@article {pmid40568145,
year = {2025},
author = {Brezner, S and Garushyants, SK and Wolf, YI and Koonin, EV and Snir, S},
title = {Evolution of gene order in prokaryotes is driven primarily by gene gain and loss.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.04.03.647019},
pmid = {40568145},
issn = {2692-8205},
abstract = {UNLABELLED: Evolution of bacterial and archaeal genomes is highly dynamic including extensive gene gain via horizontal gene transfer and gene loss as well as different types of genome rearrangements, such as inversions and translocations, so that gene order is not highly conserved even among closely related organisms. We sought to quantify the contributions of different genome dynamics processes to the evolution of the gene order relying on the recently developed "jump" model of gene translocation. The jump model has been completely solved analytically and provides the exact distribution of syntenic gene block lengths (SBL) in compared genomes based on gene translocations alone. Comparing the SBL distribution predicted by the jump model with the distributions empirically observed for multiple groups of closely related bacterial and archaeal genomes, we obtained robust estimates of the genome rearrangement to gene flux (gain and loss) ratio. In most groups of bacteria and archaea, this ratio was found to be on the order of 0.1 indicating that the loss of synteny in the evolution of bacteria and archaea is driven primarily by gene gain and loss rather than by gene translocation.

SIGNIFICANCE: Evolution of bacterial and archaeal genomes is a highly dynamic process that includes extensive gene gain via horizontal gene transfer and gene loss as well as different types of genome rearrangements, so that gene order is not highly conserved even among closely related organisms. We developed a theoretical framework to quantify the contributions of different genome dynamics processes to the evolution of the gene order and found that in most groups of bacteria and archaea, the genome rearrangement to gene flux (combined gain and loss) is on the order of 0.1. Thus, the loss of genomic synteny in the evolution of bacteria and archaea appears to be driven primarily by gene gain and loss rather than by gene translocation.},
}

@article {pmid40565594,
year = {2025},
author = {Saccone, S and Brancato, D and Bruno, F and Coniglio, E and Sturiale, V and Federico, C},
title = {Origin and Evolution of Genes in Eukaryotes: Mechanisms, Dynamics, and Functional Implications.},
journal = {Genes},
volume = {16},
number = {6},
pages = {},
doi = {10.3390/genes16060702},
pmid = {40565594},
issn = {2073-4425},
mesh = {Humans ; *Evolution, Molecular ; Animals ; *Eukaryota/genetics ; Gene Duplication ; Gene Transfer, Horizontal ; Selection, Genetic ; },
abstract = {The origin and evolution of genes are central themes in evolutionary biology and genomics, shedding light on how molecular innovations shape biological complexity and adaptation. This review explores the principal mechanisms underlying gene emergence in eukaryotes, including gene duplication, de novo gene birth, horizontal gene transfer, viral gene domestication, and exon shuffling. We examine the population dynamics that govern the fixation of new genes, their functional integration, and the selective forces acting upon them-from purifying selection to adaptive innovation. Examples such as NOTCH2NL and SRGAP2C, which originated through recent segmental duplications followed by neofunctionalization, illustrate how duplicate-derived de novo genes can play a key role in human brain development. In addition, we highlight the emerging relevance of nuclear architecture in determining the evolutionary fate of new genes, offering a spatial dimension to gene innovation. We also discuss methodological approaches for detecting new genes and inferring selection, and finally, we highlight the emerging role of the human pangenome in revealing hidden gene diversity and its implications for evolutionary and biomedical research. Understanding gene innovation not only enhances our grasp of evolutionary processes but also informs clinical studies on disease susceptibility and human uniqueness.},
}

Humans
*Evolution, Molecular
Animals
*Eukaryota/genetics
Gene Duplication
Gene Transfer, Horizontal
Selection, Genetic

