to humans. We discuss the human and ecological factor driving pAQU-MAN spread and control in aquaculture settings.},
}

@article {pmid40800620,
year = {2025},
author = {Partanen, V and Dekić Rozman, S and Karkman, A and Muurinen, J and Hiltunen, T and Virta, M},
title = {Use of sequence barcodes for tracking horizontal gene transfer of antimicrobial resistance genes in a microbial community.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf113},
pmid = {40800620},
issn = {2730-6151},
abstract = {One of the most important knowledge gaps in the antimicrobial resistance crisis is the lack of understanding regarding how genes spread from their environmental origins to bacteria pathogenic to humans. In this study our aim was to create a system that allows the conduction of experiments in laboratory settings that mimic the complexity of natural communities with multiple resistance genes and mobile genetic elements circulating at the same time. Here we report a new sequence-based barcode system that allows simultaneous tracking of the spread of antimicrobial resistance genes from multiple genetic origins. We tested this concept with an experiment in which we added an antimicrobial resistance gene to different genetic environments in alive and dead donors and let the gene spread naturally in an artificial microbial community under different environmental conditions to provide examples of factors that can be investigated. We used emulsion, paired-isolation, and concatenation polymerase chain reaction to detect the new gene carriers and metagenomic analysis to see changes in the genetic environment. We observed the genes moving and were able to recognise the barcode from the gene sequences, thus validating the idea of barcode use. We also saw that temperature and gene origin had effects on the number of new host species. Our results confirmed that our system worked and can be further developed for more complicated experiments.},
}

@article {pmid40796329,
year = {2025},
author = {Weng, YM and Martinez, JI and Markee, A and Plotkin, D and Sondhi, Y and Mongue, AJ and Frandsen, PB and Kawahara, AY},
title = {Gene family evolution suggests correlated dietary adaptations in butterflies and moths.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evaf156},
pmid = {40796329},
issn = {1759-6653},
abstract = {Butterflies and moths (Lepidoptera) are a megadiverse lineage of more than 160,000 described species. Their evolutionary success is thought to be tightly correlated with the radiation of flowering plants, but mechanisms on how these insects evolved to feed on so many different plant hosts remain largely unknown. Previous studies found emergent gene families of odorant receptors and peptidases in the ancestor of Lepidoptera, suggesting these genetic innovations may be linked to lepidopteran diversification. Here, we examined 62 genomes and identify lineage-specific gene families within the Lepidoptera and its three major clades. We found 54, 88, 77 and four functionally annotated gene families specific to Lepidoptera, Glossata, Ditrysia, and Apoditrysia, respectively. These families are involved in chemosensation, digestion, detoxification, immunity and other diverse functions. Notably, there is a marked increase in gene families presumably associated with chemosensation and immunity in Glossata and Ditrysia which encompass more than 98% of Lepidoptera diversity. We also identified horizontal gene transfer (HGT) events of two putative digestion gene families (Catalytic LigB subunit of aromatic ring-opening dioxygenase and Glycosyl hydrolases family 32) and a detoxification gene family (Cysteine synthase-like) to the common ancestors of Lepidoptera and Ditrysia, respectively. These HGT events likely played a crucial role in facilitating dietary transitions from algae, diatoms, and aquatic plant debris to fungi and primitive terrestrial plants in early Lepidoptera, ultimately enabling their adaptation to feed on and diversify with angiosperms since the emergence of Ditrysia.},
}

@article {pmid40796304,
year = {2025},
author = {Qing, Y and Liao, Z and An, D and Zeng, Y and Zhu, Q and Zhang, X},
title = {Comparative genomics reveals the genetic diversity and plasticity of Clostridium tertium.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxaf201},
pmid = {40796304},
issn = {1365-2672},
abstract = {AIMS: Clostridium tertium, increasingly recognized as the emerging human pathogen frequently isolated from environmental and clinical specimens, remains genetically underexplored despite its clinical relevance. This study aims to explore the genetic characteristics of C. tertium by genomic analysis.

METHODS AND RESULTS: This study presented a comprehensive genomic investigation of 45 C. tertium strains from the GenBank database. Genome sizes (3.27-4.55 Mbp) and coding gene counts varied markedly across strains. Phylogenetic analyses based on 16S rRNA gene and core genome uncovered distinct intra-species lineages, including evolutionarily divergent clusters likely shaped by niche specialization. Pan-genomic analysis confirmed an open genome, with accessory and strain-specific genes enriched in functions related to environmental adaptation and regulation. Functional annotation further identified diverse virulence factor genes (e.g. clpP, nagK) and antibiotic resistance genes (e.g. vatB, tetA(P)) co-occurring with mobile genetic elements (MGEs), suggesting that horizontal gene transfer (HGT) may be a key driver of genome plasticity in C. tertium. Notably, one-third of the strains carried CRISPR-Cas systems, indicating the defense potential against exogenous genetic elements.

CONCLUSIONS: C. tertium exhibited extensive genetic diversity and genome plasticity, probably driven by MGE-mediated HGT, defense mechanisms of CRISPR-Cas systems, and functional adaptation related to virulence and resistance. These traits may underlie its ability to colonize diverse environments and acquire pathogenicity and resistance.},
}

@article {pmid40794833,
year = {2025},
author = {Frail, S and Steele-Ogus, M and Doenier, J and Moulin, SLY and Braukmann, T and Xu, S and Yeh, E},
title = {Genomes of nitrogen-fixing eukaryotes reveal an alternate path for organellogenesis.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {33},
pages = {e2507237122},
doi = {10.1073/pnas.2507237122},
pmid = {40794833},
issn = {1091-6490},
support = {T32GM007276//HHS | NIH (NIH)/ ; 5T32AI007328-32//HHS | NIH (NIH)/ ; NA//Burroughs Wellcome Fund (BWF)/ ; NA//Chan Zuckerberg Initiative (CZI)/ ; },
mesh = {*Nitrogen Fixation/genetics ; Symbiosis/genetics ; *Diatoms/genetics ; Phylogeny ; *Genome ; Gene Transfer, Horizontal ; Cyanobacteria/genetics ; Evolution, Molecular ; },
abstract = {Endosymbiotic gene transfer (EGT) and import of host-encoded proteins have been considered hallmarks of organelles necessary for stable integration of two cells. However, newer endosymbiotic models have challenged the origin and timing of such genetic integration during organellogenesis. Epithemia diatoms contain diazoplasts, obligate endosymbionts derived from cyanobacteria that are closely phylogenetically related to UCYN-A, a recently described nitrogen-fixing organelle. Diazoplasts function as permanent membrane compartments in Epithemia hosts, but it is unknown if genetic integration has occurred. We report genomic analyses of two Epithemia diatom species, freshwater Epithemia clementina and marine E. pelagica, which are highly divergent but share a common ancestor at the origin of the endosymbiosis <35Mya. We find minimal evidence for genetic integration. Segments of fragmented and rearranged DNA from the diazoplast were detected integrated into the E. clementina nuclear genome, but the transfers that have occurred so far are nonfunctional. No DNA or gene transfers were detected in E. pelagica. In E. clementina, 6 host-encoded proteins of unknown function were identified in the diazoplast proteome, far fewer than detected in recently acquired endosymbiotic organelles. Overall, Epithemia diazoplasts are a valuable counterpoint to existing organelle models, demonstrating that endosymbionts can function as integral compartments-maintained over millions of years of host speciation-absent significant genetic integration. The minimal genetic integration makes diazoplasts valuable blueprints for bioengineering endosymbiotic compartments de novo.},
}

*Nitrogen Fixation/genetics
Symbiosis/genetics
*Diatoms/genetics
Phylogeny
*Genome
Gene Transfer, Horizontal
Cyanobacteria/genetics
Evolution, Molecular

@article {pmid40794100,
year = {2025},
author = {Gewurz, D and Kim, S and Bartu, L and Sharma, A and Harrison, JC and Lee, I and Rondeau, NC and Miranda, JL and Mailloux, BJ and Hamilton, KA and Lopatkin, AJ},
title = {Plasmid prevalence is independent of antibiotic resistance in environmental Enterobacteriaceae.},
journal = {Microbial genomics},
volume = {11},
number = {8},
pages = {},
doi = {10.1099/mgen.0.001453},
pmid = {40794100},
issn = {2057-5858},
mesh = {*Plasmids/genetics ; *Enterobacteriaceae/genetics/drug effects/isolation & purification ; Anti-Bacterial Agents/pharmacology ; Whole Genome Sequencing ; Microbial Sensitivity Tests ; *Drug Resistance, Bacterial/genetics ; Conjugation, Genetic ; },
abstract = {The rapid rise of antibiotic-resistant pathogens poses a critical threat to the treatment of infectious diseases. While the spread of antibiotic resistance genes (ARGs) via plasmid conjugation has been extensively studied both in the lab and the clinic, the prevalence and diversity of plasmids in drug-susceptible isolates (e.g. isolates that do not contain ARGs) remain poorly understood. Yet, plasmids in susceptible isolates play a pivotal role as reservoirs, potentially capturing and disseminating ARGs in situ. To better understand the potential impact of these strains, we investigated the prevalence and characteristics of plasmids in >200 Enterobacteriaceae, including those that are primarily drug susceptible, isolated from diverse environmental sources. Using whole-genome sequencing and a novel bioinformatic pipeline, we quantified the number of large plasmids per isolate and examined the relationship between plasmid abundance and host antibiotic susceptibility profiles. Strikingly, we found a high abundance of plasmids in susceptible strains, with no correlation between plasmid number and susceptibility level to a variety of clinically relevant antibiotics. Moreover, plasmid abundance did not influence a strain's ability to accept additional plasmids via conjugation. These findings reveal that plasmids are widespread in susceptible strains regardless of ARG content and underscore their potential to act as conduits for future resistance dissemination.},
}

*Plasmids/genetics
*Enterobacteriaceae/genetics/drug effects/isolation & purification
Anti-Bacterial Agents/pharmacology
Whole Genome Sequencing
Microbial Sensitivity Tests
*Drug Resistance, Bacterial/genetics
Conjugation, Genetic

@article {pmid40792260,
year = {2025},
author = {Jiang, Y and Shu, L and Wen, H and Wei, Y and Liu, S and Ye, C and Cheng, L and Zeng, Z and Liu, J},
title = {Enhancement of bla IMP-carrying plasmid transfer in Klebsiella pneumoniae by hospital wastewater: a transcriptomic study.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1626123},
pmid = {40792260},
issn = {1664-302X},
abstract = {INTRODUCTION: Klebsiella pneumoniae is a critical ESKAPE pathogen that presents a significant challenge to public health because of its multidrug-resistant strains. This study investigates the impact and mechanisms of hospital wastewater on the horizontal gene transfer of carbapenem resistance genes, particularly bla IMP, in K. pneumoniae.

METHODS: LB broth was prepared using sterile filtered wastewater as the substrate to investigate the impact of wastewater on the transfer of carbapenem-resistant gene bla IMP in K. pneumoniae. The mechanisms of sewage effects on the horizontal transfer of bla IMP were explored by integrating transcriptome sequencing with the detection of extracellular membrane permeability, intracellular reactive oxygen species (ROS), and other test results.

RESULTS: Hospital wastewater significantly enhances the conjugation frequency of plasmids containing bla IMP, showing a two-fold increase in wastewater-based LB broth compared to regular LB broth. In comparison to regular LB broth culture, the wastewater-based LB broth culture group showed significant alterations in the expression of 1,415 genes, with 907 genes upregulated and 508 genes downregulated. Genes related to conjugation transfer systems and the type IV secretion system were significantly upregulated, indicating a potential role in promoting plasmid transfer. Moreover, the treatment of wastewater resulted in elevated intracellular ROS production and increased permeability of bacterial outer membranes, potentially facilitating the spread of antibiotic resistance genes.

DISCUSSION: This research shows that hospital wastewater facilitates the transfer of drug-resistant plasmids containing bla IMP and elucidates its potential mechanisms. A more detailed investigation into these mechanisms may facilitate the prevention of resistance transmission between healthcare and environmental contexts and inform future strategies for managing carbapenem resistance.},
}

@article {pmid40791418,
year = {2025},
author = {Hamrock, FJ and Guest, T and Daum, MN and Connell, O and Ershova, AS and Hokamp, K and Fleming, AB and Gebhardt, MJ and Westermann, AJ and Kröger, C},
title = {DNA uptake and twitching motility are controlled by the small RNA Arp through repression of pilin translation in Acinetobacter baumannii.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.07.19.665661},
pmid = {40791418},
issn = {2692-8205},
abstract = {UNLABELLED: Acinetobacter baumannii is a major opportunistic pathogen capable of natural transformation, a process driven by type IV pili (T4P) that facilitates horizontal gene transfer and accelerates the spread of antimicrobial resistance. While the transcriptional regulation of T4P is increasingly understood, post-transcriptional mechanisms controlling pilus assembly remain unexplored. Here, we identify and characterise a small RNA, Arp (Acinetobacter repressor of pilin), as a post-transcriptional repressor of T4P-mediated functions in A. baumannii . In a previous Hi-GRIL-seq experiment, we detected specific ligation events between Arp and the ribosome binding site of the pilA mRNA, encoding the major pilin subunit PilA. In-line probing and translational reporter assays revealed that Arp represses pilA translation by sequestering the Shine-Dalgarno sequence and the first 17 codons of the mRNA. Overexpression of Arp significantly impairs DNA uptake and twitching motility, two hallmark T4P-dependent phenotypes. Together, our findings identify a native A. baumannii sRNA that modulates natural competence by targeting pilin synthesis, revealing a new regulatory layer that could be exploited to disrupt horizontal gene transfer in multidrug-resistant strains.

SIGNIFICANCE STATEMENT: Acinetobacter baumannii is a multidrug-resistant WHO #1 priority pathogen that acquires antibiotic resistance genes through natural transformation, a process dependent on type IV pili (T4P). This work reveals Arp, the first native post-transcriptional repressor of natural competence in A. baumannii , uncovering a novel regulatory layer that modulates horizontal gene transfer. The widespread presence of arp in pathogenic Acinetobacter strains suggests that sRNA is an important regulator in those organisms. Furthermore, these findings broaden our understanding of RNA-based regulation in this priority pathogen and open potential avenues for interfering with antibiotic resistance dissemination.},
}

@article {pmid40790092,
year = {2025},
author = {Andrade-Oliveira, AL and Prodocimi, F and Silva, R and Rossi, CC and Giambiagi-deMarval, M},
title = {Optimized Plasmid Extraction Uncovers Novel and Mobilizable Plasmids in Staphylococcus nepalensis Sharing Antimicrobial Resistance Across Different Bacterial Genera.},
journal = {Current microbiology},
volume = {82},
number = {10},
pages = {446},
pmid = {40790092},
issn = {1432-0991},
support = {E-26/010.000172/2016; 010.00128/2016; E-26.210.875/2016//Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro/ ; 101056/2018; 001463/2019; 211.554/2019; 201.071/2020//Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro/ ; 200.895/2021//Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro/ ; E-26/204.925/2022//Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro/ ; APQ-01339-25//Fundação de Amparo à Pesquisa do Estado de Minas Gerais/ ; APQ-03498-22//Fundação de Amparo à Pesquisa do Estado de Minas Gerais/ ; 408564/2023-7//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 304839/2022-1//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 23038.002486/2018-26//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; },
mesh = {*Plasmids/genetics/isolation & purification ; *Staphylococcus/genetics/drug effects/isolation & purification/classification ; *Anti-Bacterial Agents/pharmacology ; Phylogeny ; *Drug Resistance, Bacterial/genetics ; Animals ; Gene Transfer, Horizontal ; Whole Genome Sequencing ; Microbial Sensitivity Tests ; Brazil ; },
abstract = {Plasmids are key vectors in the dissemination of antimicrobial resistance (AMR), often transcending species and genus boundaries through horizontal gene transfer. Staphylococcus nepalensis, typically regarded as a commensal species, has emerged as a potential reservoir of resistance genes. In this study, we optimized plasmid extraction protocols to enhance the recovery of low-copy plasmids and applied whole-genome sequencing to characterize plasmids from a S. nepalensis strain isolated from the oral microbiota of a healthy cat in Brazil. Plasmid-enriched extraction using the Qiagen miniprep kit, with an additional enzymatic lysis step, significantly improved assembly outcomes, enabling the recovery of four complete plasmids. Three of them carried mobilizable antimicrobial resistance genes (aadK, cat, and tetK), conferring resistance to streptomycin, chloramphenicol, and tetracycline, respectively. Comparative and phylogenetic analyses revealed a high sequence similarity between these plasmids and mobile elements found in diverse pathogenic and environmental bacteria, including Staphylococcus aureus, S. epidermidis, Enterococcus sp., and Pseudomonas aeruginosa, indicating plasmid circulation across bacterial genera. Additionally, one novel plasmid was identified, displaying limited similarity to any known sequence and suggesting the existence of uncharacterized plasmid lineages in commensal staphylococci. These findings highlight the underestimated role of S. nepalensis as a hidden reservoir of mobilizable resistance genes and reinforce the need to surveil non-pathogenic bacteria in AMR monitoring frameworks.},
}

*Plasmids/genetics/isolation & purification
*Staphylococcus/genetics/drug effects/isolation & purification/classification
*Anti-Bacterial Agents/pharmacology
Phylogeny
*Drug Resistance, Bacterial/genetics
Animals
Gene Transfer, Horizontal
Whole Genome Sequencing
Microbial Sensitivity Tests
Brazil

@article {pmid40788082,
year = {2025},
author = {Kumari, S and Narendrakumar, L and Chawla, M and Das, S and Koley, H and Das, B},
title = {Investigating the molecular transmission dynamics of blaNDM in antibiotic-selective environments.},
journal = {Journal of bacteriology},
volume = {},
number = {},
pages = {e0013325},
doi = {10.1128/jb.00133-25},
pmid = {40788082},
issn = {1098-5530},
abstract = {Carbapenem resistance mediated by blaNDM-encoded metallo-beta-lactamases is often linked to ISAba125, an insertion sequence from the IS30 family, which is widely distributed among critical and high-priority bacterial pathogens. The rapid dissemination of ISAba125-linked blaNDM in both nosocomial and community-acquired infections presents a serious challenge to healthcare systems and pharmaceutical industries. Despite the urgency of this issue, the factors driving blaNDM spread and the molecular mechanisms governing ISAba125 mobility remain poorly understood. In this study, we engineered the genomes of Vibrio cholerae and Escherichia coli to investigate the mobility of blaNDM under controlled conditions both with and without the genetically linked ISAba125. We also examined the transmission efficiency and the stability of blaNDM in environments with and without sublethal antibiotic concentrations. Our in vitro findings were validated in a rabbit ileal loop model. The results revealed that antibiotic pressure significantly influences the mobility of blaNDM, shedding light on the molecular dynamics of its transmission. These insights are crucial for developing strategies to curb the spread of blaNDM and mitigate the growing threat of carbapenem resistance in bacterial pathogens.IMPORTANCEInsertion sequences are the simplest form of mobile genetic elements that play a critical role in the adaptation of bacteria, allowing them to rapidly acquire new traits like resistance genes that enhance their survival. ISAba125 is one such insertion sequence that facilitates the spread of blaNDM, contributing to the global challenge of carbapenem resistance. In this study, we developed reporter strains that could be used as a valuable tool for investigating the dynamics of ISAba125-linked blaNDMsh-ble and evaluated the transposition frequency of ISAba125-linked blaNDMsh-ble in the presence and absence of sublethal concentration of antibiotics. Our results demonstrated that ISAba125 enhances the spread of blaNDMsh-ble under sublethal concentration of antibiotics that induces SOS response.},
}

@article {pmid40784676,
year = {2025},
author = {Luo, L and Chen, X and Liu, B and Nie, Y and Wu, XL},
title = {Strengthen or Weaken: Evolutionary Directions of Cross-Feeding After Formation.},
journal = {Environmental microbiology reports},
volume = {17},
number = {4},
pages = {e70175},
pmid = {40784676},
issn = {1758-2229},
support = {32130004//National Natural Science Foundation of China/ ; 32161133023//National Natural Science Foundation of China/ ; 32170113//National Natural Science Foundation of China/ ; 2024YFA0919000//National Key Research and Development Program of China/ ; },
mesh = {*Biological Evolution ; *Microbial Consortia/physiology ; *Bacteria/genetics/metabolism ; *Microbial Interactions ; Symbiosis ; },
abstract = {Interactions between species and the evolution of strains are important biotic factors determining the microbial community dynamics, with these two processes being deeply intertwined. Cross-feeding is a prevailing mutualistic interaction in natural microbial communities in which metabolites secreted by one microbe can be utilised by another. Constructing synthetic microbial consortia based on cross-feeding is a promising strategy for bioremediation and bioproduction. But how to improve the performance and the stability of consortia remains a challenge. This review discusses the features of two opposite evolutionary directions of cross-feeding consortia over time, providing insights into the factors affecting the evolutionary process. While coevolving, cross-feeding may strengthen with stronger metabolic coupling, deeper growth dependence, and/or deeper evolutionary dependence; then the consortia become reinforced. Conversely, unsuitable environmental conditions can lead to the direct collapse of the cross-feeding consortia due to metabolic decoupling, partner extinction, or cheater dominance. The loss of the fitness advantage and the constraints on the evolutionary ability can also lead to the weakening of cross-feeding. Cross-feeding partners can affect the evolution of focal strains from different aspects, such as niche space, selective pressure, horizontal gene transfer, and evolutionary rate. Analysing cross-feeding from an evolutionary perspective will advance our understanding of microbial community dynamics and enable rational designs of efficient and stable synthetic microbial consortia.},
}

*Biological Evolution
*Microbial Consortia/physiology
*Bacteria/genetics/metabolism
*Microbial Interactions
Symbiosis

@article {pmid40780628,
year = {2025},
author = {Feng, X and Li, S and Huang, D and Tan, N and Li, X and Xia, S and Hu, L and Cai, R and Li, Y and Wang, J and Luo, M and Li, H and Ye, X and Lv, Z and Shi, X and Wu, S and Dyer, N and Li, H and Hu, Q and Zhou, Z},
title = {Emergence of carbapenem-resistant XDR Salmonella enterica in pediatric patients in South China: a genomic perspective study.},
journal = {International journal of antimicrobial agents},
volume = {},
number = {},
pages = {107589},
doi = {10.1016/j.ijantimicag.2025.107589},
pmid = {40780628},
issn = {1872-7913},
abstract = {BACKGROUND AND AIM: Carbapenem-resistant Salmonella enterica (CRSE), mostly driven by plasmids, poses a growing public health threat, especially in pediatric populations. This study investigates a cluster of pediatric CRSE infections in pediatric populations, characterizes genomic features of CRSE isolates, assesses global CRSE prevalence, and explores plasmid-mediated horizontal gene transfer.

METHODS: An epidemiological investigation of 18 pediatric CRSE cases was conducted. Genomic analysis included resistome profiling, plasmid typing, and phylogenetic clustering to assess genetic diversity. A global analysis of 530,113 Salmonella genomes identified carbapenemase-carrying isolates. Plasmid transfer experiments between S. enterica and E. coli were performed to evaluate horizontal gene transmission.

RESULTS: Respiratory co-infections (67% of cases, primarily RSV and HPIVs) were associated with severe clinical outcomes. Genomic analysis revealed multiple genetically distinct CRSE clones carrying blaNDM-5, predominantly on IncI-gamma/K1 and IncHI2A plasmids. Plasmid-mediated transfer of carbapenem resistance genes between S. enterica and E. coli was confirmed. Global surveillance identified 228 carbapenemase-positive Salmonella isolates (2000-2023) across 35 genetically diverse populations and 24 countries, demonstrating widespread dissemination.

CONCLUSION: Respiratory co-infections may exacerbate CRSE severity in children, while plasmid circulation drives carbapenem resistance transmission. The high genetic diversity and global distribution of CRSE highlight urgent needs for integrated surveillance, antimicrobial stewardship, and interventions targeting co-infections and environmental reservoirs.},
}

@article {pmid40779699,
year = {2025},
author = {Bao, Y and Ho, YW and Shen, Z and Lam, EY and Fang, JKH and Leung, KMY and Lee, PKH},
title = {Ecological Roles and Shared Microbes Differentiate the Plastisphere from Natural Particle-Associated Microbiomes in Urban Rivers.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c06538},
pmid = {40779699},
issn = {1520-5851},
abstract = {The "plastisphere," comprising microbes associated with microplastics (MPs), may have substantial ecological impacts on riverine ecosystems. However, little is known about how the microbiomes associated with anthropogenic MPs compare with those associated with natural particles (NPs) in urban rivers with varying MP pollution levels. We therefore conducted a comparative analysis of the metagenomes associated with MPs and NPs (100-5000 μm) and river water (RW) across 10 urban river systems. Although we found similarities in taxonomic and functional compositions between the microbiomes associated with MPs and NPs, the plastisphere exhibited distinct associations with specialized taxa and life-history strategies. These unique traits enhanced the potential of the plastisphere for complex carbohydrate and plastic degradation, nitrate and nitric oxide reduction, and antibiotic resistance and virulence compared with the NP or RW microbiomes. Furthermore, MPs supported the sharing of unique microbes with the surrounding RW; these shared microbes possessed enhanced horizontal gene transfer capabilities and potentially could disperse traits of the plastisphere into the broader RW microbiomes. This study highlights the distinct ecological roles and shared microbes of the plastisphere, indicating that MP pollution may substantially and uniquely impact the function and health of riverine ecosystems.},
}

@article {pmid40778777,
year = {2025},
author = {Phimphong, T and Hashimoto, S and Songwattana, P and Wongdee, J and Greetatorn, T and Teamtisong, K and Boonchuen, P and Masuda, S and Shibata, A and Shirasu, K and Sibounnavong, P and Tittabutr, P and Boonkerd, N and Sato, S and Gully, D and Giraud, E and Piromyou, P and Teaumroong, N},
title = {Diversity of bradyrhizobial T3SS systems and their roles in symbiosis with peanut (Arachis hypogaea) and Vigna species (V. radiata and V. mungo).},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0060025},
doi = {10.1128/aem.00600-25},
pmid = {40778777},
issn = {1098-5336},
abstract = {Symbiosis between Bradyrhizobium strains isolated from Lao People's Democratic Republic (Lao PDR) and intercropped legumes (Arachis hypogaea, Vigna radiata, and V. mungo) was regulated by the type III secretion system (T3SS), which delivers effector proteins (T3Es) into host plant cells to modulate nodulation. To explore this mechanism, we sequenced and analyzed seven Bradyrhizobium genomes, identifying putative T3Es across five T3SS groups (G.1-G.5), which were classified based on the sequence of rhcN, a conserved ATPase gene essential for T3SS function. Phylogenetic analysis of rhcN more closely reflected the evolutionary relationships of nodulation genes than those based on 16S rRNA or whole-genome comparisons, underscoring its symbiotic relevance. Functional assays using rhcN mutants revealed group-specific effects on nodulation; G.1 strains showed neutral effects on A. hypogaea, negative effects on V. radiata, and positive effects on V. mungo. G.2 strains consistently promoted nodulation across all hosts and lacked effectors related to SUMO (small ubiquitin-like modifier) pathways, which have been implicated in host defense regulation. G.3 strains reduced nodulation in A. hypogaea but enhanced it in Vigna species. G.4 strains suppressed nodulation in A. hypogaea, and G.5 strains inhibited nodulation across all tested legumes. These findings highlight the diversity in T3SS organization, effector composition, and symbiotic responses among native Bradyrhizobium strains. The identification of known and uncharacterized effectors suggests roles in host compatibility and specificity. These strains, along with their effector profiles, provide a foundation for future functional studies to better understand T3SS-mediated interactions and support the development of targeted inoculants for legume hosts.IMPORTANCEThis study advances our understanding of legume-Bradyrhizobium symbiosis by examining the genetic organization and evolutionary patterns of T3SS genes. Our findings revealed that T3SS gene evolution does not always align with phylogenies based on 16S rRNA or whole-genome sequences, suggesting that horizontal gene transfer and functional adaptation may shape diversification. The observed variation in T3SS architecture and effector profiles among the five distinct Bradyrhizobium groups was correlated with host-specific nodulation outcomes in A. hypogaea, V. radiata, and V. mungo. We also identified novel candidate genes influencing symbiotic signaling and compatibility. These insights into the diversity and function of T3SS components contribute to a broader understanding of host-microbe communication and may support the development of more targeted and efficient rhizobial inoculants for sustainable legume cultivation and improved biological nitrogen fixation.},
}

@article {pmid40773239,
year = {2025},
author = {Gifford, RJ},
title = {Pervasive horizontal transfer of adeno-associated virus capsid genes.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {32},
pages = {e2505928122},
doi = {10.1073/pnas.2505928122},
pmid = {40773239},
issn = {1091-6490},
support = {MC_UU_12014/12//UKRI | Medical Research Council (MRC)/ ; },
mesh = {*Dependovirus/genetics ; *Gene Transfer, Horizontal ; Animals ; *Capsid Proteins/genetics ; Humans ; *Capsid ; Genetic Vectors/genetics ; Recombination, Genetic ; Phylogeny ; Evolution, Molecular ; Cattle ; Genetic Therapy ; },
abstract = {Adeno-associated viruses (AAVs) are nonpathogenic DNA viruses with potent gene delivery capabilities, making them essential tools in gene therapy and biomedical research. Despite their therapeutic importance, key aspects of AAV natural biology remain obscure, complicating efforts to explain rare AAV-associated diseases and optimize gene therapy vectors. By analyzing sequence data from virus isolates and endogenous viral elements (EVEs), I reveal a striking evolutionary pattern: While AAV sublineages, defined by the replication-associated (rep) gene, have broadly codiverged with host groups over millions of years, capsid (cap) diversity has been shaped by extensive recombination. In particular, one capsid lineage, Mammalian-wide (M-wide), has spread horizontally across diverse rep lineages and host taxa through multiple recombination events. Furthermore, several AAVs with M-wide capsids-including AAV-4, AAV-12, and bovine AAV (BAAV)-originate from historical adenovirus (Ad) stocks, raising the possibility that laboratory conditions contributed to capsid transfer. Distinguishing natural from laboratory-driven recombination is essential for understanding AAV ecology and its implications for gene therapy. A systematic sequencing effort in human and primate populations is needed to assess the extent of recombinant capsid acquisition, determine the impact of laboratory-driven recombination on circulating AAV diversity, and track ongoing recombination events that could affect vector safety and efficacy.},
}

*Dependovirus/genetics
*Gene Transfer, Horizontal
Animals
*Capsid Proteins/genetics
Humans
*Capsid
Genetic Vectors/genetics
Recombination, Genetic
Phylogeny
Evolution, Molecular
Cattle
Genetic Therapy

@article {pmid40771950,
year = {2025},
author = {Qi, Y and Lu, Z and Meng, Z and Wang, X and Chen, H and Li, M and Qu, C and Zhang, P and Liu, Y and Liu, J},
title = {Diversity and antibiotic resistance of cultivable bacteria in bulk tank milk from dairy farms in Shandong Province, China.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1649876},
pmid = {40771950},
issn = {2297-1769},
abstract = {INTRODUCTION: This study systematically analyzed bacterial diversity and antimicrobial resistance (AMR) profiles in bulk tank milk from five dairy farms (n = 30) in Shandong Province, China, to assess public health risks associated with microbial contamination and provide critical data for regional quality control and AMR risk assessment in dairy production systems.

METHODS: Total bacterial counts were quantified, revealing significant inter-farm variation (P < 0.05) with a range of 3.94-6.68 log CFU/mL. Among 129 bacterial isolates, genus-level dominance and species prevalence were identified. Antimicrobial susceptibility testing (AST) against 10 agents was performed using integrated resistance criteria combining Clinical and Laboratory Standards Institute (CLSI) standards and epidemiological cutoff values (ECOFFs). Nine resistance genes targeting seven antibiotic classes were detected via PCR.

RESULTS: The highest resistance rate was observed for sulfadiazine (53.2%) and the lowest for levofloxacin (6.0%). Multidrug resistance was detected in 23% (20/87) of isolates, with 14 strains meeting ECOFFs-based resistance criteria. PCR analysis showed sul1 (70.5%) and ant(4')-Ia (54.3%) as the most prevalent resistance genes, while mcr-1, lnu (B), and bla NDM-1 were absent in all isolates. Regional resistance variations correlated significantly with farm management practices.

DISCUSSION: These findings underscore the impact of historical antibiotic use on AMR dissemination. Enhanced AMR surveillance in raw milk, improved antibiotic stewardship, and targeted interventions are crucial to mitigate public health risks from microbial contamination and horizontal gene transfer of resistance determinants.},
}

@article {pmid40770992,
year = {2025},
author = {Moody, ERR and Williams, TA and Álvarez-Carretero, S and Szöllősi, GJ and Pisani, D and Lenton, TM and Donoghue, PCJ},
title = {The emergence of metabolisms through Earth history and implications for biospheric evolution.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {380},
number = {1931},
pages = {20240097},
pmid = {40770992},
issn = {1471-2970},
support = {//John Templeton Foundation/ ; //Leverhulme Trust/ ; /BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {*Archaea/metabolism/genetics ; *Biological Evolution ; *Bacteria/metabolism/genetics ; Earth, Planet ; Phylogeny ; *Metabolic Networks and Pathways/genetics ; Gene Transfer, Horizontal ; },
abstract = {We investigate the evolution of microbial metabolisms from the last universal common ancestor to the extant biota through comparative phylogenomics, reconciling the evolution of the genes that underpin metabolic pathways with a time-calibrated tree of life. We find that the majority of metabolic pathways were established within the first 2 billion years of Earth history, with pathways accreting at different rates. Methanogenesis and acetogenesis are recovered to be among the earliest energy metabolisms, whereas photosynthetic pathways achieved completeness by 2 Ga, much later than most previous studies have envisaged. Horizontal exchange of metabolic genes is widespread, but it has occurred largely among closely related lineages and for some pathways there is a strong signal of vertical inheritance. We also find that the rate of horizontal gene transfer has been higher in Bacteria than in Archaea through evolutionary history. Finally, we evaluate how our reconstructed history of metabolism can help to constrain hypotheses of biospheric evolution, considering the entropic and Darwinized Gaia hypotheses as well as a simple neutral model for the assembly of biogeochemical cycles.This article is part of the discussion meeting issue 'Chance and purpose in the evolution of biospheres'.},
}

*Archaea/metabolism/genetics
*Biological Evolution
*Bacteria/metabolism/genetics
Earth, Planet
Phylogeny
*Metabolic Networks and Pathways/genetics
Gene Transfer, Horizontal

@article {pmid40770987,
year = {2025},
author = {Padalko, A and Karavaeva, V and Zamarreno Beas, J and Neukirchen, S and Sousa, FL},
title = {Bioenergetics evolution: the link between Earth's and Life's history.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {380},
number = {1931},
pages = {20240102},
pmid = {40770987},
issn = {1471-2970},
support = {//H2020 European Research Council/ ; //Vienna Science and Technology Fund/ ; },
mesh = {*Energy Metabolism ; *Biological Evolution ; Earth, Planet ; *Bacteria/metabolism/genetics ; Phylogeny ; Archaea/genetics/metabolism ; *Bacterial Physiological Phenomena ; },
abstract = {The history of life intrigues both researchers and society, as it is human nature to question our origins. Our understanding of microbial evolution comes mainly from genomic data and geological evidence. Recent advances in sequencing technologies are revealing vast insights into microbial diversity, especially among uncultured lineages. While metagenomics indicates the existence of novel lineages, their ecological functions remain unknown. To unlock these mysteries, we need to shift focus from genomics to understanding their physiology. A barrier to understanding environmental microbes lies in our limited knowledge of their energy-harnessing and conservation strategies. Phylogenetic trees built from universal genes can group thousands of lineages but fail to capture the entire genome or reflect key physiological traits, especially with lateral gene transfer complicating evolutionary patterns. To deepen our knowledge of microbial evolution, a promising strategy combines large-scale comparative phylogenetic analyses of genes related to physiology with experimental data. Geochemical records of ancient energy sources can act as evolutionary constraints. This top-down approach would help rule out traits that could not be ancient, narrowing the physiological possibilities of early microbial life. Focusing on how microbes harnessed energy during evolution could bridge the gap between geochemistry and microbiology, providing testable predictions about bioenergetic transitions.This article is part of the discussion meeting issue 'Chance and purpose in the evolution of biospheres'.},
}

*Energy Metabolism
*Biological Evolution
Earth, Planet
*Bacteria/metabolism/genetics
Phylogeny
Archaea/genetics/metabolism
*Bacterial Physiological Phenomena

@article {pmid40770776,
year = {2025},
author = {Kauer, L and Sapountzis, P and Imholt, C and Berens, C and Kuehn, R},
title = {Microbial exchange at the wildlife-livestock interface: insights into microbial composition, antimicrobial resistance and virulence factor gene dynamics in grassland ecosystems.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {84},
pmid = {40770776},
issn = {2524-4671},
abstract = {The transmission of antimicrobial resistance genes (ARGs) and virulence factors (VFs) between wildlife and livestock is an emerging concern for animal and human health, especially in shared ecosystems. ARGs enhance bacterial survival against antibiotics, while VFs contribute to infection processes, and the microbiome composition influences host health. Understanding microbial exchange at the wildlife-livestock interface is essential for assessing risks to both animal and human health. This study addresses the gap in knowledge by investigating the microbial composition, ARGs, and VFs in fecal matter from livestock (Bos taurus, Ovis aries) and wildlife (Microtus arvalis) cohabiting grassland pastures. Sampling was conducted within the DFG Biodiversity Exploratories, which provides valuable and extensive long-term ecological datasets and enables the study of diverse environmental parameters. Using metagenomic sequencing and 16 S rRNA amplicon analysis, we compared bacterial diversity, antimicrobial resistance profiles, and virulence gene presence across the three host species. Metagenomic analysis revealed host-specific differences in bacterial community composition. Livestock samples exhibited higher microbial diversity than those from M. arvalis, likely due to greater environmental exposure and management practices. The most common VFs in livestock were associated with immune modulation, whereas motility-related VFs were prevalent in M. arvalis. ARG profiles differed among hosts, suggesting rare events rather due to environmental acquisition than direct transmission between the hosts. The limited numbers of ARGs and VFs shared between the species indicate that horizontal gene transfer events between wildlife and livestock are infrequent. Notably, M. arvalis harbored diverse ARGs, including resistance to tetracycline and vancomycin, which were likely acquired from the environment rather than from direct livestock contact. These findings highlight the significant role of environmental reservoirs in shaping microbial communities and the spread of resistance. This research underscores the need for enhanced surveillance and ecosystem management strategies to mitigate the risk associated with antimicrobial resistance and the potential impacts on both animal and human health.},
}

@article {pmid40770694,
year = {2025},
author = {Ha, YH and Cho, A and Kim, TH and Gil, HY},
title = {De Novo assembly and characterization of Aria alnifolia Chloroplast and mitochondrial genomes reveal homologous conformational changes mediated by repeat regions and gene transfer.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {730},
pmid = {40770694},
issn = {1471-2164},
support = {KNA 1-1-13, 14-1//Korea National Arboretum/ ; KNA 1-1-13, 14-1//Korea National Arboretum/ ; KNA 1-1-13, 14-1//Korea National Arboretum/ ; KNA 1-1-13, 14-1//Korea National Arboretum/ ; },
mesh = {Phylogeny ; *Genome, Chloroplast ; *Genome, Mitochondrial ; *Repetitive Sequences, Nucleic Acid ; Gene Transfer, Horizontal ; Evolution, Molecular ; *Rosaceae/genetics/classification ; Base Composition ; Chloroplasts/genetics ; },
abstract = {BACKGROUND: Aria alnifolia is an ornamental landscape species widely distributed in East Asia. However, its mitochondrial genome remains largely unexplored. We used PacBio long reads and Illumina short reads to sequence and assemble the organelle genomes, aiming to understand the evolutionary relationship between the plastids and mitochondria of A. alnifolia. This study focused on the homologous conformational changes mediated by repeat regions and gene transfer between organelle genomes. We also conducted comparative genomic and phylogenetic analyses with other Rosaceae species to clarify the evolutionary placement of A. alnifolia within the family.

RESULTS: The mitochondrial genome is 455,361 bp long with a GC content of 45.2%, while the chloroplast genome is 160,303 bp long with a GC content of 36.5%. The mitochondrial genome contains 59 genes, including 35 protein-coding genes, 4 rRNA genes, and 20 tRNA genes. The chloroplast genome comprises 128 genes, with 84 protein-coding genes, 8 rRNA genes, and 37 tRNA genes. The subcircular structure of the mitochondrial genome was inferred from two double-branch structures (DBSs) among 12 identified DBSs in A. alnifolia using a combination of long and short reads. In the mitochondrial genome, 128 simple sequence repeats were identified, compared to 69 in the chloroplast genome. Additionally, both organelles contained 239 dispersed repeats of at least 30 bp. We also confirmed gene transfer between the chloroplasts and mitochondria through shared repeats. Furthermore, we observed a region in the mitochondrial genome with high similarity to the chloroplast-encoded psaA gene, suggesting a possible inter-organellar gene transfer event. Phylogenetic analysis of the mitochondrial genomes revealed that A. alnifolia is closely related to Pyrus communis, albeit with low resolution.

CONCLUSION: This study provides one of the first comprehensive analyses of the organelle genomes (chloroplast and mitochondria) in the genus Aria. These results serve as a valuable reference for future taxonomic and molecular evolutionary studies of the Rosaceae family.},
}

Phylogeny
*Genome, Chloroplast
*Genome, Mitochondrial
*Repetitive Sequences, Nucleic Acid
Gene Transfer, Horizontal
Evolution, Molecular
*Rosaceae/genetics/classification
Base Composition
Chloroplasts/genetics

@article {pmid40768349,
year = {2025},
author = {Zbinden, M and Huisman, JS and Blitvic, N and Stocker, R and Słomka, J},
title = {Fluid flow generates bacterial conjugation hot spots by increasing the rate of shear-driven cell-cell encounters.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {32},
pages = {e2505446122},
doi = {10.1073/pnas.2505446122},
pmid = {40768349},
issn = {1091-6490},
support = {Pivot Fellowship//Simons Foundation (SF)/ ; Pivot Fellowship//Simons Foundation (SF)/ ; 542395FY22//Simons Foundation (SF)/ ; GBMF9197//Gordon and Betty Moore Foundation (GBMF)/ ; LT0045/2023-L//Human Frontier Science Program (HFSP)/ ; 51NF40_180575//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (SNF)/ ; 51NF40_225148//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (SNF)/ ; PZ00P2_202188//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (SNF)/ ; CRSII5-186422//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (SNF)/ ; 205321_207488//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (SNF)/ ; PHY-2309135//National Science Foundation (NSF)/ ; PHY-2309135//National Science Foundation (NSF)/ ; PHY-2309135//National Science Foundation (NSF)/ ; },
mesh = {*Escherichia coli/genetics/physiology ; *Conjugation, Genetic ; Plasmids/genetics ; },
abstract = {Conjugation accelerates bacterial evolution by enabling bacteria to acquire genes horizontally from their neighbors. Plasmid donors must physically encounter and connect with recipients to allow plasmid transfer, and different environments are characterized by vastly different encounter rates between cells, based on mechanisms ranging from simple diffusion to fluid flow. However, how the environment affects the conjugation rate by setting the encounter rate has been largely neglected, mostly because existing experimental setups do not allow for direct control over cell encounters. Here, we describe the results of conjugation experiments in Escherichia coli in which we systematically varied the magnitude of shear flow using a cone-and-plate rheometer to control the encounter rate. We found that the conjugation rate increases with shear until it peaks at an optimal shear rate ([Formula: see text]), reaching a conjugation rate fivefold higher than the baseline set by diffusion-driven encounters. This optimum marks the transition from a regime in which shear promotes conjugation by increasing the rate of cell-cell encounters to a regime in which shear disrupts conjugation. Regions of high fluid shear are widespread in aquatic systems, in the gut of host organisms, and in soil, and our results indicate that these regions could be hot spots of bacterial conjugation in the environment.},
}

*Escherichia coli/genetics/physiology
*Conjugation, Genetic
Plasmids/genetics

@article {pmid40763289,
year = {2025},
author = {AbdulHak, A and Zedan, HH and El-Mahallawy, HA and Sayed, AA and Mohamed, HO and Zafer, MM},
title = {The genomic configurations driving antimicrobial resistance and virulence in colistin resistant Pseudomonas aeruginosa from an Egyptian Tertiary Oncology Hospital.},
journal = {PLOS global public health},
volume = {5},
number = {8},
pages = {e0004976},
pmid = {40763289},
issn = {2767-3375},
abstract = {Pseudomonas aeruginosa, recognized by the World Health Organization as a critical priority pathogen, exhibits significant genomic plasticity and a high potential for developing resistance to multiple antimicrobials. This study provides comprehensive genomic insights into colistin-resistant P. aeruginosa isolates obtained from cancer patients. Phenotypic assays were conducted to evaluate antibiotic susceptibility, biofilm formation, efflux pump activity, swarming motility, and pigment production. Whole genome sequencing of the collected isolates was performed using Oxford-Nanopore technology to examine sequence types, resistome profiles, virulence-associated genes, and mobile genetic elements. Our findings reveled that out of 52 isolates, 10 (19.2%) were resistant to colistin. Ceftolozane/tazobactam demonstrated full efficacy against 60% of colistin resistant P. aeruginosa isolates. Within this colistin resistant subset, high-risk clones ST308 and ST773 emerged as dominant, both harboring blaNDM-1 and exhibiting extensive resistance profiles, including resistance to colistin and, in some cases, ceftolozane/tazobactam. The first detection of ST1143 and ST1693 in Egypt carrying blaOXA-1028 and blaOXA-904, respectively was documented, neither of which had been previously reported in the country. The accessory genome, accounting for up to 34.6% of the total genome, highlights the remarkable genomic plasticity of P. aeruginosa, and its capacity for horizontal acquisition of resistance and virulence genes via mobile genetic elements, such as integrative and conjugative elements (ICEs). Virulome analysis revealed the presence of the exoU gene in high-risk clones, a marker closely linked to hypervirulence in infection models, whereas other sequence types were associated with less virulent factors, such as exoS. Despite phenotypic variability in biofilm formation, pigment production, and motility, the underlying genetic determinants of these traits were highly conserved. Mutational analysis revealed mutations in the regulatory system PhoPQ as the primary mechanism of colistin resistance, with no mcr genes detected. In conclusion, the substantial genomic plasticity of P. aeruginosa, reflected by an extensive accessory genome facilitates horizontal gene transfer (HGT), and significantly influences antimicrobial resistance and virulence. Colistin resistance was predominantly mediated by chromosomal mutations. Virulome and resistome analyses underscores the high pathogenicity and resistance potential of high-risk clones ST773 and ST308. The detection of horizontally acquired elements, such as integrative and conjugative elements (ICEs) carrying resistance genes such as blaNDM-1, underscores their role in disseminating resistance determinants. These findings emphasize the need urgent for targeted antimicrobial stewardship and surveillance strategies within Egyptian healthcare settings.},
}

@article {pmid40762257,
year = {2025},
author = {Homsombat, T and Yoshii, K and Fukada, Y and Koiwai, K and Hirono, I and Kondo, H},
title = {Comparative Genomics of Edwardsiella piscicida in the Japanese Flounder (Paralichthys olivaceus): Discovery and Implications of a Novel Genomic Island.},
journal = {Journal of fish diseases},
volume = {},
number = {},
pages = {e70035},
doi = {10.1111/jfd.70035},
pmid = {40762257},
issn = {1365-2761},
support = {JPMJSA1806//Science and Technology Research Partnership for Sustainable Development/ ; },
abstract = {Edwardsiella piscicida is a significant pathogen that poses a particular threat to Japanese flounder (Paralichthys olivaceus) aquaculture in Japan and other countries. The damage is caused by the pathogen's ability to evade host immune defences and establish intracellular infections, intensified by its genomic plasticity and capacity for horizontal gene transfer. To investigate evolutionary adaptations between one older (2019) and four recent (2023) E. piscicida strains from the same geographical locations, we performed comparative genomic analysis of five isolates using high-quality hybrid genome assemblies and compared them with 27 Edwardsiella reference genomes. Pangenome analysis identified distinct novel genomic islands (GIs) specific to the 2023 strains. These GIs (~100 kb in size) shared 85 gene clusters encoding multiple antibiotic resistance genes, phage defence systems, mobilisation genes, and mercury resistance. In addition, they encoded integrases, transposases, and conjugative transfer genes, suggesting they function as integrative and conjugative elements (ICEs), a type of mobile genetic element. Phenotypic characterisation showed the 2023 strains carrying novel GI increased antibiotic resistance, but no significant difference in virulence in Japanese flounder infection trials. These findings highlight the recent genomic diversification of E. piscicida in aquaculture and the importance of monitoring emerging GIs driving antibiotic resistance and environmental persistence.},
}