@article {pmid40565227,
year = {2025},
author = {Fu, W and Wang, Y and Ge, Y and Gao, H and Sun, X and Deng, Z and Wang, L and Chen, S and He, X and Wu, G},
title = {Molecular Insight into the Recognition of DNA by the DndCDE Complex in DNA Phosphorothioation.},
journal = {International journal of molecular sciences},
volume = {26},
number = {12},
pages = {},
doi = {10.3390/ijms26125765},
pmid = {40565227},
issn = {1422-0067},
support = {32170030//National Natural Science Foundation of China/ ; 2020YFA0907300//National Key R&D Program of China/ ; 2022YFA0912200//National Key R&D Program of China/ ; },
mesh = {Escherichia coli/metabolism/genetics ; *Escherichia coli Proteins/metabolism/chemistry/genetics ; Protein Binding ; *DNA, Bacterial/metabolism/chemistry ; *DNA/metabolism/chemistry ; Streptomyces lividans/metabolism/genetics ; *Bacterial Proteins/metabolism/chemistry ; Models, Molecular ; },
abstract = {In a vast variety of prokaryotes such as Escherichia coli and Streptomyces lividans, the DNA degradation (Dnd) CDE protein complex (consisting of DndC, DndD, and DndE), together with the DndA/IscS protein and the DndFGH complex, function as a defense barrier to prevent the invasion of non-self-DNA. The DndCDE complex introduces phosphorothioation (PT) modifications into DNA, and the DndFGH complex specifically cleaves non-PT DNA and, thus, restricts horizontal gene transfer and phage invasion. Despite the central importance of the DndCDE complex in DNA PT modification, which catalyzes the oxygen-sulfur swap on DNA, our understanding of this key complex remains poor. Here, we employed protein structure prediction to provide a reasonably reliable prediction of the structure of the DndCDE complex and a 23 bp DNA-DndCDE complex. We found that among the three proteins in the DndCDE complex, DndC, especially its "specificity loop", plays a key role in recognizing the consensus PT modification sequence. In addition, the DndD protein is found to possess a highly conserved structural surface on its globular domain, presumably mediating the dimerization of DndD as well as the DndCDE complex. Furthermore, our normal mode analysis showed that there exists a dynamic transition between a closed and an open state for the DndCDE complex, facilitating its association and release of DNA. Our conclusions were corroborated by biochemical assays using purified proteins. On the whole, we provide molecular insights into the assembly and DNA-recognition mechanism of a central protein complex involved in DNA phosphorothioation.},
}

Escherichia coli/metabolism/genetics
*Escherichia coli Proteins/metabolism/chemistry/genetics
Protein Binding
*DNA, Bacterial/metabolism/chemistry
*DNA/metabolism/chemistry
Streptomyces lividans/metabolism/genetics
*Bacterial Proteins/metabolism/chemistry
Models, Molecular