@article {pmid40759899,
year = {2025},
author = {Zhao, Y and Li, L and Huang, Y and Xu, X and Liu, Z and Li, S and Zhu, L and Hu, B and Zhang, T},
title = {Global soil antibiotic resistance genes are associated with increasing risk and connectivity to human resistome.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {7141},
pmid = {40759899},
issn = {2041-1723},
support = {22193062//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Humans ; *Soil Microbiology ; Gene Transfer, Horizontal ; Escherichia coli/genetics/drug effects/isolation & purification ; Phylogeny ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Microbial/genetics ; *Genes, Bacterial ; Metagenomics ; Genome, Bacterial ; Soil/chemistry ; *Drug Resistance, Bacterial/genetics ; Feces/microbiology ; Metagenome ; },
abstract = {Soil is a reservoir of antibiotic resistance genes (ARGs), and understanding its connection to human antibiotic resistome is crucial for the One Health framework. Rank I ARGs appear key to deciphering this relationship, but their global distribution and attribution in soil remain unclear. To fill this gap, we analyze 3965 metagenomic data (12 habitats, including soil, feces, sewage) and 8388 genomes of Escherichia coli isolates. Results show that soil ARG risk has increased over time (from 2008 to 2021). We introduce a "connectivity" metric that evaluates cross-habitat ARGs connectivity through sequence similarity and phylogenetic analysis, and reveal higher genetic overlap with clinical E. coli genomes (1985-2023) over time suggesting an increasing link between soil and human resistome. A comparison of 45 million genome pairs suggests that cross-habitat horizontal gene transfer (HGT) is crucial for the connectivity of ARGs between humans and soil. Finally, we compile clinical antibiotic resistance datasets (covering 126 countries from 1998 to 2022) and find significant correlations between soil ARG risk, potential HGT events and clinical antibiotic resistance (R[2] = 0.40-0.89, p < 0.001). Overall, our work provides insights into the ARGs connectivity between soil and humans, and could help identify strategies to prevent dissemination of antibiotic resistance.},
}

Humans
*Soil Microbiology
Gene Transfer, Horizontal
Escherichia coli/genetics/drug effects/isolation & purification
Phylogeny
Anti-Bacterial Agents/pharmacology
*Drug Resistance, Microbial/genetics
*Genes, Bacterial
Metagenomics
Genome, Bacterial
Soil/chemistry
*Drug Resistance, Bacterial/genetics
Feces/microbiology
Metagenome

@article {pmid40759277,
year = {2025},
author = {Guo, Z and Ma, H and Liu, Y and Xie, J and Liu, X and Chang, Y and Wang, Z and Cui, P},
title = {Metagenomic analysis reveals Northwest Pacific Ocean as a reservoir and evolutionary hub of antibiotic resistance genes.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {384},
number = {},
pages = {126938},
doi = {10.1016/j.envpol.2025.126938},
pmid = {40759277},
issn = {1873-6424},
abstract = {Antibiotic resistance genes (ARGs) were identified as a novel type of environmental contaminants. Ocean is thought to be one of the ultimate environments where ARGs gathered. Marine ecosystems represent vast reservoirs of ARGs, yet their dynamics in open-ocean environments remain poorly characterized. Through large-scale metagenomic profiling of the Kuroshio Extension, a hydrographically dynamic region in the Northwest Pacific, we identified a striking enrichment of ARGs (1.81 × 10[-3] ratio) at a frontal zone site (S30). The ARG abundance at this site exceeded coastal levels by 90-fold. Notably, multidrug resistance genes dominated this hotspot, with efflux pumps contributing 62 % of the resistance mechanisms, a pattern distinct from the target-alteration strategies prevalent in other regions. The site exhibited unique microbial consortia, including pathogenic Acinetobacter (30.2 % abundance) carrying clinically critical determinants (msbA, adeJ). Co-occurrence networks revealed horizontal transfer risks, linking clinical pathogen and nature carrier to multiple ARGs. Crucially, we discovered three novel plasmid-borne resistance genes circulating in >15 % of microbial populations, demonstrating open-ocean ARG diversification independent of direct anthropogenic inputs. These findings redefine oceanic frontiers as crucibles of resistance evolution, demanding urgent integration into global antimicrobial stewardship strategies.},
}

@article {pmid40758767,
year = {2025},
author = {Lerminiaux, N and Fakharuddin, K and Longtin, Y and McGill, E and Mitchell, R and Mataseje, L and On Behalf Of The Canadian Nosocomial Infection Surveillance Program, },
title = {Plasmid genomic epidemiology of bla NDM carbapenemase-producing Enterobacterales in Canada from 2010 to 2023.},
journal = {Microbial genomics},
volume = {11},
number = {8},
pages = {},
pmid = {40758767},
issn = {2057-5858},
mesh = {*beta-Lactamases/genetics ; Canada/epidemiology ; Humans ; *Plasmids/genetics ; *Enterobacteriaceae Infections/epidemiology/microbiology ; Whole Genome Sequencing ; *Bacterial Proteins/genetics ; *Enterobacteriaceae/genetics/enzymology/isolation & purification ; Cross Infection/epidemiology/microbiology ; Genome, Bacterial ; Gene Transfer, Horizontal ; },
abstract = {Carbapenems are broad-spectrum antibiotics that are losing effectiveness against infections caused by multidrug-resistant Enterobacterales that have acquired carbapenemase genes. The New Delhi metallo-β-lactamase (bla NDM) is one of the most common carbapenemases in Canada and around the globe. These genes are frequently found on conjugative plasmids, which can disseminate through horizontal gene transfer. We applied whole-genome sequencing to characterize 1,032 bla NDM carbapenemase-producing Enterobacterales isolates collected by the Canadian Nosocomial Infection Surveillance Program from 2010 to 2023. Using a combination of short-read and long-read sequencing, we obtained 226 complete and circular bla NDM-encoding plasmids. Unlike other carbapenemases in Canada, we found that bla NDM plasmids were very diverse; there was a lack of dominant clusters identified using MOB-suite, and clustering methods were not able to accurately predict plasmid clusters for short-read-only data. The majority of bla NDM plasmids were IncF-type (69.0%, 156/226). Both bla NDM and bla OXA-48-type carbapenemase genes were found in 11.4% (118/1,032) of isolates, and we identified several instances of both carbapenemase genes co-harboured on the same plasmid replicon (n=9). Our findings highlight that plasmid transfer has not played a major role in bla NDM transmission across Canada and that long-read sequencing is essential for resolving bla NDM plasmid structure and cluster membership.},
}

*beta-Lactamases/genetics
Canada/epidemiology
Humans
*Plasmids/genetics
*Enterobacteriaceae Infections/epidemiology/microbiology
Whole Genome Sequencing
*Bacterial Proteins/genetics
*Enterobacteriaceae/genetics/enzymology/isolation & purification
Cross Infection/epidemiology/microbiology
Genome, Bacterial
Gene Transfer, Horizontal

@article {pmid40757871,
year = {2025},
author = {Mohamed, FA and Timmer, B and Hargitai, R and Melegh, S and Meszéna, R and Pál, T and Urbán, P and Herczeg, R and Gyenesei, A and Sonnevend, Á},
title = {Hypervirulent Klebsiella pneumoniae causing bloodstream infections in Hungary.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0003125},
doi = {10.1128/spectrum.00031-25},
pmid = {40757871},
issn = {2165-0497},
abstract = {Hypervirulent Klebsiella pneumoniae (hvKP) can cause severe infections even in healthy individuals. Currently, no data are available on the frequency of hvKP-induced bloodstream infections (BSI) in Hungary. Our investigation revealed that of the 157 K. pneumoniae isolated from BSI in 2020-2022 at a university hospital in Hungary, three (2%) carried the hypervirulence-associated rmpA and iutAiucABCD genes. The complete genomes of these three hvKP isolates were sequenced. They were unrelated and belonged to ST5, ST86, and ST6771, a single-locus variant of ST893, i.e., to internationally known hvKP clones. In the K. pneumoniae ST86 and ST6771 isolates, the rmpA/A2, aerobactin, and salmochelin siderophore genes were located on virulence plasmids highly similar to those of K. pneumoniae ST23 and ST86 isolated in Asia, while the K. pneumoniae ST5 isolate harboured rmpA, iroBCDN, and yersiniabactin locus on a chromosomally integrated ICEKp1 element. Comparison of the core genome MLST of the three Hungarian hvKP isolates to genomes belonging to the same ST/CC deposited in the Bigsdb database of the Pasteur Institute revealed that, although no direct epidemiological link could be established, KP48326 K. pneumoniae ST86, isolated in Pécs, clustered with a Greek isolate (ID-48733). The emergence of K. pneumoniae belonging to known hypervirulent clones in Hungary, albeit sporadic, is alarming and underscores the importance of continued whole-genome-based epidemiological surveillance.IMPORTANCEThis study represents the first investigation of the prevalence of hypervirulent K. pneumoniae (hvKP) in bloodstream infections in Hungary, conducted at the University Hospital of Pécs. Our findings emphasize the need to accurately identify hvKP strains, integrating both phenotypic and genotypic screening. Whole genome sequencing revealed genetic diversity among the Hungarian hvKP isolates, confirming the emergence of globally disseminating hvKP clones-ST86, CC893, and ST5-in Hungary. The localization of hypervirulence-related genes on mobile genetic elements, e.g., on virulence plasmids or on ICEKp1 similar to those found in hvKP isolates from different continents, underscores the significant role of horizontal gene transfer in the spread of hvKP. Overall, the study enhances our understanding of hvKP epidemiology and underscores the importance of continued molecular surveillance and control measures to mitigate the threat of hvKP infections in Hungary.},
}

@article {pmid40752531,
year = {2025},
author = {Liu, Q and Zhuo, R and He, W and Li, C},
title = {The new SCCmec type methicillin-resistant Staphylococcus aureus carried CRISPR-cas system isolated from a pig in China.},
journal = {Microbial pathogenesis},
volume = {207},
number = {},
pages = {107943},
doi = {10.1016/j.micpath.2025.107943},
pmid = {40752531},
issn = {1096-1208},
mesh = {Animals ; *Methicillin-Resistant Staphylococcus aureus/genetics/isolation & purification/drug effects/classification ; Swine/microbiology ; *CRISPR-Cas Systems/genetics ; China ; *Staphylococcal Infections/veterinary/microbiology ; Plasmids/genetics ; Drug Resistance, Multiple, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; *Swine Diseases/microbiology ; Gene Transfer, Horizontal ; Microbial Sensitivity Tests ; },
abstract = {Methicillin-resistant Staphylococcus aureus (MRSA) lineages circulate globally in healthcare, community, and livestock-associated (LA) settings. Nine MRSA isolates were recovered from swine in China, all exhibiting resistance to ampicillin and multidrug resistance phenotypes. Among eight ST9-t899 isolates, SCCmec type XII(9C2) predominated. However, we identified a novel staphylococcal cassette chromosome mec (SCCmec) type, designated XIII (9A), in an LA-MRSA strain (LS45). Structural analysis revealed SCCmec XIII(9A) comprises a CRISPR-Cas system (cas10-csm2-csm3-csm4-csm5-csm6). Functional analysis demonstrated this CRISPR-Cas system provided partial protection against phage infection at low multiplicities of infection (MOIs ≤10[-7]), but conferred no detectable immunity against spacer-matched plasmids, with no significant change in cas10 expression during plasmid challenge. The co-location of this novel SCCmec element and a functional CRISPR-Cas system within an LA-MRSA strain demonstrates that S. aureus can maintain a defense system active against phages while accommodating SCCmec-mediated horizontal gene transfer. These findings provide new insights into the genomic adaptations of MRSA across different hosts.},
}

Animals
*Methicillin-Resistant Staphylococcus aureus/genetics/isolation & purification/drug effects/classification
Swine/microbiology
*CRISPR-Cas Systems/genetics
China
*Staphylococcal Infections/veterinary/microbiology
Plasmids/genetics
Drug Resistance, Multiple, Bacterial/genetics
Anti-Bacterial Agents/pharmacology
*Swine Diseases/microbiology
Gene Transfer, Horizontal
Microbial Sensitivity Tests

@article {pmid40752385,
year = {2025},
author = {Chen, G and Qiu, X and Guo, J and Liu, T and Zha, M and Wu, X and Zheng, X and Sheng, GP and Wang, Y},
title = {Hidden risks: Unrecognized biological toxicity and antibiotic resistance spread in peracetic acid-based advanced wastewater treatment technologies.},
journal = {Water research},
volume = {287},
number = {Pt A},
pages = {124318},
doi = {10.1016/j.watres.2025.124318},
pmid = {40752385},
issn = {1879-2448},
abstract = {The escalating concern over antibiotic resistance in wastewater demands urgent attention. While advanced treatment technologies are anticipated to enhance secondary effluent quality and mitigate this issue, the associated biological toxicity and potential for resistance spread have been largely neglected. Herein, we explored the impact of peracetic acid (PAA)-based processes on antibiotic resistance during advanced secondary effluent treatment. Our findings revealed that PAA effectively inactivated most wastewater bacteria. However, it simultaneously induced environmental biotoxicity and genotoxicity, triggering a 1.5-2-fold increase in extracellular ARGs (eARGs) release and doubling horizontal gene transfer frequency. In contrast, PAA-based advanced oxidation process (PAA-AOP) demonstrated strong efficacy in detoxifying antibiotics and minimizing harm to aquatic organisms. It reduced both intracellular and extracellular ARGs by 2-4 orders of magnitude in real wastewater and significantly inhibited the conjugative transfer and transformation frequency of ARGs (by approximately 10 times), impairing their spread. Moreover, PAA-AOP reduced the abundance of pathogenic bacteria in wastewater transconjugants, thus minimizing direct harm to humans. Additionally, a membrane flow-through system designed with PAA-AOP exhibited excellent catalytic performance and stability in removing antibiotics and ARGs. These findings provide key insights into PAA-based advanced wastewater treatment, making a significant contribution to mitigating biotoxicity and antibiotic resistance in aquatic ecosystems.},
}

@article {pmid40752173,
year = {2025},
author = {Li, WJ and Ghaly, TM and Tetu, SG and Huang, FY and Li, HZ and Li, H},
title = {Effects of agricultural inputs on soil virome-associated antibiotic resistance and virulence: A focus on manure, microplastic and pesticide.},
journal = {Journal of hazardous materials},
volume = {496},
number = {},
pages = {139380},
doi = {10.1016/j.jhazmat.2025.139380},
pmid = {40752173},
issn = {1873-3336},
abstract = {Soil viruses are increasingly recognized as crucial mediators of horizontal gene transfer, yet their role in disseminating antibiotic resistance genes (ARGs) and virulence factor genes (VFGs) under agricultural disturbances remains poorly understood. Here, we characterized the viromes and associated ARGs and VFGs in agricultural soils treated with low- and high-dose manures, microplastics, and pesticides. Using metagenomic sequencing coupled with advanced viral identification tools, we found that manure fertilization markedly altered viral community composition and increased viral diversity. Manure also enhanced the abundance of ARGs and VFGs in viromes by 2.0-9.8-fold and 2.0-8.1-fold, respectively, while microplastics and pesticides had limited impacts. Additionally, gene pathways related to human diseases and environmental adaptation were enriched in soil viromes treated with manures and high-dose pesticides. Virus-host prediction revealed that Actinomycetia dominated bacterial hosts of both ARG- and VFG-carrying viruses, with some VFG-carrying viruses linked to potential human pathogens, e.g., Escherichia albertii and Klebsiella pneumoniae. Co-occurrence network analysis indicated that these disturbances strengthened connections between bacteria, viruses, and ARGs (or VFGs). Our study provides a comprehensive profile of viromes and associated risks in agricultural soil under three disturbances, highlighting the role of viruses in spread of antibiotic resistance and pathogenic risks in agricultural soil.},
}

@article {pmid40752166,
year = {2025},
author = {Yan, H and Zhu, X and Wu, Y and Wu, E and Zhu, X and Chen, B},
title = {Soil oxygen fluctuations as a natural barrier against antibiotic resistant genes propagation: Indications from bacterial network and community assembly.},
journal = {Journal of hazardous materials},
volume = {496},
number = {},
pages = {139375},
doi = {10.1016/j.jhazmat.2025.139375},
pmid = {40752166},
issn = {1873-3336},
abstract = {The impact of redox fluctuations on ARGs propagation in antibiotic-contaminated soil is rarely investigated. In this study, we incubated tetracycline (TC)-contaminated soils under three different oxygen conditions (static anaerobic, oxygen fluctuations, and static aerobic) using a soil microcosm experiment. Soil microbial community composition analysis shows that the bacterial community exhibited higher diversity and stability under fluctuating oxygen conditions compared to continuous aerobic or anaerobic conditions. Network analysis reveals that networks under oxygen fluctuations exhibited higher stability and more competitive interactions. Neutral community model (NCM) analyses indicates that oxygen fluctuations mitigate the selection pressure of tetracycline on soil microbial communities, whereas anaerobic conditions potentiate it. Consequently, the relative abundance of tetracycline resistance genes (TRs) under oxygen fluctuations accounted for approximately 15-57 % of that in anaerobic conditions and 21-88 % in aerobic conditions. Structural equation model (SEM) further reveals that the bacterial community under oxygen fluctuations acts as a barrier to TRs propagation, whereas in aerobic and anaerobic communities, the enrichment of TRs was due to the direct effect of changes in the bacterial community and horizontal gene transfer. This study addresses that soil oxygen fluctuations act as a natural barrier against the propagation of antibiotic resistance genes.},
}

@article {pmid40751786,
year = {2025},
author = {Srivastava, A and Chot, E and Gupta, V and Singhvi, N and Shukla, P},
title = {Stress genomics of the toxigenic cyanobacteria: environmental and biotechnological perspectives.},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {8},
pages = {295},
pmid = {40751786},
issn = {1573-0972},
mesh = {*Cyanobacteria/genetics/physiology ; *Genomics ; *Genome, Bacterial ; *Biotechnology ; *Stress, Physiological/genetics ; Adaptation, Physiological/genetics ; Bacterial Proteins/genetics/metabolism ; Bacterial Toxins/genetics ; },
abstract = {The genomic investigation of toxigenic cyanobacteria reveals unique features of potential genes, proteins, and genomic regions associated with varied functions critical for their survival and stress tolerance. Cyanobacteria are prevalent photoautotrophic microorganisms forming harmful blooms in aquatic environments, with significant public health and ecological implications. Despite the availability of complete genome sequences, the stress genomics of these harmful cyanobacteria remains understudied. This review highlights the genomic "arsenal" of these resilient species, emphasizing their stress adaptation mechanisms and potential vulnerabilities. Understanding this molecular basis is essential for developing targeted strategies to mitigate their impact. The insights gained from the genomic analysis could be leveraged to express unexploited stress-related genes for enhanced stress tolerance in industrial applications. Additionally, the review underscores the importance of redirecting research focus towards the functional genomics of bloom-forming strains to uncover novel pathways and strategies for their selective eradication and to improve the productivity of beneficial cyanobacterial strains under fluctuating environmental conditions. Finally, this review is an effort towards creating an important genomic resource for such toxic cyanobacteria.},
}

*Cyanobacteria/genetics/physiology
*Genomics
*Genome, Bacterial
*Biotechnology
*Stress, Physiological/genetics
Adaptation, Physiological/genetics
Bacterial Proteins/genetics/metabolism
Bacterial Toxins/genetics

@article {pmid40749792,
year = {2025},
author = {Li, W and Sun, J and Wu, Q and Kwok, LY and Dong, G and Sun, Z},
title = {Global genomics of Lactococcus lactis: horizontal gene transfer and intergenic variation drive multiple domestication and dairy adaptation.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2025.07.053},
pmid = {40749792},
issn = {2090-1224},
abstract = {INTRODUCTION: Lactococcus lactis is a crucial lactic acid bacterium of great economically significance for cheese product. The species exhibits wildly distribution and significant genetic diversity, yet the underlying drivers of its differentiation remain elusive.

OBJECTIVES: Lactococcus lactis, exhibits complex genetic diversity, yet the mechanisms driving its differentiation and niche adaptation remain poorly understood.

METHODS: This study assembled a genome dataset of 1008 isolates of Lactococcus lactis from six major habitats across five continents. And combined with public database data, used population genomics and function genomics to analysis the population structure and adaptation.

RESULTS: To elucidate its population structure and domestication history, 1008 genomes from six diverse habitats across five continents were analyzed, revealing two major genetic branches subdivided into ten distinct lineages. Phylogenomic and ancestral analyses support a multiple domestication model, with the ancestral plant-associated lineage (L6) diversified into dairy-adapted lineages (L8-L10) through extensive horizontal gene transfer, primarily facilitated by mobile genetic elements. Notably, intergenic regions (IGRs) critically influence phenotypic diversity and genetic structure, underscoring the functional significance of non-coding sequences in microbial adaptation. Pan-genome analysis highlights extensive accessory gene and IGR diversity, with habitat-specific enrichments: dairy lineages are enriched in mobile genetic elements and carbohydrate-active enzymes, while plant isolates show reduced genetic exchange. A machine learning framework integrating single nucleotide polymorphisms, genes, and IGRs accurately predicts isolate-specific fermentation traits, enabling efficient industrial strain selection.

CONCLUSION: These findings redefine non-coding regions as key drivers of microbial domestication and provide a genomic framework to optimize Lactococcus lactis for dairy fermentation and biotechnology, bridging ecological adaptation with applied innovation.},
}

@article {pmid40749656,
year = {2025},
author = {Asghar, MU and Zhai, Y and Liu, T and Fan, P and Ain, NU and Zaidi, AH and Tariq, M and Mainar-Jaime, RC and Jeong, KC},
title = {A metagenomics-based approach to understanding the transmission of healthcare-associated antimicrobial resistance in Pakistan.},
journal = {Journal of hazardous materials},
volume = {496},
number = {},
pages = {139384},
doi = {10.1016/j.jhazmat.2025.139384},
pmid = {40749656},
issn = {1873-3336},
abstract = {Hospital environments are critical yet underexamined reservoirs for hazardous antimicrobial resistance (AMR), particularly in lower-middle-income countries (LMICs) where resource constraints often hinder comprehensive surveillance. In this study, we employed 16S rRNA gene sequencing and shotgun metagenomics to characterize the microbiome, resistome, and potential transmission routes across five clinical environments within a hospital in Pakistan: the intensive care unit (ICU), surgical ward (SW), cardiac surgery ward (CSW), cardiac ward (CW), and operating theater (OT). Microbial community analysis revealed compositional similarities among the ICU, SW, and OT, with the ICU emerging as a primary source of microbial dissemination. Species-level profiling identified hospital-associated pathogens such as Acinetobacter baumannii, Klebsiella pneumoniae, and Enterobacter cloacae, and metagenome-assembled genome (MAG) analysis enabled the linkage of antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs) to specific bacterial hosts. ARGs and MGEs displayed setting-specific patterns, with the SW harboring the highest abundance of ARGs, particularly those conferring resistance to β-lactams and biocides. Insertion sequences were the most prevalent MGEs and were commonly linked to ARGs, indicating potential horizontal gene transfer. Co-occurrence network analysis identified Staphylococcus, Enterococcus, and Escherichia as central hub taxa within the microbial communities of the ICU, SW, and OT, indicating their critical roles in potential ARG transmission. These findings provide critical insights into the environmental transmission dynamics of AMR in LMIC healthcare settings and underscore the urgent need for metagenomics-informed infection control strategies.},
}

@article {pmid40749596,
year = {2025},
author = {Park, Y and Kim, W and Bae, J and Park, W},
title = {Public goods-mediated bacterial interplay in aquatic ecosystems.},
journal = {Water research},
volume = {287},
number = {Pt A},
pages = {124310},
doi = {10.1016/j.watres.2025.124310},
pmid = {40749596},
issn = {1879-2448},
abstract = {Microbial public goods, including siderophores, heme, and catalases, underpin cooperative interactions in aquatic environments. These extracellular compounds enable resource acquisition, stress mitigation, and metabolic cross-feeding, helping aquatic microbial communities cope with environmental stress and sustain their ecological roles. Because public goods are freely available to surrounding cells, their production involves balancing individual cost and community benefit, generating conflict between cooperation and cheating. External cues such as nutrient limitation, salinity shifts, and oxidative stress modulate the production and utilization of microbial public goods. Aquatic systems are physically homogeneous and dilute, fostering metabolic interdependence by increasing reliance on externally available compounds and shaping cooperation through dependency rather than autonomy. In parallel, genomic traits such as gene loss or streamlining in oligotrophic aquatic taxa further reinforce this cooperative mode. Many aquatic microbes have lost the full genetic capacity to synthesize essential metabolites, including vitamins, siderophores, and antioxidants, making them dependent on extracellular metabolites provided by other community members. In such water environments, the production and accessibility of public goods become central to survival, fostering cross-feeding and collective stress responses. This shared resource dependence reinforces cooperation and drives community organization and functional interdependence, underscoring the ecological and evolutionary importance of public goods in shaping aquatic microbial ecosystems.},
}