@article {pmid40560800,
year = {2025},
author = {Ruf, A and Blumenkamp, P and Ludwig, C and Lippegaus, A and Brachmann, A and Klingl, A and Goesmann, A and Brinkrolf, K and Papenfort, K and Robatzek, S},
title = {Extracellular Vesicles From Xylella fastidiosa Carry sRNAs and Genomic Islands, Suggesting Roles in Recipient Cells.},
journal = {Journal of extracellular vesicles},
volume = {14},
number = {6},
pages = {e70102},
pmid = {40560800},
issn = {2001-3078},
support = {EXC 2051 - Project-ID 390713860//Deutsche Forschungsgemeinschaft/ ; INST 95/1435-1 FUGG//Deutsche Forschungsgemeinschaft/ ; RO 3550/16-1//Deutsche Forschungsgemeinschaft/ ; RO 3550/17-1//Deutsche Forschungsgemeinschaft/ ; RO 3550/18-1//Deutsche Forschungsgemeinschaft/ ; SPP2389 - Project-ID 503931087//Deutsche Forschungsgemeinschaft/ ; ERC Adv Grant 884235//H2020 European Research Council/ ; },
mesh = {*Extracellular Vesicles/metabolism/genetics ; *Genomic Islands/genetics ; *Xylella/genetics/pathogenicity/metabolism ; *RNA, Small Untranslated/genetics/metabolism ; Plant Diseases/microbiology ; Gene Transfer, Horizontal ; RNA, Bacterial/genetics/metabolism ; Bacterial Proteins/metabolism/genetics ; Virulence ; RNA-Binding Proteins/metabolism ; },
abstract = {Xylella fastidiosa (Xf) is a Gram-negative bacterial plant pathogen responsible for severe diseases in a variety of economically important crops. A critical aspect of its virulence is the production of extracellular vesicles (EVs). In this study, we discovered that DNA-binding proteins and nonribosomal RNA-binding proteins are abundant in the corona of Xf-EVs. DNA-seq revealed enrichment of three genomic islands (GIs) in EVs, which carry molecular signatures indicative of horizontal gene transfer (HGT). The most abundant GI encodes five homologous small RNAs designated sXFs. RNA sequencing revealed a distinct pattern of noncoding RNAs enriched in EVs, including four island-encoded sXFs. One of the sXF's stem-loops contains motifs for binding the RNA chaperone Hfq, which is also abundant in EVs. Predicted target analysis suggests that sXFs play a role in regulation of natural competence in bacteria. Additionally, sXF plant target prediction identifies a coiled-coil nucleotide-binding domain leucine-rich repeat receptor (CNL) immune gene that is downregulated following Xf infection and Xf-EV treatment. We propose a model where Xf releases nucleic acid carrying EVs with two functions: one to deliver RNA-related cargo that regulates gene expression in both bacterial and plant cells, and another to deliver DNA-related cargo for the genetic transfer of genomic islands. We highlight island-encoded sXFs as potential virulence factors and vesiduction as a mechanism of HGT of sXFs in Xf. Taken together, our data on Xf-EV cargoes provide a molecular framework for understanding the virulence of Xf.},
}

*Extracellular Vesicles/metabolism/genetics
*Genomic Islands/genetics
*Xylella/genetics/pathogenicity/metabolism
*RNA, Small Untranslated/genetics/metabolism
Plant Diseases/microbiology
Gene Transfer, Horizontal
RNA, Bacterial/genetics/metabolism
Bacterial Proteins/metabolism/genetics
Virulence
RNA-Binding Proteins/metabolism

@article {pmid40559614,
year = {2025},
author = {Martz, K and Alomar, D and Karim, M and Knezevic, S and D'Costa, VM},
title = {Characterization of the Diversity in Host Range of an Extensively Drug-Resistant (XDR) Type IV Secretion System-Encoding Plasmid in Acinetobacter.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {6},
pages = {},
pmid = {40559614},
issn = {2076-0817},
support = {PJ4-175369/CAPMC/CIHR/Canada ; PJT-178191/CAPMC/CIHR/Canada ; },
mesh = {*Plasmids/genetics ; *Acinetobacter baumannii/genetics/drug effects/pathogenicity ; *Drug Resistance, Multiple, Bacterial/genetics ; Humans ; *Type IV Secretion Systems/genetics ; Acinetobacter Infections/microbiology ; *Host Specificity ; Anti-Bacterial Agents/pharmacology ; },
abstract = {The World Health Organization (WHO) cites antimicrobial resistance as among the greatest threats to human health. The multidrug-resistant pathogen Acinetobacter baumannii, recognized as a priority pathogen for healthcare and research, is responsible for a diverse array of infections including respiratory tract, soft tissue and wound, and bloodstream infections. Despite this importance, the mechanisms of its pathogenesis remain poorly understood. Conjugation represents a central mechanism for bacterial adaptation and evolution and is responsible for the spread of genes that promote pathogen survival, antibiotic resistance, virulence, and biofilm formation. Our laboratory recently characterized a large group of almost 120 Type IV Secretion System (T4SS)-encoding plasmids in Acinetobacter, distributed globally across 20 countries spanning four continents, and demonstrated that an XDR A. baumannii plasmid from this family was transmissible to another A. baumannii strain. This research investigated the potential diversity of host strains for this representative member plasmid. Using the GC1 lineage strain A. baumannii AB5075-UW harbouring the XDR plasmid p1AB5075 and a series of previously characterized clinical and environmental Acinetobacter strains, conjugative analyses demonstrated transfer of the XDR plasmid to both A. baumannii strains of more genetically divergent sequence types and to non-baumannii Acinetobacter species both inside and outside the Acinetobacter calcoaceticus-baumannii (ACB) complex. Successful recipients included diverse strains of both clinical and environmental origin within the Acinetobacter genus. Collectively, this research could provide insights into an important genetic element for future surveillance.},
}