@article {pmid40749032,
year = {2025},
author = {Matle, I and Pfukenyi, DM and Maphori, N and Moatshe, N and Nkabinde, T and Motaung, A and Schmidt, T and Seakamela, E and Mwanza, M and Ngoma, L and Sirdar, M and Mbatha, KR and Magwedere, K},
title = {Monitoring, surveillance, antimicrobial resistance and genetic diversity analysis of non-typhoidal Salmonella in South Africa from 1960-2023 from animal and animal products.},
journal = {PloS one},
volume = {20},
number = {8},
pages = {e0329061},
pmid = {40749032},
issn = {1932-6203},
mesh = {South Africa/epidemiology ; Animals ; *Salmonella/genetics/drug effects/isolation & purification/classification ; Anti-Bacterial Agents/pharmacology ; *Genetic Variation ; *Drug Resistance, Bacterial/genetics ; Microbial Sensitivity Tests ; Retrospective Studies ; *Salmonella Infections/epidemiology/microbiology ; *Salmonella Infections, Animal/epidemiology/microbiology ; Humans ; Food Microbiology ; },
abstract = {Salmonellosis remains one of the most frequently reported foodborne diseases globally, with the highest burden in low-resource areas. The millions of deaths caused by Nontyphoidal Salmonella (NTS) infections emphasize the urgent need for timely, detailed, and evidence-based interventions to effectively manage and monitor NTS burdens. This study retrospectively analyzed 1,028 NTS isolates from animals, the environment, and food products in South Africa, collected between 1960 and 2023. Among the 102 serotypes identified, S. Heidelberg, isolated only between 2000-2009 and 2020-2023, accounted for 94.3% of isolations during the latter period, suggesting a recent shift in Salmonella epidemiology in the region. The highest resistance rates were observed for cefoxitin (65.7%), cephalothin (62.8%), and tetracycline (59.8%), with a significant increase in resistance to several antibiotics, including ceftriaxone and aztreonam, from 2010-2023. Genetic analysis revealed that S. Gallinarium had the highest prevalence of antibiotic resistance genes, such as tetA (71.4%), qnrA (64.3%), cat1 (64.3%), blaPSE (57.1%), and both blaCMY-2 and qnrB at 50%. The blaPSE and blaSHV genes were strongly associated with ceftriaxone resistance in S. Dublin isolates, while blaPSE and qnrS were linked to chloramphenicol resistance in S. Enteritidis and S. Dublin isolates. Additionally, 87% of the virulence genes screened were present in over 50% of the serotypes, indicating increased adaptability and potential shifts in disease dynamics. The rise in antimicrobial resistance, driven by antimicrobial misuse, horizontal gene transfer, and biofilm formation, could alter serotype dynamics and changing disease epidemiology. This trend underscores the urgent need for effective antimicrobial stewardship and surveillance to combat the spread of antibiotic resistance in Salmonella populations.},
}

South Africa/epidemiology
Animals
*Salmonella/genetics/drug effects/isolation & purification/classification
Anti-Bacterial Agents/pharmacology
*Genetic Variation
*Drug Resistance, Bacterial/genetics
Microbial Sensitivity Tests
Retrospective Studies
*Salmonella Infections/epidemiology/microbiology
*Salmonella Infections, Animal/epidemiology/microbiology
Humans
Food Microbiology

@article {pmid40748957,
year = {2025},
author = {Cui, W and Fendley, JM and Srikant, S and Shraiman, BI},
title = {A minimal model of panimmunity maintenance by horizontal gene transfer in the ecological dynamics of bacteria and phages.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {31},
pages = {e2417628122},
pmid = {40748957},
issn = {1091-6490},
support = {PHY:1748958//National Science Foundation (NSF)/ ; NSF PHY:1707973//National Science Foundation (NSF)/ ; 2919.02//Gordon and Betty Moore Foundation (GBMF)/ ; KTIP//Simons Foundation (SF)/ ; PHY:2210612//National Science Foundation (NSF)/ ; Life Sciences Research Foundation//Howard Hughes Medical Institute (HHMI)/ ; },
mesh = {*Gene Transfer, Horizontal ; *Bacteriophages/genetics/immunology ; *Bacteria/genetics/immunology/virology ; },
abstract = {Bacteria and phages have been in an ongoing arms race for billions of years. To resist phages bacteria have evolved numerous defense systems, which nevertheless are still overcome by counterdefense mechanisms of specific phages. These defense/counterdefense systems are a major element of microbial genetic diversity and have been demonstrated to propagate between strains by horizontal gene transfer (HGT). It has been proposed that the totality of defense systems found in microbial communities collectively form a distributed "pan-immune" system with individual elements moving between strains via ubiquitous HGT. Here, we formulate a Lotka-Volterra type model of a bacteria/phage community interacting via a combinatorial variety of defense/counterdefense systems and show that HGT enables stable maintenance of diverse defense/counterdefense genes in the microbial pan-genome even when individual microbial strains inevitably undergo extinction. This stability requires the HGT rate to be sufficiently high to ensure that some descendant of a "dying" strain survives, thanks to the immunity acquired through HGT from the community at large, thus establishing a new strain. This mechanism of persistence for the pan-immune gene pool is fundamentally similar to the "island migration" model of ecological diversity, with genes moving between genomes instead of species migrating between islands.},
}

*Gene Transfer, Horizontal
*Bacteriophages/genetics/immunology
*Bacteria/genetics/immunology/virology

@article {pmid40748897,
year = {2025},
author = {Ségurel, L and Ulaganathan, TS and Mathieu, S and Loiodice, M and Poulet, L and Drouillard, S and Cygler, M and Helbert, W},
title = {The porphyran degradation system is complete, phylogenetically and geographically diverse across the gut microbiota of East Asian populations.},
journal = {PloS one},
volume = {20},
number = {8},
pages = {e0329457},
pmid = {40748897},
issn = {1932-6203},
mesh = {Humans ; Asia, Eastern/ethnology ; Bacterial Proteins/genetics/metabolism ; *Bacteroides/enzymology/genetics ; *East Asian People/statistics & numerical data ; *Gastrointestinal Microbiome/genetics ; *Gene Transfer, Horizontal ; Genetic Variation ; Glycoside Hydrolases/genetics/metabolism ; Metagenome ; Phylogeny ; *Polysaccharides, Bacterial/metabolism ; *Porphyra/microbiology ; Sepharose/analogs & derivatives ; },
abstract = {The human gut microbiota can acquire new catabolic functions by integrating genetic material coming from the environment, for example from food-associated bacteria. An illustrative example of that is the acquisition by the human gut microbiota of Asian populations of genes coming from marine bacteria living on the surface of red algae that are incorporated into their diet when eating maki-sushi. To better understand the function and evolution of this set of algal genes corresponding to a polysaccharide utilization locus (PUL) dedicated to the degradation of porphyran, the main polysaccharide of the red algae Porphyra sp., we characterized it biochemically, assessed its genetic diversity and investigated its geographical distribution in large public worldwide datasets. We first demonstrated that both methylated and unmethylated fractions are catabolized without the help of external enzymes. By scanning the genomic data of more than 10,000 cultivated isolates as well as metagenomic data from more than 14,000 worldwide individuals, we found that the porphyran PUL is present in 17 different Phocaeicola/Bacteroides species (including 12 species that were not known to carry it), as well as in two Parabacteroides species and two genera from the Bacillota phylum, highlighting multiple lateral transfers within the gut microbiota. We then analyzed the prevalence of this porphyran PUL across 32 countries and showed that it exists in appreciable frequencies (>1%) only in East Asia (Japan, China, Korea). Finally, we identified three major PUL haplotypes which frequencies significantly differ between these East Asian countries. This geographic structure likely reflects the rate of bacterial horizontal transmission between individuals.},
}

Humans
Asia, Eastern/ethnology
Bacterial Proteins/genetics/metabolism
*Bacteroides/enzymology/genetics
*East Asian People/statistics & numerical data
*Gastrointestinal Microbiome/genetics
*Gene Transfer, Horizontal
Genetic Variation
Glycoside Hydrolases/genetics/metabolism
Metagenome
Phylogeny
*Polysaccharides, Bacterial/metabolism
*Porphyra/microbiology
Sepharose/analogs & derivatives

@article {pmid40748669,
year = {2025},
author = {Cui, S and Ma, W and Peng, H and Ye, Y and Qing, Y and Wei, G and Wang, J and Zhang, X},
title = {Genome-wide mining reveals the genetic plasticity of antibiotic resistance/virulence factor genes in Enterobacter hormaechei subsp. xiangfangensis.},
journal = {Journal of applied microbiology},
volume = {136},
number = {8},
pages = {},
doi = {10.1093/jambio/lxaf196},
pmid = {40748669},
issn = {1365-2672},
support = {2025JJ50123//Natural Science Foundation of China/ ; 32101368//National Natural Science Foundation of China/ ; 32200676//National Natural Science Foundation of China/ ; 2022YFE0119600//National Key Research and Development Program of China/ ; },
abstract = {AIMS: This study aims to systematically characterize the genetic basis and intra-species differentiation of antibiotic resistance/virulence factor genes (ARGs/VFGs) in Enterobacter hormaechei subsp. xiangfangensis.

METHODS AND RESULTS: A high-quality metagenome-assembled genome of E. hormaechei subsp. xiangfangensis bin99 (97.22% completeness, 1.63% contamination) was acquired. Phylogenomic and average nucleotide identity (≥95%) analyses confirmed its taxonomic assignment. Pan-genomic analysis revealed an open configuration (Heap's exponent B = 0.34) with a large accessory genome (approximate 2965 genes) and a stabilized core genome (1139 genes). Critically, a strong positive correlation (r = 0.86, P < 2.2e-16) was observed between mobile genetic elements (MGEs) and accessory gene abundance, probably suggesting horizontal gene transfer (HGT) as a potential driver of genome diversity. Functional annotation highlighted distinct roles: core genes enriched in essential metabolism, while accessory/strain-specific genes were linked to adaptation. Screening identified significant inter-strain variation in ARGs (n = 31) and VFGs (n = 35). Bin99 itself harbored 19 ARGs (e.g. multidrug: soxS, ramA, oqxB) and 40 VFGs (e.g. flagella, T6SS). Importantly, MGE abundance showed a significant positive correlation with ARGs (r = 0.67, P < 2.2e-16) but a negative correlation with VFGs (r = -0.29, P < 3.7e-9), suggesting that ARGs were frequently linked to MGEs facilitating HGT-mediated spread, while VFGs might rely less on this route.

CONCLUSIONS: The findings provide genome-wide evidence for distinct genetic plasticity underlying ARG and VFG evolution in E. hormaechei subsp. xiangfangensis, highlighting implications for resistance and virulence dissemination.},
}

@article {pmid40746326,
year = {2025},
author = {Qiu, Y and Guo, P and Tian, H and Zhou, Y and Wen, H and Liang, H},
title = {The restriction impacts of the Type III restriction-modification system on the transmission dynamics of antimicrobial resistance genes in Campylobacter jejuni.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1496275},
pmid = {40746326},
issn = {1664-302X},
abstract = {INTRODUCTION: The spread of antibiotic resistance genes among Campylobacter jejuni (C. jejuni) is a serious problem, and the effects of the restriction-modification (R-M) system on the transmission dynamics of these genes in C. jejuni remain poorly understood.

MATERIALS AND METHODS: Complete genome sequences of C. jejuni strains were extracted from the BV-BRC database until March 25, 2024. The phylogenetic and the resistance analysis were used to analyze the distribution of resistance genes in C. jejuni. The impacts of the R-M systems on the AMR genes transmission between C. jejuni strains and the possible mechanisms were explored through recombination, pangenome and mobile genetic elements analysis.

RESULTS: C. jejuni strains carrying the Type III R-M system have a significantly lower number of antimicrobial resistance (AMR) genes compared to strains without this system (p < 0.0001), with covariance value being -0.0526. The recombination analysis also shows that the median number of the number of AMR genes in the strains not possessing the Type III R-M system increases by 19.38% compared to strains carrying that system (p < 0.0001). We also find that the horizontal gene transfer frequency might have limited relationship with the Type III R-M system in C. jejuni through pangenome and mobile genetic elements analysis.

CONCLUSION: Our research indicates that the Type III R-M system might restrict the transmission of AMR genes potentially by affecting recombination in C. jejuni, which provides a theoretical basis for addressing the drug resistance problem.},
}

@article {pmid40745981,
year = {2025},
author = {Yu, W and Yu, D and Xiong, M and Liu, YJ and Wang, FQ and Xiong, LB},
title = {Metabolic Engineering of Acinetobacter baylyi ADP1 for L-Leucine Production.},
journal = {Journal of basic microbiology},
volume = {},
number = {},
pages = {e70075},
doi = {10.1002/jobm.70075},
pmid = {40745981},
issn = {1521-4028},
support = {//This study was supported by the National Key Research and Development Program of China (2022YFA0912200), the National Natural Science Foundation of China (No. 32100067), the Academic Mentorship for Scientific Research Cadre Project (AMSCP-24-01), the Research Fund of Shanghai University of Medicine & Health Sciences (SSF-22-25-001), the Research Fund of Shanghai Jinshan District Health Commission (JSKJ-KTMS-2022-15) and the Research Fund of Shanghai Jinshan District Science and Technology Committee (2022-WS-22)./ ; },
abstract = {Acinetobacter baylyi ADP1 has garnered attention as a promising synthetic biology chassis due to its compact genome, rapid growth, innate competence for horizontal gene transfer, and ease of genetic manipulation. To assess its potential for natural product biosynthesis, we engineered ADP1 for the production of l-leucine. First, feedback inhibition was relieved by overexpressing the endogenous leuA and ilvBN genes, alongside the replacement of transcriptional attenuation regions within the leuBCD operon. These interventions derepressed the native biosynthetic pathway, resulting in a substantial increase in l-leucine titers from 0.10 to 0.82 g/L. Next, we augmented the eda gene in the Entner-Doudoroff pathway, while disrupting poxB, which diverts carbon toward acetate, further promoting l-leucine biosynthesis. To resolve carbon competition between the tricarboxylic acid (TCA) cycle and l-leucine synthesis, an inducible sRNA-based system was developed to dynamically repress TCA cycle-associated genes. This balanced the cell growth with l-leucine anabolism, ultimately achieving a titer of 1.16 g/L with a yield of 0.08 g/g glucose. Interestingly, the l-leucine feedback regulation diverges markedly from classical prokaryotic chassis like Escherichia coli and Corynebacterium glutamicum, in which feedback-resistant variants of leuA and ilvBN are typically required to overcome repression. In contrast, in ADP1, overexpression of the native, wild-type genes was sufficient to drive efficient product synthesis. Moreover, the unique glucose catabolism network in ADP1 limits its pyruvate availability, supplementing pyruvate and minimizing carbon loss proved critical for optimizing l-leucine production. Collectively, our findings offer mechanistic insights into chassis-specific metabolic regulation and optimizing precursor supply in nonmodel organisms.},
}

@article {pmid40744236,
year = {2025},
author = {Zhang, S and Al-Gashgari, B and Medina, JS and Wang, C and Narayanasamy, S and Xiong, Y and Wang, K and Hong, PY},
title = {Extracellular DNA-associated dissemination of antimicrobial resistance in anaerobic versus aerobic membrane bioreactor.},
journal = {Bioresource technology},
volume = {437},
number = {},
pages = {133054},
doi = {10.1016/j.biortech.2025.133054},
pmid = {40744236},
issn = {1873-2976},
abstract = {Extracellular DNA (eDNA) in the environment can escalate antimicrobial resistance threats arising from natural transformation-based horizontal gene transfer (HGT). Reclaimed wastewater is a source of eDNA, particularly those associated with antibiotic resistance genes (ARGs), may vary depending on the wastewater treatment technology. Here, a comparison study was conducted in aerobic and anaerobic membrane bioreactors (AeMBR and AnMBR). A full-scale AeMBR and a pilot-scale AnMBR were analyzed through long-term sampling and time-series batch tests. Long-term sampling showed that AeMBR sludge increased eDNA content by 2.5 times compared to AnMBR sludge. Specifically, time-series batch tests showed eDNA levels in aerobic sludge followed a logistic growth model but not anaerobic sludge. The water matrix of AeMBR sludge increased natural transformation by 1.6-fold change compared to that of AnMBR sludge. This increase in natural transformation rates was mediated by reactive oxygen species (ROS) in the AeMBR sludge. Metagenomic analysis revealed that the AnMBR system maintained consistent extracellular ARG (eARG) ecological diversity from influent to effluent, whereas the AeMBR system significantly altered eARG diversity. This study provides vital insights into the behavior of eDNA arising from different wastewater treatment processes. Understanding these differences is crucial for optimizing treatment strategies to reduce the environmental impact of eDNA-associated dissemination of antibiotic resistance.},
}

@article {pmid40744195,
year = {2025},
author = {Deng, Z and Zhao, Y and Ren, Z and Hao, N and Sun, P and Zhao, W},
title = {Ecological distribution, dissemination potential, and health risks of antibiotic resistance genes and mobile genetic elements in soils across diverse land-use types in China.},
journal = {Environmental research},
volume = {285},
number = {Pt 2},
pages = {122459},
doi = {10.1016/j.envres.2025.122459},
pmid = {40744195},
issn = {1096-0953},
abstract = {Antibiotic resistance genes (ARGs) have emerged as critical environmental contaminants, while mobile genetic elements (MGEs) act as key vectors facilitating their horizontal transfer, collectively posing growing challenges to ecosystem and public health. This study presents a comprehensive metagenomic investigation of ARGs and MGEs across 180 soil samples from five major land use types in China: farmland, forest, grassland, urban planting, and bare land. Among 862 identified ARG subtypes, 28 were detected in over 95 % of samples, indicating the presence of ecologically dominant and widely disseminated resistance elements. By integrating taxonomic profiling, metagenomic assembly, and multiple statistical methods-including Kruskal-Wallis testing, redundancy analysis (RDA), PERMANOVA, and co-occurrence network analysis-we revealed distinct distributional patterns and ecological associations of ARGs and MGEs across land use gradients. Forest and agricultural soils exhibited higher ARG diversity and abundance, while urban and barren soils showed reduced resistome complexity. Network analysis identified key ARG-MGE co-occurrence modules and hub elements that may promote horizontal gene transfer, particularly under anthropogenic disturbance. Taxonomic annotation highlighted Actinomycetota and Pseudomonadota as dominant ARG hosts. A multi-indicator health risk framework incorporating environmental prevalence, gene mobility, and host pathogenicity classified 267 ARG subtypes as posing medium to high potential risks. These findings enhance our understanding of land use-mediated ARG dissemination and provide a scientific basis for targeted environmental monitoring and mitigation strategies.},
}

@article {pmid40743960,
year = {2025},
author = {Wu, X and Tang, Z and Li, Y and Du, Z and Li, W and Wang, S and Huang, C},
title = {Biochar promotes removal of intracellular and extracellular antibiotic resistance genes in sludge compost: Reshaping microbial communities.},
journal = {Journal of environmental management},
volume = {392},
number = {},
pages = {126781},
doi = {10.1016/j.jenvman.2025.126781},
pmid = {40743960},
issn = {1095-8630},
abstract = {Antibiotic resistance genes (ARGs), as emerging pollutants, jeopardize ecological and public health. Extracellular ARGs (eARGs) pose heightened risks due to their mobility, accelerating resistance spread. However, studying eARGs remains challenging given extracellular DNA's environmental instability. While aerobic composting of sewage sludge reduces ARGs, resurgence of certain genes (e.g., sulfonamide resistance) in later stages may exacerbate resistance risks. This study investigated the effects of sludge-derived biochar and commercial biochar on the reduction of intracellular and extracellular sulfonamide ARGs during sludge composting. After the addition of both biochars, intracellular ARGs (iARGs) gradually decreased as composting progressed, while eARGs initially increased before subsequently declining. The biochars reshaped the microbial community in sludge composting, significantly increasing the number of differentially enriched microbial species, altering community assembly processes, and reducing bacterial diversity and richness-key factors in ARGs reduction. The addition of both biochars also decreased the abundance of intl1, and combined with the inactivation of certain microorganisms and disruption of cell membranes, effectively suppressed the horizontal gene transfer (HGT) of eARGs. However, compared to commercial biochar, the application of sludge-derived biochar led to an increase in potential host microorganisms for ARGs, highlighting a potential risk associated with the production of biochar from sludge. Additionally, the biochars modified environmental factors such as moisture and organic content, further enhancing eARG removal. This study proposes a "waste-to-waste" circular economy model. By reusing sludge-derived biochar in composting, it not only suppresses the spread of ARGs but also achieves high-value utilization of sludge, enabling synergistic pollution control.},
}

@article {pmid40743727,
year = {2025},
author = {Vinogradov, E and Zou, L and Stupak, J and Martynova, Y and Arbour, M and St Michael, F and Williams, D and Beaudoin, G and Li, J and Chen, W and Zou, W and Peters, DL},
title = {Capsular Polysaccharide of Acinetobacter baumannii MRSN 31196 (a KL1 Variant Strain) and its Degradation by a Recombinant Depolymerase from Bacteriophage vB_AbaP_B5.},
journal = {Carbohydrate research},
volume = {556},
number = {},
pages = {109621},
doi = {10.1016/j.carres.2025.109621},
pmid = {40743727},
issn = {1873-426X},
abstract = {Acinetobacter baumannii MRSN 31196 was assigned as KL1, but has now been reassigned as KL1-v as new polymerase wzy and acetyl transferase (atr25) genes are discovered outside of its gene locus due to horizontal gene transfer. Its capsular polysaccharide (CPS), namely K1v, was isolated by a standard water-phenol extraction and an aqueous base extraction. K1v is degradable by a recombinant phage depolymerase B5 which is known to hydrolyze A. baumannii K9 CPS. The structure of oligosaccharides obtained were determined by NMR and mass spectroscopic analysis. The results showed that the K1v structure is closely related to K1 CPS, with the same sugar composition and linkages except β-QuiNAcNR-(1-3)-GlcNAc in K1v replaced β-QuiNAcNR-(1-4)-GlcNAc in K1, due to an altered Wzy. However, the atr25 gene is likely silenced, or the transferase activity is inhibited, as K1v is not O-acetylated. We also found that the N-acetyl and N-3-hydroxybutyryl (HBu) substitutions (R) in QuiNAcNR has approximately a 1:1 ratio. The mass spectroscopic analysis provided evidence that structural blocks with consecutive QuiNAcNAc or QuiNAcNHBu are present in the polysaccharide. The K1v CPS structure has the following trisaccharide repeating unit.},
}

@article {pmid40743684,
year = {2025},
author = {Wang, H and Gao, J and Cui, Y and Wang, Y and Guo, Y and Chen, H},
title = {Short-chain per/polyfluoroalkyl substances alternatives enhance horizontal gene transfer risks in nitrification systems under quaternary ammonium compounds antimicrobials co-stress despite lower acute toxicity than perfluorooctanoic acid.},
journal = {Water research},
volume = {287},
number = {Pt A},
pages = {124274},
doi = {10.1016/j.watres.2025.124274},
pmid = {40743684},
issn = {1879-2448},
abstract = {The ecological risks posed by per/polyfluoroalkyl substances (PFAS) and quaternary ammonium compounds (QACs), as emerging contaminants, to the aquatic environment have recently attracted considerable attention. However, it is still unclear whether and how the combined stress of PFAS and QACs affects wastewater treatment system performance and modulates the transmission of resistance genes (RGs). In this paper, it was investigated that the ecological impacts of perfluorooctanoic acid (PFOA) and its alternatives, perfluorobutanesulfonic acid (PFBS) and perfluorohexanoic acid (PFHxA), on nitrification systems with/without diallyl dimethylammonium chloride (DADMAC), a typical QACs disinfectant, during 120 days. Results showed that 3 mg/L PFOA significantly reduced ammonia removal efficiency, while 0-3 mg/L PFBS and PFHxA had no significant impacts. Interestingly, the addition of 0.3 mg/L DADMAC mitigated the inhibitory effect of PFOA on ammonia oxidation and elevated the abundance of complete ammonia oxidizers amoA and ammonia-oxidizing bacteria amoA genes by 15.8 %-52.9 % and 45.0 %-113.9 %, respectively, through looser protein structures of extracellular polymeric substances and more RGs activated. Under single stress, the abundance of total RGs exhibited first decreasing and then increasing trends with increasing concentrations of all three PFAS, and 3 mg/L PFOA enriched the highest. Under combined stress, PFOA led to the highest abundance of RGs by adding 0.3 mg/L DADMAC, while PFBS resulted in the highest abundance of RGs by adding 3 mg/L DADMAC. Notably, the system with PFBS was observed to have the highest abundance of mobile genetic elements (MGEs), followed by PFHxA, particularly inducing intracellular MGEs in sludge to maintain richness and continuity during combined stress stages. Moreover, MGEs were found to have the most positive contribution to the multiplication of antibiotic resistance genes in all three systems. Overall, although PFBS and PFHxA are regarded as typical alternatives to PFOA and are significantly less toxic to the nitrification systems compared with PFOA, both alternatives resulted in higher levels of MGEs, especially posing a more severe risk of horizontal gene transfer in the combined stress environment. Thus, this requires a focus on the RGs transmission risks of using PFAS and its alternatives in disinfectant-intensive environments.},
}