*Plasmids/genetics
*Acinetobacter baumannii/genetics/drug effects/pathogenicity
*Drug Resistance, Multiple, Bacterial/genetics
Humans
*Type IV Secretion Systems/genetics
Acinetobacter Infections/microbiology
*Host Specificity
Anti-Bacterial Agents/pharmacology

@article {pmid40559557,
year = {2025},
author = {Enciso-Martínez, Y and Barrios-Villa, E and Ballesteros-Monrreal, MG and Navarro-Ocaña, A and Valencia, D and González-Aguilar, GA and Martínez-Téllez, MA and Palomares-Navarro, JJ and Ayala-Zavala, F},
title = {Virulence and Antibiotic Resistance of aEPEC/STEC Escherichia coli Pathotypes with Serotype Links to Shigella boydii 16 Isolated from Irrigation Water.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/pathogens14060549},
pmid = {40559557},
issn = {2076-0817},
mesh = {Humans ; Virulence ; Serogroup ; *Shigella boydii/genetics/isolation & purification/drug effects/pathogenicity/classification ; Phylogeny ; Anti-Bacterial Agents/pharmacology ; *Water Microbiology ; *Drug Resistance, Bacterial ; HeLa Cells ; *Shiga-Toxigenic Escherichia coli/genetics/drug effects/isolation & purification/pathogenicity/classification ; Agricultural Irrigation ; Virulence Factors/genetics ; Microbial Sensitivity Tests ; },
abstract = {Irrigation water can serve as a reservoir and transmission route for pathogenic Escherichia coli, posing a threat to food safety and public health. This study builds upon a previous survey conducted in Hermosillo, Sonora (Mexico), where 445 samples were collected from a local Honeydew melon farm and associated packing facilities. Among the 32 E. coli strains recovered, two strains, A34 and A51, were isolated from irrigation water and selected for further molecular characterization by PCR, due to their high pathogenic potential. Both strains were identified as hybrid aEPEC/STEC pathotypes carrying bfpA and stx1 virulence genes. Adhesion assays in HeLa cells revealed aggregative and diffuse patterns, suggesting enhanced colonization capacity. Phylogenetic analysis classified A34 within group B2 as associated with extraintestinal pathogenicity and antimicrobial resistance, while A51 was unassigned to any known phylogroup. Serotyping revealed somatic antigens shared with Shigella boydii 16, suggesting possible horizontal gene transfer or antigenic convergence. Antibiotic susceptibility testing showed resistance to multiple β-lactam antibiotics, including cephalosporins, linked to the presence of blaCTX-M-151 and blaCTX-M-9. Although no plasmid-mediated quinolone resistance genes were detected, resistance may involve efflux pumps or mutations in gyrA and parC. These findings are consistent with previous reports of E. coli adaptability in agricultural environments, suggesting potential genetic adaptability. While our data support the presence of virulence and resistance markers, further studies would be required to demonstrate mechanisms such as horizontal gene transfer or adaptive evolution.},
}

Humans
Virulence
Serogroup
*Shigella boydii/genetics/isolation & purification/drug effects/pathogenicity/classification
Phylogeny
Anti-Bacterial Agents/pharmacology
*Water Microbiology
*Drug Resistance, Bacterial
HeLa Cells
*Shiga-Toxigenic Escherichia coli/genetics/drug effects/isolation & purification/pathogenicity/classification
Agricultural Irrigation
Virulence Factors/genetics
Microbial Sensitivity Tests