@article {pmid40739812,
year = {2025},
author = {Nie, C and Liu, F and Li, Z and Shen, Y and Hou, Y and Han, P and Tong, M},
title = {Boosting Low-Dose Ferrate(VI) Activation by Layered FeOCl for the Efficient Removal of Antibiotic-Resistant Bacteria and Antibiotic Resistance Genes via Enhancing Fe(IV)/Fe(V) Generation.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c03869},
pmid = {40739812},
issn = {1520-5851},
abstract = {Antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in aquatic environments pose threats to ecosystem safety and human health, which could not be efficiently removed by conventional disinfection techniques. Herein, layered FeOCl with coordinatively unsaturated Fe sites were fabricated and used to activate Fe(VI) for the efficient ARB/ARG removal in the present study. We found that highly reactive Fe(IV)/Fe(V) intermediates were generated in the FeOCl/Fe(VI) system, rapidly disinfecting 1 × 10[7] CFU mL[-1] ARB to below the limit of detection within only 6 min. Via the combination of in situ characterization and theoretical calculations, we revealed that Fe(VI) was preferentially adsorbed onto Fe sites on the (010) plane of FeOCl and subsequently activated to produce reactive Fe(IV)/Fe(V) through direct electron transfer. Meanwhile, O2[•-] generated from O2 activation on the FeOCl surface enhanced Fe(VI) conversion to Fe(IV)/Fe(V). During the disinfection process, intracellular/extracellular ARGs and DNA bases were simultaneously degraded, inhibiting the potential horizontal gene transfer process. The FeOCl/Fe(VI) system could effectively disinfect ARB under complex water matrices and in real water samples including tap water, lake water, and groundwater. When integrated into a continuous-flow reactor, the FeOCl/Fe(VI) system with excellent stability successively disinfected ARB. Overall, the FeOCl/Fe(VI) system showed great promise for eliminating ARB/ARGs from water.},
}

@article {pmid40738105,
year = {2025},
author = {Rodriguez-Rodriguez, L and Pfister, J and Schuck, L and Martin, AE and Mercado-Santiago, LM and Tagliabracci, VS and Forsberg, KJ},
title = {Metagenomic selections reveal diverse antiphage defenses in human and environmental microbiomes.},
journal = {Cell host & microbe},
volume = {33},
number = {8},
pages = {1381-1395.e7},
doi = {10.1016/j.chom.2025.07.005},
pmid = {40738105},
issn = {1934-6069},
abstract = {To prevent phage infection, bacteria have developed an arsenal of antiphage defenses. Evidence suggests that many examples in nature have not been described. Using plasmid libraries expressing small DNA inserts and functional selections for antiphage defense in Escherichia coli, we identified over 200 putative defenses from 14 bacterial phyla in 9 human and soil microbiomes. Many defenses were unrecognizable based on sequence or predicted structure and thus could only be identified via functional assays. In mechanistic studies, we show that some defenses encode nucleases that distinguish phage DNA via diverse chemical modifications. We also identify outer membrane proteins that prevent phage adsorption and a set of unknown defenses with diverse antiphage profiles and modalities. Most defenses acted against at least two phages, indicating that broadly acting systems are widely distributed. Collectively, these findings highlight the diversity and interoperability of antiphage defense systems.},
}

@article {pmid40738074,
year = {2025},
author = {Yang, X and Heng, H and Zhang, H and Peng, M and Chan, EW and Shum, HP and Zhang, R and Chen, S},
title = {IncFIBK/FIIK conjugative iuc3-carrying virulence plasmids of clinical hypervirulent Klebsiella pneumoniae are multi-drug resistant.},
journal = {Microbiological research},
volume = {300},
number = {},
pages = {128288},
doi = {10.1016/j.micres.2025.128288},
pmid = {40738074},
issn = {1618-0623},
mesh = {*Klebsiella pneumoniae/genetics/pathogenicity/drug effects/isolation & purification ; *Plasmids/genetics ; *Drug Resistance, Multiple, Bacterial/genetics ; *Klebsiella Infections/microbiology ; Virulence/genetics ; *Virulence Factors/genetics ; Humans ; Anti-Bacterial Agents/pharmacology ; Conjugation, Genetic ; Animals ; Multigene Family ; Hydroxamic Acids/metabolism ; Genetic Variation ; Siderophores/metabolism ; Bacterial Proteins/genetics ; },
abstract = {Aerobactin encoding loci is the key virulence factor in the virulence plasmid of Klebsiella pneumoniae (Kp). The iuc1 and iuc2 loci are most commonly detected and well-studied, while the iuc3 lineage is less understood. The study investigated comprehensively the iuc3-carrying plasmids in Kp strains providing insights into the diversity, transmission potential and contribution to Kp virulence. The iuc3 was encoded on plasmids ranging from 177,328 bp to 249,880 bp, primarily of the IncFIBK/FIIK5 type, often carrying multi-drug resistance (MDR) regions. Conjugation experiments demonstrated the transferability of iuc3-carrying plasmids, conferring additional resistance to recipient strains. Siderophore production assays indicated that the iuc3 gene cluster significantly enhanced iron acquisition in transconjugants. Analysis of 69,969 Kp isolates from the NCBI Pathogen Detection database identified 872 iuc3-carrying strains across 205 STs and 69 KLs, indicating widespread genetic diversity. These strains were increasingly detected in human clinical samples over time, with additional reservoirs in animals, food, and the environment. The findings underscore the public health threat posed by iuc3-carrying Kp strains, emphasizing the need for surveillance and control measures to prevent the spread of MDR-HvKp clones. This study highlights the complex interplay between plasmid-mediated resistance, virulence, and the potential for horizontal gene transfer in Klebsiella spp.},
}

*Klebsiella pneumoniae/genetics/pathogenicity/drug effects/isolation & purification
*Plasmids/genetics
*Drug Resistance, Multiple, Bacterial/genetics
*Klebsiella Infections/microbiology
Virulence/genetics
*Virulence Factors/genetics
Humans
Anti-Bacterial Agents/pharmacology
Conjugation, Genetic
Animals
Multigene Family
Hydroxamic Acids/metabolism
Genetic Variation
Siderophores/metabolism
Bacterial Proteins/genetics

@article {pmid40738036,
year = {2025},
author = {Seethalakshmi, PS and Anas, A and Devika Raj, K and Jasmin, C and Menon, N and George, G and Sathyendranath, S},
title = {Genomic insights into antibiotic-resistant Vibrio species from clinical and coastal environmental sources in India.},
journal = {Marine pollution bulletin},
volume = {221},
number = {},
pages = {118496},
doi = {10.1016/j.marpolbul.2025.118496},
pmid = {40738036},
issn = {1879-3363},
abstract = {The occurrence and impact of pathogenic Vibrio sp. in coastal waters are strongly influenced by climate change indicators such as ocean warming, sea-level rise, and extreme weather events. This study aimed to compare the virulence and antimicrobial resistance (AMR) profiles of Vibrio cholerae from clinical and environmental sources across India's coastal regions. We also examined pathogenic traits in other marine Vibrio sp. We hypothesized that Vibrio spp. from different environments would show distinct virulence and AMR patterns shaped by their ecological context. To investigate this, we conducted antimicrobial susceptibility testing and whole-genome sequencing (WGS) on both clinical and environmental isolates. Our findings reveal that environmental V. cholerae from coastal waters possess genes promoting host adhesion and haemolytic activity. Similarly, Vibrio alginolyticus and Vibrio vulnificus harboured virulence factors aiding tissue attachment and invasion. Resistance profiling showed environmental V. cholerae were resistant to fluoroquinolones and macrolides, while clinical isolates were resistant to aminoglycosides and sulphonamides. The presence of antibiotic-resistant Vibrio in marine environments poses a significant public health risk, especially given frequent human interactions with coastal waters for recreation, fishing, and transport. Climate change may exacerbate the proliferation and movement of these pathogens across aquatic and terrestrial systems, increasing the likelihood of human exposure. Moreover, the potential for horizontal gene transfer of resistance genes among pathogenic marine bacteria further highlights the need for surveillance and mitigation strategies to address the growing threat of AMR in marine ecosystems.},
}

@article {pmid40737558,
year = {2025},
author = {Bhatt, S and Kumar, N and Akhter, Y and Chatterjee, S},
title = {Investigating RND efflux pumps in Sphingobium yanoikuyae P4: the role of nonpathogenic bacteria in antibiotic resistance gene spread amid environmental contamination.},
journal = {Journal of biomolecular structure & dynamics},
volume = {},
number = {},
pages = {1-16},
doi = {10.1080/07391102.2025.2540826},
pmid = {40737558},
issn = {1538-0254},
abstract = {The widespread and inappropriate application of antibiotics across human and veterinary medicine has generated pressing global health threats, principally the emergence of antimicrobial resistance (AMR) and the contamination of the environment with antibiotics. A fundamental mechanism fueling environmental AMR is the proliferation and horizontal dissemination of antibiotic resistance genes (ARGs), with efflux transporter proteins functioning as central intermediaries. Surprisingly, nonpathogenic bacteria, which are usually regarded as harmless, now pose a substantial risk to society due to the presence of efflux transporters, which make them AMR contributors. In this study, the genomic analysis of the nonpathogenic soil bacterium Sphingobium yanoikuyae P4 revealed an RND (Resistance-Nodulation-Division) efflux pump containing the relevant domains responsible for antibiotic efflux. Molecular docking studies revealed high affinities between the efflux pump and various antibiotics, including fluoroquinolones, beta-lactams, and sulfonamides, raising the possibility of their efflux into the environment. Antibiotic susceptibility tests showed reduced susceptibility due to the action of this efflux transporter. Furthermore, the genome analysis suggested the presence of mobile genetic elements and plasmid-associated sequences, indicating possible horizontal gene transfer. The data highlights that both nonpathogenic and pathogenic bacteria are crucial for capturing and transmitting antibiotic-resistance genes. These results confirm the disregard for existing concerns over the substantial role of nonpathogenic environmental bacteria in the ecological resistome and warrant the need to consider such microorganisms in monitoring and controlling AMR.},
}

@article {pmid40736339,
year = {2025},
author = {Tan, R and Song, Y and Yin, J and Shi, D and Li, H and Chen, T and Wang, Y and Jin, M and Li, J and Yang, D},
title = {Decoding the SCFA-CpxAR-OMP Axis as a Dietary Checkpoint against Antimicrobial Resistance Transmission across Gut-Environment Interfaces.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf156},
pmid = {40736339},
issn = {1751-7370},
abstract = {The transmission of environmental-originated antibiotic resistance genes (ARGs) into the human gut via the food chain or water has transformed the intestinal tract into a critical reservoir and dissemination hub for ARGs. Moreover, human to human oral-fecal transmission is likely to intensify this dissemination cycle. Gut microbiota harboring ARGs not only drive clinical infections but also exacerbate diverse pathologies, including inflammatory bowel disease and metabolic disorders. Furthermore, amplified ARGs can re-enter environmental compartments through fecal discharge, establishing a persistent bidirectional "gut-environment" resistance transmission cycle. In this study, we demonstrate that short-chain fatty acids (SCFAs), key metabolites derived from gut microbiota, potently suppress the horizontal transfer of ARGs. A high-fiber diet reshaped gut microbial composition, elevating SCFA production by 2.3-fold and reducing ARGs dissemination rates by up to 5.8-fold in vivo. The anti-conjugation activity of SCFAs was further validated through in vitro observations and in vivo models. Mechanistically, we propose the CpxAR-OMP pathway as a previously uncharacterized regulatory axis, wherein SCFAs inhibit ARGs transfer by downregulating conjugation-associated promoters (trfAp and trbBp) and disrupting membrane function via CpxAR-mediated suppression of OMPs expression. To our knowledge, this work provides comprehensive evidence of SCFAs in curbing exogenous ARGs dissemination within the gut ecosystem, deciphers the CpxAR-OMP-driven molecular mechanism, and proposes dietary fiber intervention as a feasible strategy to mitigate antimicrobial resistance across the "One-Health" continuum.},
}

@article {pmid40735512,
year = {2025},
author = {Boutzoukas, A and Doi, Y},
title = {The global epidemiology of carbapenem-resistant Acinetobacter baumannii.},
journal = {JAC-antimicrobial resistance},
volume = {7},
number = {4},
pages = {dlaf134},
pmid = {40735512},
issn = {2632-1823},
abstract = {Carbapenem-resistant Acinetobacter baumannii (CRAb) is a challenging, environmentally hardy organism with a propensity to spread within hospitals and a predilection to infect critically ill, vulnerable patients. With its potential for rapid transmission, limited treatment options, and substantial mortality, CRAb is recognized as a critical, top-priority pathogen. Since its initial discovery in 1985, CRAb has disseminated globally, presenting a significant public health threat. CRAb is now endemic in many regions in Europe, South America, Asia, and Africa and globally contributes to over 50 000 deaths each year. Its ability to adhere to hospital surfaces, withstand desiccation, and form biofilms leads to widespread outbreaks. At-risk populations include those hospitalized and ventilated, and the most frequent presentations are respiratory and bloodstream infections. Carbapenem resistance in CRAb is primarily mediated by plasmid-borne carbapenemase genes, especially bla OXA-23. These genes, carried by several epidemic international clones, including IC1 and IC2, have facilitated the global dissemination of CRAb through horizontal gene transfer in healthcare settings. Mortality rates are >20% and vary substantially by region and by type of infection, with bloodstream infections carrying >40% mortality. Despite its significant impact, the development of treatments for CRAb remains inadequate. The novel agent sulbactam-durlobactam holds promise for improved patient outcomes, but ongoing therapeutic development, infection prevention, and antimicrobial stewardship are critical to combat this formidable pathogen. Here, we review the emergence and dissemination of CRAb, its molecular epidemiology and resistance mechanisms, summarize contemporary global clinical epidemiology and patient outcomes, and briefly describe existing and future therapeutics.},
}

@article {pmid40733744,
year = {2025},
author = {Zahid, A and Ismail, H and Wilson, JC and Grice, ID},
title = {Bioengineering Outer-Membrane Vesicles for Vaccine Development: Strategies, Advances, and Perspectives.},
journal = {Vaccines},
volume = {13},
number = {7},
pages = {},
pmid = {40733744},
issn = {2076-393X},
support = {NA//Earbus Foundation of Western Australia/ ; },
abstract = {Outer-membrane vesicles (OMVs), naturally secreted by Gram-negative bacteria, have gained recognition as a versatile platform for the development of next-generation vaccines. OMVs are essential contributors to bacterial pathogenesis, horizontal gene transfer, cellular communication, the maintenance of bacterial fitness, and quorum sensing. Their intrinsic immunogenicity, adjuvant properties, and scalability establish OMVs as potent tools for combating infectious diseases and cancer. Recent advancements in genetic engineering and biotechnology have further expanded the utility of OMVs, enabling the incorporation of multiple epitopes and antigens from diverse pathogens. These developments address critical challenges such as antigenic variability and co-infections, offering broader immune coverage and cost-effective solutions. This review explores the unique structural and immunological properties of OMVs, emphasizing their capacity to elicit robust immune responses. It critically examines established and emerging engineering strategies, including the genetic engineering of surface-displayed antigens, surface conjugation, glycoengineering, nanoparticle-based OMV engineering, hybrid OMVs, and in situ OMV production, among others. Furthermore, recent advancements in preclinical research on OMV-based vaccines, including synthetic OMVs, OMV-based nanorobots, and nanodiscs, as well as emerging isolation and purification methods, are discussed. Lastly, future directions are proposed, highlighting the potential integration of synthetic biology techniques to accelerate research on OMV engineering.},
}

@article {pmid40732295,
year = {2025},
author = {Bharathi, D and Lee, J},
title = {Recent Trends in Bioinspired Metal Nanoparticles for Targeting Drug-Resistant Biofilms.},
journal = {Pharmaceuticals (Basel, Switzerland)},
volume = {18},
number = {7},
pages = {},
pmid = {40732295},
issn = {1424-8247},
support = {RS-2025-00513239//National Research Foundation of Korea/ ; RS-2024-00450423//Korea Health Industry Development Institute/Republic of Korea ; },
abstract = {Multidrug-resistant (MDR) biofilm infections characterized by densely packed microbial communities encased in protective extracellular matrices pose a formidable challenge to conventional antimicrobial therapies and are a major contributor to chronic, recurrent and device-associated infections. These biofilms significantly reduce antibiotic penetration, facilitate the survival of dormant persister cells and promote horizontal gene transfer, all of which contribute to the emergence and persistence of MDR pathogens. Metal nanoparticles (MNPs) have emerged as promising alternatives due to their potent antibiofilm properties. However, conventional synthesis methods are associated with high costs, complexity, inefficiency and negative environmental impacts. To overcome these limitations there has been a global push toward the development of sustainable and eco-friendly synthesis approaches. Recent advancements have demonstrated the successful use of various plant extracts, microbial cultures, and biomolecules for the green synthesis of MNPs, which offers biocompatibility, scalability, and environmental safety. This review provides a comprehensive overview of recent trends and the latest progress in the green synthesis of MNPs including silver (Ag), gold (Au), platinum (Pt), and selenium (Se), and also explores the mechanistic pathways and characterization techniques. Furthermore, it highlights the antibiofilm applications of these MNPs emphasizing their roles in disrupting biofilms and restoring the efficacy of existing antimicrobial strategies.},
}

@article {pmid40732194,
year = {2025},
author = {Liu, F and Cao, B and Dai, H and Li, G and Li, S and Gao, W and Zhao, R},
title = {High-Resolution Core Gene-Associated Multiple Nucleotide Polymorphism (cgMNP) Markers for Strain Identification in the Wine Cap Mushroom Stropharia rugosoannulata.},
journal = {Microorganisms},
volume = {13},
number = {7},
pages = {},
pmid = {40732194},
issn = {2076-2607},
support = {2022YFD1200605//the National Key R&D Program of China project/ ; },
abstract = {Stropharia rugosoannulata, an ecologically valuable and economically important edible mushroom, faces challenges in strain-level identification and breeding due to limited genomic resources and the lack of high-resolution molecular markers. In this study, we generated high-quality genomic data for 105 S. rugosoannulata strains and identified over 2.7 million SNPs, unveiling substantial genetic diversity within the species. Using core gene-associated multiple nucleotide polymorphism (cgMNP) markers, we developed an efficient and transferable framework for strain discrimination. The analysis revealed pronounced genetic differentiation among cultivars, clustering them into two distinct phylogenetic groups. Nucleotide diversity (π) across 83 core genes varied significantly, highlighting both highly conserved loci under purifying selection and highly variable loci potentially associated with adaptive evolution. Phylogenetic analysis of the most variable gene, Phosphatidate cytidylyltransferase mitochondrial, identified 865 SNPs, enabling precise differentiation of all 85 cultivars. Our findings underscore the utility of cgMNP markers in addressing challenges posed by horizontal gene transfer and phylogenetic noise, demonstrating their robustness in cross-species applications. By providing insights into genetic diversity, evolutionary dynamics, and marker utility, this study establishes a foundation for advancing breeding programs, conservation strategies, and functional genomics in S. rugosoannulata. Furthermore, the adaptability of cgMNP markers offers a universal tool for high-resolution strain identification across diverse fungal taxa, contributing to broader fungal phylogenomics and applied mycology.},
}

@article {pmid40732100,
year = {2025},
author = {Mourão, AV and Fernandes, D and de Sousa, T and Calouro, R and Saraiva, S and Igrejas, G and Poeta, P},
title = {Aquatic Resistome in Freshwater and Marine Environments: Interactions Between Commensal and Pathogenic in the Context of Aquaculture and One Health.},
journal = {Microorganisms},
volume = {13},
number = {7},
pages = {},
pmid = {40732100},
issn = {2076-2607},
support = {UI/00772//Fundacao para a Ciencia e a Tecnologia/ ; LA/P/0059/2020//Fundacao para a Ciencia e a Tecnologia/ ; },
abstract = {Aquatic resistomes are important reservoirs of antibiotic resistance genes (ARGs) and their precursors, which can proliferate and dissipate in pathogenic microorganisms that affect humans and animals, especially due to anthropogenic pressures such as the intensive use of antibiotics in aquaculture, often without effective regulation. This review addresses the mechanisms of horizontal gene transfer (HGT) in the dissemination of ARGs through mobile genetic elements (MGEs). In freshwater, genera such as Aeromonas, Pseudomonas and Microcystis stand out as vectors of ARGs. In the context of One Health, it is essential to implement sound public policies and strict regulations on the use of antibiotics in aquaculture, and the use of monitoring tools such as environmental DNA (eDNA) and metagenomics allows for the early detection of ARGs, contributing to the protection of human, animal and environmental health.},
}

@article {pmid40730864,
year = {2025},
author = {McCallum, GE and Hall, JPJ},
title = {The hospital sink drain microbiome as a melting pot for AMR transmission to nosocomial pathogens.},
journal = {npj antimicrobials and resistance},
volume = {3},
number = {1},
pages = {68},
pmid = {40730864},
issn = {2731-8745},
support = {MR/W02666X/1/MRC_/Medical Research Council/United Kingdom ; MR/W02666X/1/MRC_/Medical Research Council/United Kingdom ; },
abstract = {The hospital sink drain microbiome can harbour opportunistic pathogens and antimicrobial resistance genes (ARGs). Aspects of this habitat, such as exposure to disinfectants, antibiotics, nutrients, and body fluids could exacerbate horizontal gene transfer of ARGs and clinically impactful pathogen resistance. Here, we explore features of the hospital sink drain that may favour ARG acquisition and transmission, highlight studies providing evidence of transfer, and consider strategies to mitigate these risks.},
}

@article {pmid40729388,
year = {2025},
author = {Riaz, MR and Sosa Marquez, I and Lindgren, H and Levin, G and Doyle, R and Romero, MC and Paoli, JC and Drnevich, J and Fields, CJ and Geddes, BA and Marshall-Colón, A and Heath, KD},
title = {Mobile gene clusters and coexpressed plant-rhizobium pathways drive partner quality variation in symbiosis.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {31},
pages = {e2411831122},
pmid = {40729388},
issn = {1091-6490},
support = {IOS-1645875//NSF (NSF)/ ; DBI-2022049//NSF (NSF)/ ; IOS-2243821//NSF (NSF)/ ; na//Consejo Nacional de Humanidades, Ciencias y Tecnologías (Conahcyt)/ ; na//UofI | UIUC | Carl R. Woese Institute for Genomic Biology (IGB)/ ; IOS- 2243818//NSF (NSF)/ ; },
mesh = {*Symbiosis/genetics ; *Sinorhizobium meliloti/genetics ; *Multigene Family ; Root Nodules, Plant/microbiology/genetics ; Genetic Variation ; Transcriptome ; *Rhizobium/genetics ; Gene Regulatory Networks ; },
abstract = {Plant-microbe symbioses such as the legume-rhizobium mutualism are vital in the web of ecological relationships within both natural and managed ecosystems, influencing primary productivity, crop yield, and ecosystem services. The outcome of these interactions for plant hosts varies quantitatively and can range from highly beneficial to even detrimental depending on natural genetic variation in microbial symbionts. Here, we take a systems genetics approach, harnessing the genetic diversity present in wild rhizobial populations to predict genes and molecular pathways crucial in determining partner quality, i.e., the benefits of symbiosis for legume hosts. We combine traits, dual-RNAseq of both partners from active nodules, pangenomics/pantranscriptomics, and Weighted Gene Co-expression Network Analysis (WGCNA) for a panel of 20 Sinorhizobium meliloti strains that vary in symbiotic partner quality. We find that genetic variation in the nodule transcriptome predicts host plant biomass, and WGCNA reveals networks of genes in plants and rhizobia that are coexpressed and associated with high-quality symbiosis. Presence-absence variation of gene clusters on the symbiosis plasmid (pSymA), validated in planta, is associated with high or low-quality symbiosis and is found within important coexpression modules. Functionally our results point to management of oxidative stress, amino acid and carbohydrate transport, and NCR peptide signaling mechanisms in driving symbiotic outcomes. Our integrative approach highlights the complex genetic architecture of microbial partner quality and raises hypotheses about the genetic mechanisms and evolutionary dynamics of symbiosis.},
}

*Symbiosis/genetics
*Sinorhizobium meliloti/genetics
*Multigene Family
Root Nodules, Plant/microbiology/genetics
Genetic Variation
Transcriptome
*Rhizobium/genetics
Gene Regulatory Networks

@article {pmid40727556,
year = {2025},
author = {Wang, Z and Zhao, S and Chen, G and Sun, S and Liu, Y and Chen, H and Meng, L and Han, Z and Zheng, D},
title = {Biodegradation of high-molecular-weight polycyclic aromatic hydrocarbons by a novel species of the genus Devosia isolated from the deep-sea region of the Kermadec Trench.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1584496},
pmid = {40727556},
issn = {1664-302X},
abstract = {Polycyclic aromatic hydrocarbons (PAHs) are categorized as persistent organic pollutants due to their high toxicity and environmental persistence. In this study, a deep-sea bacterium, designed Naph2[T], was isolated from the sediments of the Kermadec Trench using PAH-enriched cultures. A comparative analysis of Overall Genome Relatedness Indices (OGRI) values between Naph2[T] and closely related strains within the genus Devosia indicated that the isolate represents a novel species, designated as Devosia polycyclovorans sp. nov. (type strain Naph2[T] = MCCC 1K09447[T]). This conclusion is further supported by physiological and biochemical analyses. Naph2[T] exhibited the ability to degrade high-molecular-weight PAHs such as pyrene and benzo[a]pyrene, a feature not previously reported for any strain within the genus Devosia. The degradation degree of Naph2[T] for pyrene and benzo[a]pyrene reached 58 and 48% at a concentration of 300 mg/L and 200 mg/L, respectively, in 5 days. Genomic analysis revealed key genes associated with PAH degradation, including aromatic ring-hydroxylating dioxygenase (RHD), nagAa, and downstream gene clusters such as pht, pob, and pca. Comparative genomic studies showed that Naph2[T] harbors a greater number of PAH degradation genes than other species within the Devosia genus, demonstrate that it may have acquired these capabilities through horizontal gene transfer. Transcriptome data revealed significant upregulation of pcaG and pcaH, which encode enzymes involved in the degradation of 3,4-dihydroxybenzoic acid, a downstream intermediate of polycyclic aromatic hydrocarbon metabolism. These findings not only provide novel insights into the ecological roles of the genus Devosia, but also highlight the potential of this new species for PAH bioremediation applications.},
}

@article {pmid40725502,
year = {2025},
author = {Hu, T and Zhou, F and Wang, L and Hu, X and Li, Z and Li, X and Zhou, D and Wang, H},
title = {Mitogenome Characteristics and Intracellular Gene Transfer Analysis of Four Adansonia Species.},
journal = {Genes},
volume = {16},
number = {7},
pages = {},
pmid = {40725502},
issn = {2073-4425},
support = {No. 25L193//Integration and Optimization of Ancient Tree and Famous Tree Protection and Rural Tourism Development in Zhumadian City/ ; },
mesh = {*Genome, Mitochondrial/genetics ; Phylogeny ; Evolution, Molecular ; *Gene Transfer, Horizontal ; },
abstract = {Adansonia L. (1753) belongs to the family Malvaceae and is commonly known as the baobab tree. This species holds significant cultural and ecological value and is often referred to as the 'tree of life.' Although its nuclear genome has been reported, the mitogenome has not yet been studied. Mitogenome research is crucial for understanding the evolution of the entire genome. In this study, we assembled and analyzed the mitogenomes of four Adansonia species by integrating short-read and long-read data. The results showed that the mitogenomes of all four Adansonia species were resolved as single circular sequences. Their total genome lengths ranged from 507,138 to 607,344 bp and contained a large number of repetitive sequences. Despite extensive and complex rearrangements between the mitogenomes of Adansonia and other Malvaceae species, a phylogenetic tree constructed based on protein-coding genes clearly indicated that Adansonia is more closely related to the Bombax. Selection pressure analysis suggests that the rps4 gene in Adansonia may have undergone positive selection compared to other Malvaceae species, indicating that this gene may play a significant role in the evolution of Adansonia. Additionally, by analyzing intracellular gene transfer between the chloroplast, mitochondria, and nuclear genomes, we found that genes from the chloroplast and mitochondria can successfully transfer to each chromosome of the nuclear genome, and the psbJ gene from the chloroplast remains intact in both the mitochondrial and nuclear genomes. This study enriches the genetic information of Adansonia and provides important evidence for evolutionary research in the family Malvaceae.},
}

*Genome, Mitochondrial/genetics
Phylogeny
Evolution, Molecular
*Gene Transfer, Horizontal

@article {pmid40724928,
year = {2025},
author = {Mažeikienė, I and Frercks, B and Kurgonaitė, M and Rasiukevičiūtė, N and Mačionienė, I},
title = {Genomic Insights into Vaccinium spp. Endophytes B. halotolerans and B. velezensis and Their Antimicrobial Potential.},
journal = {International journal of molecular sciences},
volume = {26},
number = {14},
pages = {},
pmid = {40724928},
issn = {1422-0067},
mesh = {*Endophytes/genetics/metabolism ; *Bacillus/genetics/metabolism/isolation & purification/classification ; *Genome, Bacterial ; *Anti-Infective Agents/pharmacology/metabolism ; Genomics/methods ; Phylogeny ; Blueberry Plants/microbiology ; Gene Transfer, Horizontal ; },
abstract = {Plant microbiota contributes to nutrient absorption, and the production of hormones and vitamins, and plays a crucial role in responding to environmental stress. We hypothesized that Vaccinium spp. harbour a unique microbiota that enables them to coexist in extreme environments such as saline, nutrient-poor, and waterlogged conditions. Upon examining Bacillus spp. endophytes isolated from blueberries, cranberries and lingonberries in vitro, we identified B. halotolerans (Bil-LT1_1, Bil-LT1_2) and B. velezensis (Cran-LT1_8, Ling-NOR4_15) strains that inhibit the growth of five pathogenic fungi and five foodborne bacteria. Whole-genome sequencing provided insights into genome organization and plasticity, helping identify mobile elements and genes potentially acquired through horizontal gene transfer. Functional annotation identified genes associated with plant colonization, stress tolerance, biocontrol activity, and plant growth promotion. Comparative genomic analyses revealed key biosynthetic gene clusters (BGCs) responsible for producing antifungal metabolites, including lipopeptides and polyketides. Genes supporting plant nutrition, growth, and environmental adaptation were present also in these strains. Notably, isolated endophytes exhibited particularly high levels of genomic plasticity, likely due to horizontal gene transfer involving gene ontology (GO) pathways related to survival in polymicrobial and foreign environments.},
}

*Endophytes/genetics/metabolism
*Bacillus/genetics/metabolism/isolation & purification/classification
*Genome, Bacterial
*Anti-Infective Agents/pharmacology/metabolism
Genomics/methods
Phylogeny
Blueberry Plants/microbiology
Gene Transfer, Horizontal

@article {pmid40724597,
year = {2025},
author = {Borgio, JF},
title = {Hybrid Genome and Clinical Impact of Emerging Extensively Drug-Resistant Priority Bacterial Pathogen Acinetobacter baumannii in Saudi Arabia.},
journal = {Life (Basel, Switzerland)},
volume = {15},
number = {7},
pages = {},
pmid = {40724597},
issn = {2075-1729},
abstract = {Acinetobacter baumannii is listed by the World Health Organization as an emerging bacterial priority pathogen, the prevalence and multidrug resistance of which have been increasing. This functional genomics study aimed to understand the drug-resistance mechanisms of an extensively drug-resistant (XDR) A. baumannii strain (IRMCBCU95U) isolated from a transtracheal aspirate sample from a female patient with end-stage renal disease in Saudi Arabia. The whole genome of IRMCBCU95U (4.3 Mbp) was sequenced using Oxford Nanopore long-read sequencing to identify and compare the antibiotic-resistance profile and genomic features of A. baumannii IRMCBCU95U. The antibiogram of A. baumannii IRMCBCU95U revealed resistance to multiple antibiotics, including cefepime, ceftazidime, ciprofloxacin, imipenem, meropenem and piperacillin/tazobactam. A comparative genomic analysis between IRMCBCU95U and A. baumannii K09-14 and ATCC 19606 identified significant genetic heterogeneity and mosaicism among the strains. This analysis also demonstrated the hybrid nature of the genome of IRMCBCU95U and indicates that horizontal gene transfer may have occurred between these strains. The IRMCBCU95U genome has a diverse range of genes associated with antimicrobial resistance and mobile genetic elements (ISAba1 and IS26) associated with the spread of multidrug resistance. The presence of virulence-associated genes that are linked to iron acquisition, motility and transcriptional regulation confirmed that IRMCBCU95U is a priority human pathogen. The plasmid fragment IncFIB(pNDM-Mar) observed in the strain is homologous to the plasmid in Klebsiella pneumoniae (439 bp; similarity: 99.09%), which supports its antimicrobial resistance. From these observations, it can be concluded that the clinical A. baumannii IRMCBCU95U isolate is an emerging extensively drug-resistant human pathogen with a novel combination of resistance genes and a plasmid fragment. The complex resistome of IRMCBCU95U highlights the urgent need for genomic surveillance in hospital settings in Saudi Arabia to fight against the spread of extensively drug-resistant A. baumannii.},
}

@article {pmid40724253,
year = {2025},
author = {Ortega-Sanz, I and Rajkovic, A},
title = {Microplastics-Assisted Campylobacter Persistence, Virulence, and Antimicrobial Resistance in the Food Chain: An Overview.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {14},
pages = {},
pmid = {40724253},
issn = {2304-8158},
support = {G000123N//Research Foundation - Flanders/ ; 965173//European Union/ ; },
abstract = {Recent studies have detected microplastics (MPs) in seafood and various food products worldwide, including poultry, fish, salt, beverages, fruits, and vegetables. This widespread contamination makes human exposure through consumption unavoidable and raises concerns for food safety and human health. MPs provide physical support to microorganisms for biofilm formation, protecting them from extreme conditions and facilitating their persistence in the environment. However, little is known about the impact of MPs in the transmission of foodborne pathogens and subsequent spread of infectious diseases like campylobacteriosis, the most common foodborne illness caused by a bacterium, Campylobacter. This review explores the sources of MP contamination in the food chain and offers a comprehensive overview of MP presence in animals, food products, and beverages. Moreover, we compile the available studies linking MPs and Campylobacter and examine the potential impact of these particles on the transmission of Campylobacter along the food chain with a particular focus on poultry, the main source and reservoir for the pathogen. While the environmental and toxicological effects of MPs are increasingly understood, their influence on the virulence of Campylobacter and the spread of antimicrobial resistance remains underexplored. Further studies are needed to develop standardized methods for isolating and identifying MPs, enabling comprehensive investigations and more effective monitoring and risk mitigation strategies.},
}

@article {pmid40723966,
year = {2025},
author = {Atriano Briano, RA and Badillo-Larios, NS and Niño-Moreno, P and Pérez-González, LF and Turrubiartes-Martínez, EA},
title = {Molecular Characterization of Vancomycin-Resistant Enterococcus spp. from Clinical Samples and Identification of a Novel Sequence Type in Mexico.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {7},
pages = {},
pmid = {40723966},
issn = {2079-6382},
abstract = {Background:Enterococcus spp. is the third leading cause of healthcare-associated infections in the American continent, often because of the virulence factors that protect the bacterium against host defenses and facilitate tissue attachment and genetic material exchange. In addition, vancomycin, considered a last-resort treatment, has shown reduced efficacy in Enterococcus spp. strains. However, the relationship between bacterial resistance and virulence factors remains unclear. This study intends to evaluate the prevalence of glycopeptide-resistant genotypes and virulence factors in Enterococcus spp. strains. Methods: Over six months, 159 Enterococcus spp. strains causing nosocomial infections were analyzed. Multiplex PCR was performed to identify species, glycopeptide-resistant genotypes, and 12 virulence factors. Results: The most abundant species identified were Enterococcus faecalis and E. faecium. Vancomycin resistance was observed in 10.7% of the isolates, and the vanA genotype was present in 47% of resistant samples. The main virulence factors detected were acm (54%), which is related to cell adhesion; gel E (66%), a metalloproteinase linked to tissue damage; and the sex pheromones cpd (64%) and ccf (84%), which are involved in horizontal gene transfer. A significant association was found between the prevalence of acm, ccf, and cpd in VRE isolates, indicating the potential dissemination of genes to emerging strains via horizontal gene transfer. In addition, a new E. faecium, which displayed five virulence factors and harbored the vanA sequence type, was identified and registered as ST2700. Conclusions:Enterococcus faecalis and E. faecium are clinically critical due to multidrug resistance and virulence factors like acm, which aids host colonization. Genes ccf and cpd promote resistance spread via horizontal transfer, while the emerging ST2700 strain requires urgent monitoring to curb its virulent, drug-resistant spread.},
}

@article {pmid40723946,
year = {2025},
author = {Saengsawang, P and Tanonkaew, R and Kimseng, R and Nissapatorn, V and Wintachai, P and Rodríguez-Ortega, MJ and Mitsuwan, W},
title = {Whole Genome Sequence Analysis of Multidrug-Resistant Staphylococcus aureus and Staphylococcus pseudintermedius Isolated from Superficial Pyoderma in Dogs and Cats.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {7},
pages = {},
pmid = {40723946},
issn = {2079-6382},
support = {RGNS 65-187//Office of the Permanent Secretary, Ministry of Higher Education, Science, Research and Innova-tion (OPS MHESI), Thailand Science Research/ ; WU-COE-65-05//Centre of Excellence in Innovation of Essential Oil and Bioactive Compounds/ ; },
abstract = {Background: Pyoderma is a superficial bacterial infection that is considered the formation of pus-containing lesions on the skin occurring in animals. Staphylococci, including Staphylococcus aureus and Staphylococcus pseudintermedius, that cause pyoderma in pet animals is a global health concern. The objectives of this study were to investigate antibiotic-resistant staphylococci isolated from pyoderma in dogs and cats and to analyse whole genome sequences of multidrug-resistant (MDR) staphylococci. Methods: A total of 56 pyoderma swabbing samples from 42 dogs and 14 cats located in Southern Thailand was collected to isolate staphylococci. Antibiotic susceptibility and antibiotic-resistant genes of staphylococcal isolates were investigated. Furthermore, the representative MDR isolates were investigated using whole genome sequence analysis. Results: 61 isolates were identified as staphylococci, which can be classified into 12 different species, mostly including 13 S. intermedius (13.26%), 13 S. saprophyticus (13.26%), 8 S. sciuri (8.16%), and Staphylococcus cohnii (8.16%). Remarkably, the main pyoderma-causing species that were isolated in this study were S. aureus (5.10%) and S. pseudintermedius (3.06%). Most staphylococci were resistant to penicillin G (30%), and the blaZ gene was found to be the highest prevalence of the resistance genes. Both MDR-S. aureus WU1-1 and MDR-S. pseudintermedius WU48-1 carried capsule-related genes as main virulence factor genes. Interestingly, MDR-S. pseudintermedius WU48-1 was resistant to seven antibiotic classes, which simultaneously carried blaZ, mecA, aac, dfrK, aph3, and tetM. Genes related to antibiotic efflux were the highest proportion of the mechanism found in both representatives. Remarkably, SCCmec cassette genes were found in both isolates; however, the mecA gene was found only in MDR-S. pseudintermedius WU48-1. In addition, these were mostly carried by macrolide- and tetracycline-resistance genes. Mobile gene transfer and horizontal gene transfer events frequently contain genes involved in the antibiotic target alteration mechanism. Conclusions: This study found that MDR staphylococci, especially S. aureus and S. pseudintermedius, are important in animals and owners in terms of One Health concern. The information on whole genome sequences of these MDR staphylococci, particularly antimicrobial resistance genes, mobile genetic elements, and horizontal gene transfer events, can help to understand gene transmission and be applied for antibiotic resistance surveillance in veterinary medicine.},
}

@article {pmid40723873,
year = {2025},
author = {Gatto, KP and Targueta, CP and Vittorazzi, SE and Lourenço, LB},
title = {Could Horizontal Gene Transfer Explain 5S rDNA Similarities Between Frogs and Worm Parasites?.},
journal = {Biomolecules},
volume = {15},
number = {7},
pages = {},
pmid = {40723873},
issn = {2218-273X},
support = {2014/23542-6//Fapesp/ ; },
mesh = {Animals ; *Gene Transfer, Horizontal ; Phylogeny ; *RNA, Ribosomal, 5S/genetics ; *DNA, Ribosomal/genetics ; *Anura/genetics ; *Xenopus laevis/genetics/parasitology ; },
abstract = {Horizontal gene transfer (HGT), the non-Mendelian transfer of genetic material between organisms, is relatively frequent in prokaryotes, whereas its extent among eukaryotes remains unclear. Here, we raise the hypothesis of a possible cross-phylum HGT event involving 5S ribosomal DNA (rDNA). A specific type of 5S rDNA sequence from the anuran Xenopus laevis was highly similar to a 5S rDNA sequence of the genome of its flatworm parasite Protopolystoma xenopodis. A maximum likelihood analysis revealed phylogenetic incongruence between the gene tree and the species trees, as the 5S rDNA sequence from Pr. xenopodis was grouped along with the sequences from the anurans. Sequence divergence analyses of the gene region and non-transcribed spacer also agree with an HGT event from Xenopus to Pr. xenopodis. Additionally, we examined whether contamination of the Pr. xenopodis genome assembly with frog DNA could explain our findings but found no evidence to support this hypothesis. These findings highlight the possible contribution of HGT to the high diversity observed in the 5S rDNA family.},
}

Animals
*Gene Transfer, Horizontal
Phylogeny
*RNA, Ribosomal, 5S/genetics
*DNA, Ribosomal/genetics
*Anura/genetics
*Xenopus laevis/genetics/parasitology

@article {pmid40723416,
year = {2025},
author = {Zhang, H and Wu, T and Ruan, H},
title = {Unveiling Genomic Islands Hosting Antibiotic Resistance Genes and Virulence Genes in Foodborne Multidrug-Resistant Patho-Genic Proteus vulgaris.},
journal = {Biology},
volume = {14},
number = {7},
pages = {},
pmid = {40723416},
issn = {2079-7737},
support = {2022KJ004//Tianjin Education Commission Scientific Research Project/ ; },
abstract = {Proteus vulgaris is an emerging multidrug-resistant (MDR) foodborne pathogen that poses a significant threat to food safety and public health, particularly in aquaculture systems where antibiotic use may drive resistance development. Despite its increasing clinical importance, the genomic mechanisms underlying antimicrobial resistance (AMR) and virulence transmission in foodborne Proteus vulgaris remain poorly understood, representing a critical knowledge gap in One Health frameworks. To investigate its AMR and virulence transmission mechanisms, we analyzed strain P3M from Penaeus vannamei intestines through genomic island (GI) prediction and comparative genomics. Our study provides the first comprehensive characterization of mobile genetic elements in aquaculture-derived Proteus vulgaris, identifying two virulence-associated GIs (GI12/GI15 containing 25/6 virulence genes) and three AMR-linked GIs (GI7/GI13/GI16 carrying 1/1/5 antibiotic resistance genes (ARGs)), along with a potentially mobile ARG cluster flanked by IS elements (tnpA-tnpB), suggesting horizontal gene transfer capability. These findings elucidate previously undocumented genomic mechanisms of AMR and virulence dissemination in Proteus vulgaris, establishing critical insights for developing One Health strategies to combat antimicrobial resistance and virulence in foodborne pathogens.},
}

@article {pmid40722006,
year = {2025},
author = {Qiu, J and Tao, H and Li, H and Liu, X and Liu, R and Nawaz, MN and Wang, X and Ma, L},
title = {The environmental adaptation of acidophilic archaea: promotion of horizontal gene transfer by genomic islands.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {696},
pmid = {40722006},
issn = {1471-2164},
support = {42277193//National Natural Science Foundation of China/ ; 42277193//National Natural Science Foundation of China/ ; },
mesh = {*Gene Transfer, Horizontal ; *Genomic Islands ; *Archaea/genetics/physiology ; Genome, Archaeal ; *Adaptation, Physiological/genetics ; Base Composition ; Phylogeny ; Genomics ; RNA, Transfer/genetics/chemistry ; },
abstract = {Acid mine drainage (AMD) is an extremely acidic leachate highly contaminated with metal ions, yet it harbors a significantly high abundance of archaea. Genomic islands (GIs), as one of the productions of horizontal gene transfer (HGT), play an important role in the environmental adaptation and evolutionary processes of archaea. However, the distribution, structure, and function of GI within the genomes of archaea remain poorly understood. In this study, through the bioinformatic analysis of archaea in AMD, including Ferroplasma acidiphilum ZJ isolated from laboratory and 25 acidophilic archaea collected from NCBI database, 176 GIs were predicted and annotated. Furthermore, we analyzed their structural features and provided insights into the role of HGT in environmental adaptation. The size and distribution of GIs in the genomes were found to be random. In the majority of GIs, the GC content was lower than the average GC content of the strain genome, suggesting that GIs were typically looped out of the genomes with poor stability and transferred into those with higher stability. tRNAs with classical stem-loop secondary structures have been found at the ends of several GIs, suggesting that GIs frequently integrate near tRNAs. In contrast to functional genes directly involved in cellular life processes, GIs were more likely to carry genes related to genetic information and metabolism. Several GIs were identified to carry genes involved in iron oxidation, mercury reduction, and various toxin-antitoxin systems, which enhance the adaptability of the strains to highly acidic environments.},
}

*Gene Transfer, Horizontal
*Genomic Islands
*Archaea/genetics/physiology
Genome, Archaeal
*Adaptation, Physiological/genetics
Base Composition
Phylogeny
Genomics
RNA, Transfer/genetics/chemistry

@article {pmid40721230,
year = {2025},
author = {Chen, A and Liu, K and Wu, X and Qi, T and Lv, Z and Lu, Y and Tao, Y and Liu, C},
title = {Proliferation of Resistance Genes in Wastewater Pipe Under Tetracycline and Cu Stress.},
journal = {Water environment research : a research publication of the Water Environment Federation},
volume = {97},
number = {7},
pages = {e70155},
doi = {10.1002/wer.70155},
pmid = {40721230},
issn = {1554-7531},
support = {51808285//National Natural Science Foundation of China/ ; SJCX 24-0503//Postgraduate Research & Practice Innovation Program of Jiangsu Province/ ; },
mesh = {*Copper/toxicity/pharmacology ; *Tetracycline/pharmacology/toxicity ; *Wastewater/microbiology ; *Water Pollutants, Chemical/toxicity ; *Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; *Drug Resistance, Bacterial/genetics ; Bacteria/genetics/drug effects ; },
abstract = {Antibiotics and heavy metals can accumulate in wastewater pipe, and they could affect the proliferation of resistance genes in pipe. This study investigated the effects of tetracycline (TC) and Cu stress on extracellular polymeric substances (EPS) of sediments and the proliferation process and mechanism of typical antibiotic resistance genes (ARGs) and heavy metal resistance genes (HMRGs) in pipe. The results showed that TC and Cu induced microorganisms to secrete more tightly bound EPS (TB-EPS) in sediments. Under the 20 days exposure of 10,000 μg/L TC, TB-EPS increased by 49.38% compared with that without TC. Under TC and Cu stress, microorganisms secreted more functional groups associated with proteins and polysaccharides, and the secondary structure of proteins (α-helix and β-sheet) was changed, which improved the stability and aggregation of cell structure. Under the single and combined stress of TC and Cu, the relative abundance of most resistance genes in the sediment of wastewater pipe increased significantly (p ≤ 0.05). And TC and Cu stress increased the abundance of genes encoding for efflux pumps (tet(A), tet(G), copA, and copB) and promoted intl1-mediated horizontal gene transfer. This study could provide the theoretical basis for reducing the further spread of resistance genes in wastewater pipe.},
}

*Copper/toxicity/pharmacology
*Tetracycline/pharmacology/toxicity
*Wastewater/microbiology
*Water Pollutants, Chemical/toxicity
*Anti-Bacterial Agents/pharmacology
Genes, Bacterial
*Drug Resistance, Bacterial/genetics
Bacteria/genetics/drug effects

@article {pmid40719986,
year = {2025},
author = {Pandey, M and Rajput, M and Singh, P and Shukla, VK and Dixit, R},
title = {Human long non-coding RNAs acquired from bacteria via horizontal gene transfer promote gallbladder cancer.},
journal = {Molecular biology reports},
volume = {52},
number = {1},
pages = {762},
doi = {10.1007/s11033-025-10870-z},
pmid = {40719986},
issn = {1573-4978},
mesh = {Humans ; *RNA, Long Noncoding/genetics ; *Gene Transfer, Horizontal/genetics ; *Gallbladder Neoplasms/genetics/microbiology ; Phylogeny ; *Bacteria/genetics ; Gene Expression Regulation, Neoplastic ; Evolution, Molecular ; Transcriptome/genetics ; Gene Expression Profiling/methods ; },
abstract = {BACKGROUND: Gallbladder cancer, the most common malignancy of the bile duct, has a poorly understood etiopathogenesis. Non-coding RNAs are implicated in various cancers, but their role in gallbladder carcinogenesis remains unclear.

METHODS: Transcriptomic data from gallbladder cancer patients were analyzed to identify differentially expressed long non-coding RNAs (lncRNAs). These data underwent cross-species phylogenetic analysis and BLAST comparison with bacterial and ancient human genomes, including Homo heidelbergensis and Homo neanderthalensis. Pathway analysis, gene-gene interactions, and data and text mining were performed for non-conserved, non-coding genes.