@article {pmid40558211,
year = {2025},
author = {Enshaie, E and Nigam, S and Patel, S and Rai, V},
title = {Livestock Antibiotics Use and Antimicrobial Resistance.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/antibiotics14060621},
pmid = {40558211},
issn = {2079-6382},
abstract = {Background/Objectives: Antibiotic resistance or antimicrobial resistance (AMR) in livestock is a growing global concern that threatens both human and animal health. The overuse and misuse of antibiotics in livestock production have led to an increased propensity for the development of AMR bacterial strains in animals, which can be spread to humans through the consumption of contaminated animal products, direct contact, or environmental exposure. This review aims to summarize the development and transmission of AMR in livestock, explore its underlying mechanisms and impact on human and animal health, and discuss current practices and potential strategies for mitigation and prevention. Methods: For this narrative review, we searched articles on PubMed and Google Scholar using the terms antibiotic resistance, livestock, and environment, alone or in combination. Results: The history of antibiotic use in livestock and its link to increased AMR, along with the involved mechanisms, including the enzymatic breakdown of antibiotics, alterations in bacterial targets, horizontal gene transfer, and efflux pumps, are important. Antibiotics in livestock are used for growth promotion, disease prevention and control, and metaphylactic use. The role of livestock and the environment as reservoirs for resistant pathogens, their impact on human health, chronic infections, allergic reactions, toxicity, and the development of untreatable diseases is important to understand AMR. Conclusions: Given the widespread use of antibiotics and the potential consequences of AMR, collaborative global efforts, increased public awareness, coordinated regulations, and advancements in biological technology are required to mitigate the threat AMR poses to human and animal health. Regulatory solutions and the development of new therapeutic alternatives like antimicrobial peptides and bacteriophage therapy, and preventive measures such as DNA and mRNA vaccines, are future perspectives.},
}

@article {pmid40558188,
year = {2025},
author = {Mohammed, EAH and Kovács, B and Kuunya, R and Mustafa, EOA and Abbo, ASH and Pál, K},
title = {Antibiotic Resistance in Aquaculture: Challenges, Trends Analysis, and Alternative Approaches.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/antibiotics14060598},
pmid = {40558188},
issn = {2079-6382},
support = {TKP2021-NKTA-32//National Research, Development, and Innovation Fund of Hungary/ ; },
abstract = {Antibiotic resistance in aquaculture has emerged as a global crisis, representing a serious threat to the health of aquatic animals, environment, and human. The extensive use of antibiotics in aquaculture has led to rapid development of resistant bacterial strains, resulting in environmental contamination and the dissemination of resistant genes. Understanding of the research trends, key contributors, and thematic evolution of this field is essential for guiding future studies and policy interventions. The study aimed to conduct a bibliometric analysis of research on antibiotic resistance development in aquaculture, identifying key areas of research, leading contributors, emerging challenges, and alternative solutions. Data were extracted from the Web of Science (WoS) database covering the period from 2000 to 2025. A systematic search strategy was employed, utilizing terms including "antibiotic resistance" AND "bacteria," AND "aquaculture". Relevant publications were extracted from the WoS using these keywords. R-tool was then used to analyze the obtained metadata including keywords, citation patterns, and co-authored country. The analysis revealed a remarkable increase in publications over the past 25 years, with key contributions from China, India, and the USA. The most significant articles focused on the presence of multidrug resistant bacteria in the aquatic environments and, antibiotic-resistant genes, and horizontal gene transfer. Probiotics are the alternative solution to overcome the antibiotic resistance and enhance aquaculture sustainability. Future research should focus on the interdisciplinary collaboration, novel antimicrobial alternatives, and global monitoring approaches.},
}