RESULTS: Of 16 differentially expressed lncRNAs, seven showed phylogenetic links to bacterial genomes, suggesting acquisition through horizontal gene transfer (HGT) during human evolution. These lncRNAs were present in ancient human species with sequence variations. Functional analysis revealed their role in regulating biological and genetic processes, potentially promoting gallbladder carcinogenesis.

CONCLUSIONS: This is the first study to propose that seven human lncRNAs, likely of bacterial origin, were acquired through HGT during evolution. These lncRNAs regulate transcriptional and post-transcriptional processes, potentially inducing gallbladder carcinogenesis, thus highlighting a novel link between evolutionary genetics and cancer.},
}

Humans
*RNA, Long Noncoding/genetics
*Gene Transfer, Horizontal/genetics
*Gallbladder Neoplasms/genetics/microbiology
Phylogeny
*Bacteria/genetics
Gene Expression Regulation, Neoplastic
Evolution, Molecular
Transcriptome/genetics
Gene Expression Profiling/methods

@article {pmid40719955,
year = {2025},
author = {Purohit, HV},
title = {Nucleoid-associated proteins: molecular mechanisms in microbial adaptation.},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {8},
pages = {277},
pmid = {40719955},
issn = {1573-0972},
mesh = {*Bacterial Proteins/metabolism/genetics ; Gene Expression Regulation, Bacterial ; *Bacteria/genetics/metabolism ; *Adaptation, Physiological ; *DNA-Binding Proteins/metabolism/genetics ; Stress, Physiological ; Bacterial Physiological Phenomena ; },
abstract = {Nucleoid-associated proteins (NAPs) are essential regulators of bacterial chromosomal organization and gene expression, enabling microbes to adapt to environmental fluctuations. Bacteria are under increasing pressure from oxidative stress, temperature changes, osmotic fluctuations, and nutritional constraints, all of which are consequences of climate change. Major NAPs including H-NS, Fis, HU, IHF, Lrp, and Dps contribute significantly to microbial resilience by regulating genes that respond to stress and reshape chromosomal architecture. The ability to withstand extreme environments depends on these proteins, which mediate gene silencing, transcriptional activation, and DNA protection. In addition to their essential function in stress adaption, NAPs have tremendous promise for biotechnological developments. Their ability to regulate gene expression in reaction to stimuli in the environment can be used to create microbial strains that are more resistant to stress, which would be useful in fields such as bioremediation, farming, and industrial fermentation. Their impact on dormancy regulation and horizontal gene transfer opens doors for better microbial engineering techniques and the fight against antibiotic resistance. Enhancing heterologous gene expression, optimizing metabolic pathways, and designing biosensors responsive to changing environmental conditions are all possible through fine-tuning NAP activity in synthetic biology. Extremophilic NAP variations, their relationships with global regulators, and their possible utility in developing microbial systems that can withstand climate change are the topics of new research. An in-depth molecular-level understanding of these proteins may provide novel approaches to maintaining microbial-driven activities in dynamic ecosystems. Researchers can help with worldwide sustainability initiatives by creating more resilient microbial systems that can adapt to changing conditions by combining biotechnology with environmental microbiology and NAP-driven regulatory mechanisms.},
}

*Bacterial Proteins/metabolism/genetics
Gene Expression Regulation, Bacterial
*Bacteria/genetics/metabolism
*Adaptation, Physiological
*DNA-Binding Proteins/metabolism/genetics
Stress, Physiological
Bacterial Physiological Phenomena

@article {pmid40717244,
year = {2025},
author = {Mishra, S and Lercher, MJ},
title = {Horizontal Gene Transfer Inference: Gene Presence-Absence Outperforms Gene Trees.},
journal = {Molecular biology and evolution},
volume = {42},
number = {7},
pages = {},
pmid = {40717244},
issn = {1537-1719},
support = {//Deutsche Forschungsgemeinschaft/ ; },
mesh = {*Gene Transfer, Horizontal ; Phylogeny ; Models, Genetic ; Evolution, Molecular ; },
abstract = {Horizontal gene transfer is a fundamental driver of prokaryotic evolution, facilitating the acquisition of novel traits and adaptation to new environments. Despite its importance, methods for inferring horizontal gene transfer are rarely systematically compared, leaving a gap in our understanding of their relative strengths and limitations. Validating horizontal gene transfer inference methods is challenging due to the absence of a genomic fossil record that could confirm historical transfer events. Without an empirical gold standard, new inference methods are typically validated using simulated data; however, these simulations may not accurately capture biological complexity and often embed the same assumptions used in the inference methods themselves. Here, we leverage the tendency of horizontal gene transfer events to involve multiple neighboring genes to assess the accuracy of diverse horizontal gene transfer inference methods. We show that methods analyzing gene family presence/absence patterns across species trees consistently outperform approaches based on gene tree-species tree reconciliation. Our findings challenge the prevailing assumption that explicit phylogenetic reconciliation methods are superior to simpler implicit methods. By providing a comprehensive benchmark, we offer practical recommendations for selecting appropriate methods and indicate avenues for future methodological advancements.},
}

*Gene Transfer, Horizontal
Phylogeny
Models, Genetic
Evolution, Molecular

@article {pmid40715782,
year = {2025},
author = {Tonkin-Hill, G and Ruis, C and Bentley, SD and Lythgoe, KA and Bryant, JM},
title = {Within-host bacterial evolution and the emergence of pathogenicity.},
journal = {Nature microbiology},
volume = {10},
number = {8},
pages = {1829-1840},
pmid = {40715782},
issn = {2058-5276},
support = {2025515//Department of Health | National Health and Medical Research Council (NHMRC)/ ; 220540/Z/20/A//Wellcome Trust (Wellcome)/ ; },
mesh = {Humans ; *Bacteria/genetics/pathogenicity ; Gene Transfer, Horizontal ; *Bacterial Infections/microbiology/transmission ; *Evolution, Molecular ; Virulence/genetics ; *Host-Pathogen Interactions/genetics ; Genetic Variation ; Mutation ; Genome, Bacterial ; *Biological Evolution ; },
abstract = {The use of whole-genome sequencing to monitor bacterial pathogens has provided crucial insights into their within-host evolution, revealing mutagenic and selective processes driving the emergence of antibiotic resistance, immune evasion phenotypes and adaptations that enable sustained human-to-human transmission. Deep genomic and metagenomic sequencing of intra-host pathogen populations is also enhancing our ability to track bacterial transmission, a key component of infection control. This Review discusses the major processes driving bacterial evolution within humans, including both pathogenic and commensal species. Initially, mutational processes, including how mutational signatures reveal pathogen biology, and the selective pressures driving evolution are considered. The dynamics of horizontal gene transfer and intra-host pathogen competition are also examined, followed by a focus on the emergence of bacterial pathogenesis. Finally, the Review focuses on the importance of within-host genetic diversity in tracking bacterial transmission and its implications for infectious disease control and public health.},
}

Humans
*Bacteria/genetics/pathogenicity
Gene Transfer, Horizontal
*Bacterial Infections/microbiology/transmission
*Evolution, Molecular
Virulence/genetics
*Host-Pathogen Interactions/genetics
Genetic Variation
Mutation
Genome, Bacterial
*Biological Evolution

@article {pmid40714442,
year = {2025},
author = {Hong, YL and Xi, WM and Wang, YT and Yuan, Y and Shen, ZZ and Tian, M and Clarke, JL and Xie, WY and Zhao, FJ},
title = {Soil co-occurring bacterial communities serve as assembly hubs of antibiotic resistance determinants under organic fertilization.},
journal = {Journal of environmental management},
volume = {392},
number = {},
pages = {126708},
doi = {10.1016/j.jenvman.2025.126708},
pmid = {40714442},
issn = {1095-8630},
abstract = {Environmental transmission of antibiotic resistance poses a significant threat to human health by undermining the efficacy of therapeutic interventions against bacterial infections. Agricultural practices, particularly the application of organic fertilizers derived from animal manure, are major contributors to the spread of antibiotic resistance determinants (ARDs) in soil ecosystems. However, the fates of ARDs and their bacterial hosts in soil following organic fertilization as well as the impact of water management regimes remain poorly understood. We investigated the attenuation and persistence of ARDs in soil following organic fertilization under water management practices of upland, continuous flooding, and intermittent flooding. Most ARDs introduced via the organic fertilizer exhibited significant attenuation, with half-lives ranging from 19 to 50 days, primarily due to the decline of fertilizer-derived bacterial hosts. Specific ARDs, such as aph(3')-IIIa and tetO, persisted across all treatments. Upland conditions accelerated the attenuation of ARDs and their pathogenic hosts compared to flooding conditions, which prolonged their survival and promoted horizontal gene transfer. The divergent responses of ARD composition and soil bacterial communities to the environmental variables revealed a unique dissemination pattern, wherein the soil co-occurring bacterial communities served as critical hubs for the dissemination of ARDs and their bacterial hosts from organic fertilizers. The soil co-occurring bacterial communities exhibited strong interspecies interactions and high sensitivity to environmental changes. Targeted strategies to disrupt these assembly hubs may provide an effective way to mitigate the spread of antibiotic resistance from organic fertilizers to soil ecosystems.},
}

@article {pmid40714172,
year = {2025},
author = {Fan, Y and Du, M and Zhang, W and Deng, W and Yang, E and Wang, S and Yan, L and Zhang, L and Kang, S and Steenwyk, JL and An, Z and Liu, X and Xiang, M},
title = {The genomes of nematode-trapping fungi provide insights into the origin and diversification of fungal carnivorism.},
journal = {Molecular phylogenetics and evolution},
volume = {212},
number = {},
pages = {108423},
doi = {10.1016/j.ympev.2025.108423},
pmid = {40714172},
issn = {1095-9513},
abstract = {Nematode-trapping fungi (NTF), most of which belong to a monophyletic lineage in Ascomycota, cannibalize nematodes and other microscopic animals, raising questions regarding the types and mechanisms of genomic changes that enabled carnivorism and adaptation to the carbon-rich and nitrogen-poor environment created by the Permian-Triassic extinction event. To address these questions, we conducted comparative genomic analyses of 21 NTF and 21 non-NTF. Carnivorism-associated changes include expanded genes for nematode capture, infection, and consumption (e.g., adhesive proteins, CAP superfamily, eukaryotic aspartyl proteases, and serine-type peptidases). Although the link between secondary metabolite (SM) production and carnivorism remains unclear, we found that the number of SM gene clusters in NTF was significantly lower than that in non-NTF. Significantly expanded cellulose degradation gene families (GH5, GH7, AA9, and CBM1) and contracted genes for carbon-nitrogen hydrolases (enzymes that degrade organic nitrogen to ammonia) are likely associated with adaptation to carbon-rich and nitrogen-poor environments. Through horizontal gene transfer events from bacteria, NTF acquired the Mur gene cluster (participating in synthesizing peptidoglycan of the bacterial cell wall) and Hyl (a virulence factor in animals). Disruption of MurE reduced NTF's ability to attract nematodes, supporting its role in carnivorism. This study provides new insights into how NTF evolved and diversified, presumably after the Permian-Triassic mass extinction event.},
}

@article {pmid40712959,
year = {2025},
author = {Zhang, W and Guan, A and Qi, W and Mu, X and Hu, C and Qu, J},
title = {Cumulative effects of sulfamethoxazole and its metabolite on nitrogen reduction and antibiotic resistance in constructed wetlands: Microbial mechanisms and ecological risks.},
journal = {Environmental research},
volume = {285},
number = {Pt 2},
pages = {122426},
doi = {10.1016/j.envres.2025.122426},
pmid = {40712959},
issn = {1096-0953},
abstract = {Antibiotic residues in the tailwater of wastewater treatment plants (WWTPs) threaten nitrogen removal in constructed wetlands (CWs), yet the long-term impacts of fluctuating sulfamethoxazole (SMX) and its metabolite N-acetylsulfamethoxazole (N-SMX) remain unclear. Here, the dual effects of dynamic recovery in microbial nitrogen-removal functions and irreversible accumulation of antibiotic resistance genes (ARGs) under gradient SMX + N-SMX exposure (10-1000 μg L[-1] with 30-day stepwise increments) in lab-scale CWs were systematically revealed. At ≤ 100 μg L[-1], denitrification and anammox rates could recover to baseline levels, whereas 1 mg L[-1] exposure triggered a short-term surge and then cumulative inhibition of nitrogen reduction (e.g., denitrification rates was 34.7 % lower than the controls even after the SMX + N-SMX concentration reduction). Notably, sulfonamide resistance genes (sul1/sul2) increased steadily over 180 days despite the decline in SMX + N-SMX exposure (from 1 mg L[-1] to 10 μg L[-1] from day 120 to day 180), probably driven by horizontal gene transfer. Microbial analysis identified Burkholderia and Anaerolineales as dual-functional taxa linking nitrogen metabolism with ARGs propagation. Furthermore, sustained exposure suppressed the expression of denitrification genes (narG/nirK) of Methylotenera, despite its role in degrading SMX/N-SMX. These findings highlight a critical threshold: exposures <100 μg L[-1] allow the functional recovery of nitrogen reduction, but ≥1 mg L[-1] induces irreversible ARGs enrichment and disrupts microbial nitrogen cycling. This study provides mechanistic insights into the ecological risks of antibiotic fluctuations, advocating stricter control of high-concentration SMX/N-SMX in WWTP tailwater to mitigate the dissemination of resistance genes.},
}

@article {pmid40712912,
year = {2025},
author = {Zhang, X and Ding, W and Yang, J and Gao, L and Wang, Q and Wang, J and Luo, Y and Yuan, X and Sun, B and Yang, J and Zhou, Y and Sun, L},
title = {Mechanisms of outer membrane vesicles in bacterial drug resistance: Insights and implications.},
journal = {Biochimie},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.biochi.2025.07.024},
pmid = {40712912},
issn = {1638-6183},
abstract = {The emergence of antibiotic resistance has rendered the treatment of bacterial infections exceedingly challenging, with diseases caused by resistant strains often resulting in significant morbidity and mortality. Consequently, it is crucial to investigate the mechanisms underlying antibiotic resistance. Outer membrane vesicles (OMVs) are nanoscale spheres characterized by a double membrane structure, released by Gram-negative bacteria (GNB). While the mechanisms governing OMV biogenesis remain under investigation, three models have been proposed. These vesicles have been implicated in enhancing bacterial survival during antibiotic treatment and contributing to the onset and development of drug resistance through various pathways. OMVs function as a secretion system, delivering cargo that mediates intercellular communication to neighboring cells, and their closed structure facilitates this molecular delivery. Vesicles released into the extracellular compartment can protect bacteria from antibiotic treatment by promoting horizontal gene transfer, inactivating or binding antibiotics, influencing biofilm formation, and mediating bacterial gene mutations, among other mechanisms. Many studies have demonstrated that OMVs play a critical role during antibiotic exposure. An in-depth understanding of the mechanisms of OMVs in the development of bacterial drug resistance could help develop more effective therapeutic strategies to prevent persistent bacterial infections. This review focuses on summarising the latest evidence on the involvement of OMVs in the development of drug resistance, to provide ideas for future studies.},
}

@article {pmid40712751,
year = {2025},
author = {Zhang, J and Wang, H and Ni, Y and Yan, Z and Chi, D and Li, K and Zhang, R},
title = {Comparative Epidemiology and Resistance Mechanisms of Carbapenem-, Tigecycline-, and Polymyxin-Resistant Enterobacteriaceae in Pediatric Diarrhea, 2017 and 2023.},
journal = {International journal of antimicrobial agents},
volume = {},
number = {},
pages = {107580},
doi = {10.1016/j.ijantimicag.2025.107580},
pmid = {40712751},
issn = {1872-7913},
abstract = {The increasing prevalence of antimicrobial resistance (AMR) infections in children is becoming a growing global concern. AMR poses a significant challenge in pediatric diarrhea, where multidrug-resistant Enterobacteriaceae threaten treatment efficacy. This study investigates the prevalence, resistance mechanisms, and genetic characteristics of carbapenem-, tigecycline-, and polymyxin-resistant Enterobacteriaceae isolated from pediatric diarrhea cases , in 2017 (n=1059) and 2023 (n=367). The prevalence of mcr-1-positive strains declined significantly from 2.36% (25/1059) in 2017 to 0.82% (3/367) in 2023, while tet(X4)-positive strains rose from 0% to 1.91% (7/367). Carbapenemase-producers remained rare (0.28% in 2017; 1.63% in 2023), with blaNDM as the dominant carbapenemase gene. Whole genome sequencing revealed diverse antimicrobial resistance genes (ARGs) and evolving plasmid types. Notably, by 2023 all mcr-1 were carried on IncI2 plasmids. Conjugation experiments confirmed plasmids carrying mcr-1, blaNDM-5, and tet(X4) are transferable to a recipient strain, highlighting the potential for horizontal gene transfer. Our findings demonstrate a significant shift in pediatric diarrhea-associated Enterobacteriaceae resistance profiles from 2017 to 2023. The decline in mcr-1 mirrors the impact of reduced polymyxin use, whereas the rise of tet(X4) signals a new challenge. These findings underscore the dynamic nature of AMR in pediatric Enterobacteriaceae and emphasize the need for stringent antimicrobial stewardship and surveillance. A One Health approach, integrating clinical, agricultural, and environmental efforts, is crucial to mitigating AMR spread and protecting pediatric health globally.},
}

@article {pmid40712095,
year = {2025},
author = {Sarre, LA and Gastellou Peralta, GA and Romero Charria, P and Ovchinnikov, V and de Mendoza, A},
title = {Repressive Cytosine Methylation is a Marker of Viral Gene Transfer Across Divergent Eukaryotes.},
journal = {Molecular biology and evolution},
volume = {42},
number = {8},
pages = {},
pmid = {40712095},
issn = {1537-1719},
support = {//Horizon 2020 Framework Programme/ ; 950230/ERC_/European Research Council/International ; //QMUL PhD fellowship/ ; //CONACyT-IPN MRes fellowship/ ; },
abstract = {Cytosine DNA methylation patterns vary widely across eukaryotes, with its ancestral roles being understood to have included both transposable element (TE) silencing and host gene regulation. To further explore these claims, in this study, we reevaluate the evolutionary origins of DNA methyltransferases and characterize the roles of cytosine methylation on underexplored lineages, including the amoebozoan Acanthamoeba castellanii, the glaucophyte Cyanophora paradoxa, and the heterolobosean Naegleria gruberi. Our analysis of DNA methyltransferase evolution reveals a rich ancestral eukaryotic repertoire, with several eukaryotic lineages likely subsequently acquiring enzymes through lateral gene transfer (LGT). In the three species examined, DNA methylation is enriched on young TEs and silenced genes, suggesting an ancestral repressive function, without the transcription-linked gene body methylation of plants and animals. Consistent with this link with silencing, methylated genomic regions co-localize with heterochromatin marks, including H3K9me3 and H3K27me3. Notably, the closest homologs of many of the silenced, methylated genes in diverse eukaryotes belong to viruses, including giant viruses. Given the widespread occurrence of this pattern across diverse eukaryotic groups, we propose that cytosine methylation was a silencing mechanism originally acquired from bacterial donors, which was used to mitigate the expression of both transposable and viral elements, and that this function may persist in creating a permissive atmosphere for LGT in diverse eukaryotic lineages. These findings further highlight the importance of epigenetic information to annotate eukaryotic genomes, as it helps delimit potentially adaptive LGTs from silenced parasitic elements.},
}

@article {pmid40711446,
year = {2025},
author = {Ngoepe, MP and Schoeman, S and Roux, S},
title = {Challenges Associated With the Use of Metal and Metal Oxide Nanoparticles as Antimicrobial Agents: A Review of Resistance Mechanisms and Environmental Implications.},
journal = {Biotechnology journal},
volume = {20},
number = {7},
pages = {e70066},
pmid = {40711446},
issn = {1860-7314},
support = {//Department of Science and Innovation/ ; C2136/2021//Nelson Mandela University/ ; },
mesh = {*Metal Nanoparticles/chemistry/toxicity ; *Bacteria/drug effects ; *Drug Resistance, Bacterial/drug effects ; *Oxides/pharmacology/chemistry ; *Anti-Infective Agents/pharmacology ; Humans ; *Anti-Bacterial Agents/pharmacology ; *Metals/pharmacology ; },
abstract = {The use of metal and metal oxide nanoparticles has been suggested as a means of combating antibiotic-resistant bacteria (ARB). This is due to the ability of nanoparticles to target numerous sites inside the bacterial cell. Microbes can, however, develop a resistance to hazardous environments. Soil microorganisms have evolved resistance to specific metals in soil by employing alternative survival strategies, like those adopted against antibiotics. Because of this survival mechanism, bacteria have been able to develop defense mechanisms to deal with metallic nanoparticles. Resistance has evolved in human pathogens to therapies that use metallic nanoparticles, such as silver nanoparticles. Metallic nanoparticles and antibiotics have currently been proven to be ineffective against several infections. Due to these concerns, scientists are investigating whether nanoparticles might cause environmental harm and potentially breed microbes that are resistant to both inorganic and organic nanoparticles. The increased use of inorganic nanoparticles has thus been shown to result in contaminations in wastewater, facilitating horizontal gene transfer among bacterial populations. The resistance mechanism of metallic nanoparticles, role in antibiotic resistance, and a potential solution to the environment's toxicity from nanoparticles are all discussed in this review.},
}

*Metal Nanoparticles/chemistry/toxicity
*Bacteria/drug effects
*Drug Resistance, Bacterial/drug effects
*Oxides/pharmacology/chemistry
*Anti-Infective Agents/pharmacology
Humans
*Anti-Bacterial Agents/pharmacology
*Metals/pharmacology

@article {pmid40708915,
year = {2025},
author = {Li, M and Zhan, A and Rahman, TT and Jiang, T and Hou, L},
title = {From wastewater to resistance: characterization of multidrug-resistant bacteria and assessment of natural antimicrobial compounds.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1612534},
pmid = {40708915},
issn = {1664-302X},
abstract = {The development and spread of antibiotic resistance in wastewater pose significant threats to both the environment and public health. Bacteria harboring multiple antibiotic resistance genes (ARGs), including those associated with horizontal gene transfer (HGT), can serve as persistent reservoirs and vectors for antimicrobial resistance in natural ecosystems. In this study, nine antibiotic-resistant bacterial strains (U1-U9) were isolated from a wastewater treatment plant (WWTP) effluent. The isolates were identified using 16S rRNA gene sequencing and whole-genome sequencing (WGS), and their antibiotic susceptibility profiles were evaluated. All isolates exhibited resistance to multiple antibiotics, and WGS revealed that U1, U2, U4, and U7 harbored diverse ARGs, including β-lactamase genes, efflux pumps, and resistance determinants for sulfonamides, tetracyclines, and, quinolones, confirming the presence of multidrug-resistant bacteria in WWTP effluent. Phylogenetic analysis classified them into Microbacterium spp. (Actinobacteria), Chryseobacterium spp. (Bacteroidetes), Lactococcus lactis spp. (Firmicutes), and Psychrobacter spp. (Proteobacteria). To explore mitigation strategies, eleven natural compounds were screened for their effects on cell growth, biofilm formation, and motility in selected multi-drug-resistant bacteria. Among the tested compounds, curcumin and emodin showed the most consistent inhibitory activity, particularly against Microbacterium spp. strains U1 and U2, and Lactococcus lactis sp. U4. In contrast, Chryseobacterium sp. U7, a Gram-negative strain, exhibited strong resistance to all tested natural compounds, highlighting the challenge of controlling Gram-negative ARBs in wastewater settings. These findings underscore the environmental risks posed by multidrug-resistant and HGT-associated ARG-harboring bacteria in WWTP effluent. They also demonstrate the potential of natural products, such as curcumin and emodin, as alternative or complementary agents for mitigating antibiotic resistance in water systems.},
}

@article {pmid40707455,
year = {2025},
author = {Sato, Y and Bex, R and van den Berg, GCM and Santhanam, P and Höfte, M and Seidl, MF and Thomma, BPHJ},
title = {Starship giant transposons dominate plastic genomic regions in a fungal plant pathogen and drive virulence evolution.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {6806},
pmid = {40707455},
issn = {2041-1723},
mesh = {*DNA Transposable Elements/genetics ; *Genome, Fungal/genetics ; Phylogeny ; Virulence/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Ascomycota/genetics/pathogenicity ; *Plant Diseases/microbiology ; Verticillium ; },
abstract = {Starships form a recently discovered superfamily of giant transposons in Pezizomycotina fungi, implicated in mediating horizontal transfer of diverse cargo genes between fungal genomes. Their elusive nature has long obscured their significance, and their impact on genome evolution remains poorly understood. Here, we reveal a surprising abundance and diversity of Starships in the phytopathogenic fungus Verticillium dahliae. Remarkably, Starships dominate the plastic genomic compartments involved in host colonization, carry multiple virulence-associated genes, and exhibit genetic and epigenetic characteristics associated with adaptive genome evolution. Phylogenetic analyses suggest extensive horizontal transfer of Starships between Verticillium species and, strikingly, from distantly related Fusarium fungi. Finally, homology searches and phylogenetic analyses suggest that a Starship contributed to de novo virulence gene formation. Our findings illuminate the profound influence of Starship dynamics on fungal genome evolution and the development of virulence.},
}

*DNA Transposable Elements/genetics
*Genome, Fungal/genetics
Phylogeny
Virulence/genetics
*Evolution, Molecular
Gene Transfer, Horizontal
*Ascomycota/genetics/pathogenicity
*Plant Diseases/microbiology
Verticillium

@article {pmid40706788,
year = {2025},
author = {Ayaz, M and Oon, YS and Oon, YL and Khan, K and Deng, M and Li, L and Song, K and Jiang, X and Xia, Z},
title = {Microplastics transport and impact on nitrogen cycling and N2O emissions in estuaries.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {383},
number = {},
pages = {126869},
doi = {10.1016/j.envpol.2025.126869},
pmid = {40706788},
issn = {1873-6424},
abstract = {Microplastic pollution in estuarine ecosystems disrupts nitrogen cycling and enhances nitrous oxide (N2O) emissions, reinforcing the role of estuaries as greenhouse gas (GHG) hotspots. This review integrates mechanisms that modulate microplastic-induced disruptions to nitrogen cycling processes and transform estuarine biogeochemistry. It elucidates key mechanistic pathways whereby microplastic dynamics influence microbial nitrogen transformations and alter GHG fluxes. Microplastics affect nitrogen cycling through multiple mechanisms, including adsorption of nitrogenous compounds, restructuring of microbial communities, and modulation of enzymatic processes that control nitrogen transformations. Within plastisphere biofilms, microplastics foster microbial interactions that promote incomplete denitrification and nitrifier-driven N2O production, intensifying N2O fluxes from estuarine sediments and waters. The review synthesizes recent findings on microplastic degradation, genetic drift, and horizontal gene transfer, which may further reshape nitrogen cycling capacity over time. Recent advancements in microplastic characterization, including aptamer-based sensors, flow cytometry, and improved extraction methods, enhance the ability to quantify and trace microplastic impacts in estuarine environments. This review proposes an integrative conceptual model for microplastic-mediated amplification of N2O emissions in estuaries and identifies critical research and policy directions. Addressing microplastic-induced disruptions of nitrogen cycling and GHG dynamics will require integrated mitigation strategies, targeted regulatory interventions, and interdisciplinary research to support sustainable estuarine management.},
}

@article {pmid40706155,
year = {2025},
author = {Wang, YC and He, LY and Wu, HY and Qiao, LK and Huang, Z and Bai, H and Gao, FZ and Shi, YJ and Zhao, JL and Liu, YS and Ying, GG},
title = {High-risk plasmid-borne resistance genes from swine farm environments infiltrate deep soil and interact with the human gut microbiome via horizontal transfer.},
journal = {Journal of hazardous materials},
volume = {496},
number = {},
pages = {139281},
doi = {10.1016/j.jhazmat.2025.139281},
pmid = {40706155},
issn = {1873-3336},
abstract = {Swine farms serve as critical reservoirs of antibiotic resistance genes (ARGs), yet the frequency of horizontal gene transfer (HGT) remains poorly understood. In this study, we explored the gene exchange within the "swine farm-human-pig" network and assessed its risks. We identified 16,612 plasmid contigs from 107 field samples, revealing a significant presence of previously uncharacterized plasmid types. Notably, 52.88 % of acquired ARGs were located on plasmids, with 71.22 % containing at least one mobile genetic element (MGE). We quantified HGTs at the microbial community level among the human gut, pig gut, and swine farm environments. Among 4687 metagenome-assembled genomes (MAGs), 3008 were involved in 11,250 HGTs. HGT linkages were most frequently identified between microbial genomes from the swine farm and the human gut microbiome. ARGs were involved in 91 HGT events, with 645 events linked to MGEs and 16 related to virulence factors, suggesting potential cross-species transmission of clinical pathogens. The detection of 32 Rank I ARGs and the identification of increased resistome risks underscore the extensive dispersion of livestock-related contaminants into more distant environmental compartments. This study elucidates the complexities of gene exchange networks in swine farm environments, underscoring the urgent need for strategies to mitigate risks associated with the antibiotic resistome.},
}

@article {pmid40704322,
year = {2025},
author = {Nazir, A and Nazir, A and Zuhair, V and Aman, S and Sadiq, SUR and Hasan, AH and Tariq, M and Rehman, LU and Mustapha, MJ and Bulimbe, DB},
title = {The Global Challenge of Antimicrobial Resistance: Mechanisms, Case Studies, and Mitigation Approaches.},
journal = {Health science reports},
volume = {8},
number = {7},
pages = {e71077},
pmid = {40704322},
issn = {2398-8835},
abstract = {BACKGROUND AND AIMS: Antimicrobial resistance (AMR) is projected to cause 10 million deaths annually by 2050 if left unaddressed, posing a severe threat to global health and modern medicine. This review analyzes the molecular and ecological mechanisms underlying antibiotic resistance and evaluates global efforts aimed at containment to identify actionable strategies to mitigate AMR's escalating impact.

METHODS: A systematic literature review was performed using databases including PubMed, ScienceDirect, Scopus, Google Scholar, and Web of Science, focusing on peer-reviewed studies from 2000 to 2024. Search terms included "antibiotic resistance," "resistance mechanisms," "horizontal gene transfer," and "AMR epidemiology." A total of 152 articles were selected based on predefined inclusion criteria relevant to resistance mechanisms, epidemiological data, clinical outcomes, and public health interventions.

RESULTS: Findings underscore three dominant resistance pathways: target site modification, enzymatic degradation (e.g., β-lactamases), and horizontal gene transfer via plasmids and transposons. Notably, resistance to last-resort antibiotics (e.g., colistin, carbapenems) is rising in pathogens such as Klebsiella pneumoniae and Acinetobacter baumannii, with treatment failure rates exceeding 50% in some regions. Surveillance gaps and unregulated antibiotic use, especially in LMICs, further accelerate resistance spread. Only a limited number of new antibiotic classes have been approved since 2010, underscoring the innovation gap.

CONCLUSION: AMR is a quantifiable, escalating crisis that undermines decades of progress in infectious disease control. Tackling it requires coordinated action: strengthening antimicrobial stewardship, incentivizing antibiotic R&D, integrating environmental and clinical surveillance under One Health frameworks, and implementing global policy reforms. Without prompt action, AMR could surpass cancer in annual mortality by mid-century.},
}

@article {pmid40701356,
year = {2025},
author = {Hu, L and Ye, Y and Li, Y and Tan, X and Liu, X and Zhang, T and Wang, J and Du, Z and Ye, M},
title = {Bacteria-algae synergy in carbon sequestration: Molecular mechanisms, ecological dynamics, and biotechnological innovations.},
journal = {Biotechnology advances},
volume = {83},
number = {},
pages = {108655},
doi = {10.1016/j.biotechadv.2025.108655},
pmid = {40701356},
issn = {1873-1899},
mesh = {*Biotechnology/methods ; *Microalgae/metabolism ; *Carbon Sequestration ; *Bacteria/metabolism ; Carbon Dioxide/metabolism ; Photosynthesis ; Carbon/metabolism ; },
abstract = {Rising atmospheric CO2 levels require innovative strategies to increase carbon sequestration. Bacteria-algae interactions, as pivotal yet underexplored drivers of marine and freshwater carbon sinks, involve multiple mechanisms that amplify CO2 fixation and long-term storage. This review systematically describes the synergistic effects of bacteria-algae consortia spanning both microalgae (e.g., Chlorella vulgaris and Phaeodactylum tricornutum) and macroalgae (e.g., Macrocystis and Laminaria) on carbon sequestration. These effects include (1) molecular-level regulation (e.g., signal transduction via N-acyl-homoserine lactones (AHLs), and horizontal gene transfer), (2) ecological facilitation of recalcitrant dissolved organic carbon (RDOC) formation, and (3) biotechnological applications in wastewater treatment and bioenergy production. We highlight that microbial crosstalk increases algal photosynthesis by 20-40 % and contributes to 18.9 % of kelp-derived RDOC storage. Furthermore, engineered systems integrating algal-bacterial symbiosis achieve greater than 80 % nutrient removal and a 22-35 % increase in CO2 fixation efficiency (compared with axenic algal systems), demonstrating their dual role in climate mitigation and a circular economy. This review is the first to integrate molecular mechanisms (e.g., quorum sensing), ecological carbon transformation processes (e.g., the formation of RDOC), and applications in synthetic biology (e.g., CRISPR-engineered consortia) into a unified framework. Moreover, the novel strategy "microbial interaction network optimization" for enhancing carbon sinks is proposed. However, scalability challenges persist, including light limitations in photobioreactors and the ecological risks of synthetic consortia. By bridging microbial ecology with synthetic biology, this work provides a roadmap for harnessing bacteria-algae synergy to achieve carbon neutrality.},
}

*Biotechnology/methods
*Microalgae/metabolism
*Carbon Sequestration
*Bacteria/metabolism
Carbon Dioxide/metabolism
Photosynthesis
Carbon/metabolism

@article {pmid40700401,
year = {2025},
author = {Grooters, SV and Mollenkopf, DF and Wittum, TE},
title = {The genetic context of blaIMP varies among bacterial families from One Health sources.},
journal = {PloS one},
volume = {20},
number = {7},
pages = {e0327200},
pmid = {40700401},
issn = {1932-6203},
mesh = {DNA Transposable Elements/genetics ; *beta-Lactamases/genetics ; Plasmids/genetics ; Integrons/genetics ; *Bacteria/genetics/isolation & purification/drug effects ; Humans ; Gene Transfer, Horizontal ; Anti-Bacterial Agents/pharmacology ; Shewanella/genetics ; },
abstract = {The blaIMP resistance gene encodes a metallo-beta-lactamase in bacteria, which confers reduced susceptibility or resistance to all the beta-lactams, including carbapenems which are critical for treating life-threatening infections. The dissemination of blaIMP among various taxonomic families shows the diversity and range of horizontal gene transfer. Using short-read whole genome sequencing and bioinformatic tools, we determined the genetic motifs surrounding blaIMP present in 32 bacterial isolates recovered from environmental sources and agriculture facilities. blaIMP can be located extra-chromosomally on plasmids or within incomplete and complete Tn7 chromosomal structures. We identified a complete Tn7 transposon harboring the blaIMP-27 gene cassette within a class 2 integron located in chromosomal contigs of Shewanella spp. and Providencia spp. Acinetobacter spp. isolates were observed with truncated and incomplete Tn7 transposons, while conserving the class 2 integron and resistance gene cassettes. Additionally, IncQ1 plasmids carried by Proteus spp., Escherichia coli, and other Enterobacteriaceae spp. harbored class 2 integrons with blaIMP-64 and sat2 resistance gene cassettes. In an Acidovorax sp. isolate, blaIMP-27 and sat2 gene cassettes were found associated with an insertion sequence, ISL3 transposase, in an RP4 plasmid. The conserved structure of Tn7 in Shewanella spp. and Providencia spp. is consistent with these species being potential reservoirs from which other bacterial species have acquired partial Tn7 motifs, and the blaIMP-27 gene cassette. These data contribute to a broader understanding of the dissemination and temporality of blaIMP alleles and their mobile genetic elements.},
}

DNA Transposable Elements/genetics
*beta-Lactamases/genetics
Plasmids/genetics
Integrons/genetics
*Bacteria/genetics/isolation & purification/drug effects
Humans
Gene Transfer, Horizontal
Anti-Bacterial Agents/pharmacology
Shewanella/genetics

@article {pmid40699345,
year = {2025},
author = {Schöllkopf, AI and Ehrenreich, A and Liebl, W},
title = {SMC-like Wadjet system prevents plasmid transfer into Clostridium cellulovorans.},
journal = {Applied microbiology and biotechnology},
volume = {109},
number = {1},
pages = {170},
pmid = {40699345},
issn = {1432-0614},
support = {161B0930//German Federal Ministry of Education and Research/ ; 161B0930//German Federal Ministry of Education and Research/ ; 161B0930//German Federal Ministry of Education and Research/ ; },
mesh = {*Plasmids/genetics ; *Conjugation, Genetic ; *Gene Transfer, Horizontal ; *Clostridium cellulovorans/genetics ; *Chromosomes, Bacterial/genetics ; },
abstract = {This study demonstrates the impact of a Structure Maintenance of Chromosome (SMC)-like Wadjet system on the horizontal gene transfer of plasmids by conjugation to a recipient that naturally containing such a system for the first time. A Clostridium cellulovorans mutant with dramatically improved efficiency to receive plasmid DNA by conjugation was isolated and sequenced. Three spontaneous chromosomal deletions included a type II restriction-modification system, a putative CRISPR system, and a cluster of ORFs named jetABCD encoding a putative Wadjet system. Since nearly nothing is known about the role of naturally occurring Wadjet systems in their native host bacteria, markerless chromosomal deletion of jetABCD in the C. cellulovorans wildtype strain 743B was achieved and the effect on conjugative plasmid uptake was studied. The transconjugation frequency of the jetABCD mutant was increased by about five orders of magnitude compared to wildtype C. cellulovorans recipient cells. Bioinformatic analysis of genome sequences of the Bacillota phylum revealed near-complete mutually exclusive possession of either plasmids < 40 kb or jetABCD genes, indicating high efficiency of Wadjet systems in small plasmid prevention in bacteria. Importantly, the implications of this study go beyond the case of C. cellulovorans. Our study demonstrates that the eradication of Wadjet systems can dramatically improve the uptake of recombinant plasmids and thereby enhance genetic engineering of bacterial strains of interest for biotechnological applications. KEY POINTS: • Native Wadjet system inhibits plasmid transfer by conjugation in C. cellulovorans • Deleting jetABCD increased plasmid uptake by about five orders of magnitude • Possession of Wadjet systems efficiently block plasmid maintenance in Bacillota.},
}

*Plasmids/genetics
*Conjugation, Genetic
*Gene Transfer, Horizontal
*Clostridium cellulovorans/genetics
*Chromosomes, Bacterial/genetics

@article {pmid40698896,
year = {2025},
author = {Van Agtmaal, JL and Verheul, M and Vonken, L and Helsen, K and Vargas Guerrero, MG and Van Hoogstraten, SWG and Hurck, BJ and Pilla, G and Trinh, I and De Bruijn, GJ and Calum, HP and De Boer, MGJ and Pijls, BG and Arts, JJC},
title = {Antimicrobial resistance in orthopedics: microbial insights, clinical impact, and the necessity of a multidisciplinary approach-a review.},
journal = {Acta orthopaedica},
volume = {96},
number = {},
pages = {555-568},
doi = {10.2340/17453674.2025.43477},
pmid = {40698896},
issn = {1745-3682},
mesh = {Humans ; *Prosthesis-Related Infections/microbiology/drug therapy/prevention & control ; *Drug Resistance, Bacterial ; *Anti-Bacterial Agents/therapeutic use ; Antimicrobial Stewardship ; *Orthopedic Procedures ; Orthopedics ; },
abstract = {Antimicrobial resistance (AMR) is rising globally and is a threat and challenge for orthopedic surgery, particularly in managing prosthetic joint infections (PJIs). This review first explores several AMR mechanisms from a microbiological point of view, including selective pressure, horizontal gene transfer, and further dissemination. Second, the variation in the rise of AMR across countries is highlighted, including its impact on PJI. While countries with the highest AMR rates are expected to experience the most significant burden, no country will be immune to the increasing prevalence of PJI. Third, this review stresses that multidimensional strategies are needed to combat AMR's challenges in orthopedic surgery. These include raising awareness across all sectors, including healthcare professionals, the public, healthcare policymakers, and even politicians; advancing diagnostic technologies for early infection detection and classification of resistant or susceptible strains; promoting antibiotic stewardship; and developing new material technologies to prevent or cure PJI. This review highlights the urgent need for a coordinated response from clinicians, researchers, and policymakers to avoid AMR-related complications in PJI cases.},
}

Humans
*Prosthesis-Related Infections/microbiology/drug therapy/prevention & control
*Drug Resistance, Bacterial
*Anti-Bacterial Agents/therapeutic use
Antimicrobial Stewardship
*Orthopedic Procedures
Orthopedics

@article {pmid40698825,
year = {2025},
author = {Fässler, N and de Arriba, M and Biggel, M and Jelocnik, M and Borel, N and Marti, H},
title = {Development of shuttle vector-based transformation systems for veterinary and zoonotic chlamydiae.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0164125},
doi = {10.1128/spectrum.01641-25},
pmid = {40698825},
issn = {2165-0497},
abstract = {In veterinary medicine, the obligate intracellular bacteria Chlamydia (C.) abortus, Chlamydia caviae, and Chlamydia pecorum are known to cause ovine enzootic abortion, conjunctivitis in guinea pigs, and ocular/urogenital disease in koalas, respectively. Studying the biology of these bacteria has been challenging due to a dearth of genetic tools. This study aimed to establish stable transformation systems for C. abortus, C. pecorum, and C. caviae by introducing shuttle vectors carrying green fluorescent proteins. With the aim to select the most suitable green fluorescent protein for the tracking of chlamydiae in vitro, we further compared the fluorescence intensity of GFP to that of mNeonGreen. Transformed shuttle vectors comprised the native plasmid of the chlamydial species of interest, an Escherichia coli origin of replication (ori), a beta-lactamase (bla) or spectinomycin (aadA) resistance gene, and GFP or mNeonGreen for heterologous fluorescence expression. We compared the success of a C. suis-tailored transformation protocol (Protocol A) to that of an alternative protocol for C. psittaci and C. trachomatis (Protocol B), both of which employ calcium chloride for competence induction. Stable transformants were obtained for C. pecorum and C. caviae using protocols A and B, respectively, and we found that the fluorescence intensity of heterologously expressed GFP is higher than that of mNeonGreen. In contrast, pre-incubation with trypsin-EDTA prior to the application of calcium chloride was needed to obtain transformants of C. abortus. In summary, we established protocols for stable calcium chloride-mediated transformation for C. pecorum and C. abortus and expanded upon the genetic toolbox of C. caviae.IMPORTANCEChlamydiae are a diverse group of bacteria impacting human and animal health. Many of the veterinary species, such as Chlamydia abortus, Chlamydia caviae, and Chlamydia pecorum, which cause reproductive disorders and/or conjunctivitis, are zoonotic pathogens leading to a potentially life-threatening disease in humans. Our understanding of these species has been hampered due to a lack of genetic tools. In this study, we developed calcium chloride-mediated transformation protocols for each of these species: chlamydiae are mixed with shuttle vectors containing the complete species-specific plasmid sequence, an Escherichia coli origin of replication, and an antibiotic resistance gene for selection. We could further show that certain chlamydial species become more susceptible to genetic modification if they are pre-treated with trypsin-EDTA prior to the addition of calcium chloride and the vector of interest. Overall, we demonstrate that species-specific protocol refinement is indispensable to render chlamydiae competent for genetic transformation.},
}

@article {pmid40698728,
year = {2025},
author = {Qi, W and Tang, X and Huang, Y and Ma, S and Wang, J and Gao, B and Pang, J and Du, J and Wang, P and Zhan, S and Ni, BJ and Xu, S},
title = {Electron Transfer Expressway from Peroxydisulfate to O2 Mediated by Diatomic Sites Accelerating [1]O2 Production for Disinfection.},
journal = {Environmental science & technology},
volume = {59},
number = {30},
pages = {15670-15679},
doi = {10.1021/acs.est.5c01975},
pmid = {40698728},
issn = {1520-5851},
mesh = {*Disinfection ; Oxygen ; Electron Transport ; Sulfates/chemistry ; Singlet Oxygen ; Nickel ; },
abstract = {Current studies on high-density single-atom catalysts (SACs) with the coexistence of single atomic and diatomic sites have ignored the underlying contribution of diatomic sites for persulfate-based disinfection technology. Herein, high-density atomic Ni anchored on N-doped carbon (Ni1-NC) containing abundant Ni diatomic (Ni2-N6) sites, was fabricated, exhibiting superior peroxydisulfate (PDS) activation to generate singlet oxygen ([1]O2) for disinfection compared with other M1-NC, due to the fact that Ni1-NC possessed the highest negative crystal orbital Hamilton population value. A dynamic promotion effect toward disinfection, relying on the level of external O2 was discovered. This promotion effect was achieved through the cooperation of PDS and O2 which was mediated by Ni2-N6 sites bridging electron transfer from PDS to O2, thereby suppressing the energy barriers of rate-determining steps. Disinfection with decreased horizontal gene transfer was achieved by disrupting coenzyme Q, inhibiting adenosine triphosphate synthesis, and degrading extracellular polymeric substances via [1]O2. A continuous flow system based on a Ni1-NC@sponge fixed reaction bed displayed persistent disinfection for 336 h under aeration. This work presents a transboundary integrated PDS disinfection strategy combining physical aeration and chemical oxidation through tailoring diatomic sites in SACs.},
}

*Disinfection
Oxygen
Electron Transport
Sulfates/chemistry
Singlet Oxygen
Nickel

@article {pmid40696136,
year = {2025},
author = {Tobin, LA and Lam, MMC and Hamidian, M},
title = {Pan-genus analysis and typing of antimicrobial resistance plasmids in Acinetobacter.},
journal = {npj antimicrobials and resistance},
volume = {3},
number = {1},
pages = {65},
pmid = {40696136},
issn = {2731-8745},
support = {APP2009163//National Health and Medical Research Council Investigator Grant/ ; },
abstract = {Plasmids play a central role in horizontal gene transfer and bacterial adaptation, especially in the context of antimicrobial resistance (AMR) among opportunistic pathogens. Some members of the genus Acinetobacter are known for their role in hospital-acquired infections, harboring plasmids that facilitate rapid adaptation to selective pressures. However, the extent of plasmid diversity and evolutionary dynamics within Acinetobacter has not been fully elucidated. In this study, we analysed 1846 complete and non-redundant Acinetobacter plasmid sequences, identifying 166 novel Replicase (Rep) protein types and providing a significant update to the Acinetobacter Plasmid Typing (APT) scheme, which now comprises 257 Rep types. A detailed phylogenetic analysis of the prevailing R3-type Rep sequences reveals two distinct evolutionary clades (A and B) and several additional subclades. This phylogenetic structure suggests evolutionary pressures within all clades, potentially influenced by host species distribution and environmental factors. Analysis of these plasmids highlights diverse plasmid types involved in dissemination of AMR within the genus in different niches, underscoring both clinical and natural environments as reservoirs of Acinetobacter plasmids. Our findings provide a refined framework for tracking Acinetobacter plasmids, advancing our understanding of plasmid-mediated AMR spread and informing strategies to combat the spread of AMR in this critical genus.},
}

@article {pmid40694848,
year = {2025},
author = {Garcillán-Barcia, MP and de la Cruz, F and Rocha, EPC},
title = {The extended mobility of plasmids.},
journal = {Nucleic acids research},
volume = {53},
number = {14},
pages = {},
pmid = {40694848},
issn = {1362-4962},
support = {PIA/ANR-16-CONV-0005//Institut Pasteur/ ; ANR-10-LABX-62-IBEID//Laboratoire d'Excellence IBEID Integrative Biology of Emerging Infectious Diseases/ ; MCIN/AEI/10.13039/501100011033 PID2020-117923GB-I00//Spanish Ministry of Science and Innovation/ ; },
mesh = {*Plasmids/genetics ; *Gene Transfer, Horizontal ; *Bacteria/genetics ; Humans ; Conjugation, Genetic ; Interspersed Repetitive Sequences ; Bacteriophages/genetics ; },
abstract = {Plasmids play key roles in the spreading of many traits, ranging from antibiotic resistance to varied secondary metabolism, from virulence to mutualistic interactions, and from defense to antidefense. Our understanding of plasmid mobility has progressed extensively in the last few decades. Conjugative plasmids are still often the textbook image of plasmids, yet they are now known to represent a minority. Many plasmids are mobilized by other mobile genetic elements, some are mobilized as phages, and others use atypical mechanisms of transfer. This review focuses on recent advances in our understanding of plasmid mobility, from the molecular mechanisms allowing transfer and evolutionary changes of plasmids to the ecological determinants of their spread. In this emerging, extended view of plasmid mobility, interactions between mobile genetic elements, whether involving exploitation, competition, or elimination, affect plasmid transfer and stability. Likewise, interactions between multiple cells and their plasmids shape the latter patterns of transfer through transfer-mediated bacterial predation, interference, or eavesdropping in cell communication, and by deploying defense and antidefense activity. All these processes are relevant for microbiome intervention strategies, from plasmid containment in clinical settings to harnessing plasmids in ecological or industrial interventions.},
}

*Plasmids/genetics
*Gene Transfer, Horizontal
*Bacteria/genetics
Humans
Conjugation, Genetic
Interspersed Repetitive Sequences
Bacteriophages/genetics