@article {pmid40558133,
year = {2025},
author = {Ye, Z and Li, M and Jing, Y and Liu, K and Wu, Y and Peng, Z},
title = {What Are the Drivers Triggering Antimicrobial Resistance Emergence and Spread? Outlook from a One Health Perspective.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/antibiotics14060543},
pmid = {40558133},
issn = {2079-6382},
support = {2022YFF1103100//National Key Research and Development Program of China/ ; 32172314//National Natural Science Foundation of China/ ; 22193064//National Natural Science Foundation of China/ ; },
abstract = {Antimicrobial resistance (AMR) has emerged as a critical global public health threat, exacerbating healthcare burdens and imposing substantial economic costs. Currently, AMR contributes to nearly five million deaths annually worldwide, surpassing mortality rates of any single infectious disease. The economic burden associated with AMR-related disease management is estimated at approximately $730 billion per year. This review synthesizes current research on the mechanisms and multifaceted drivers of AMR development and dissemination through the lens of the One Health framework, which integrates human, animal, and environmental health perspectives. Intrinsic factors, including antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs), enable bacteria to evolve adaptive resistance mechanisms such as enzymatic inactivation, efflux pumps, and biofilm formation. Extrinsic drivers span environmental stressors (e.g., antimicrobials, heavy metals, disinfectants), socioeconomic practices, healthcare policies, and climate change, collectively accelerating AMR proliferation. Horizontal gene transfer and ecological pressures further facilitate the spread of antimicrobial-resistant bacteria across ecosystems. The cascading impacts of AMR threaten human health and agricultural productivity, elevate foodborne infection risks, and impose substantial economic burdens, particularly in low- and middle-income countries. To address this complex issue, the review advocates for interdisciplinary collaboration, robust policy implementation (e.g., antimicrobial stewardship), and innovative technologies (e.g., genomic surveillance, predictive modeling) under the One Health paradigm. Such integrated strategies are essential to mitigate AMR transmission, safeguard global health, and ensure sustainable development.},
}

@article {pmid40558095,
year = {2025},
author = {Milhomem Pilati Rodrigues, B and Janssen, L and da Silva, LA and Acacio, SSVG and Magalhães, MT and Ribeiro, BM},
title = {Experimental and evolutionary evidence for horizontal transfer of an envelope fusion protein gene between thogotoviruses and baculoviruses.},
journal = {Journal of virology},
volume = {},
number = {},
pages = {e0214824},
doi = {10.1128/jvi.02148-24},
pmid = {40558095},
issn = {1098-5514},
abstract = {Baculoviruses are insect-specific viruses with large, double-stranded DNA genomes classified into four genera. Alphabaculoviruses, which infect lepidoptera, are further divided into group I (G1-α) and group II (G2-α). The GP64 protein, essential for cell attachment and viral entry in G1-α baculoviruses, is thought to have originated through horizontal gene transfer (HGT) from thogotoviruses (family Orthomyxoviridae). This study investigates the functional substitution of GP64 by thogotovirus fusion proteins. Through RNA-seq data mining, we identified a novel thogotovirus, Melitaea didyma thogotovirus 1 (MediTHOV-1), in lepidopteran hosts. Phylodynamic analysis of G1-α baculovirus and thogotovirus glycoproteins suggests that the HGT event occurred during the Mesozoic era. To test functional substitution, we constructed recombinant Autographa californica multiple nucleopolyhedrovirus (AcMNPV) carrying either the envelope fusion protein (EFP) genes from MediTHOV-1 or Apis thogotovirus 1 (ATHOV-1), while deleted for its native gp64 gene. Our results show that, while the MediTHOV-1 glycoprotein failed to rescue AcMNPV infectivity, the ATHOV-1 fusion protein (EFP) partially restored infectivity, albeit with reduced efficiency. Cryo-electron microscopy revealed lower incorporation of ATHOV-1 EFP into viral envelopes compared to GP64. The recombinant AcMNPV carrying ATHOV-1 EFP (Ac-ATHOVGPgp64Δ) displayed delayed replication kinetics and lower viral titers. Interestingly, ATHOV-1 EFP significantly enhanced baculovirus entry and gene transduction in mosquito cells. These findings provide experimental support for the HGT hypothesis, demonstrating the functional incorporation of a thogotovirus glycoprotein into a baculovirus. This study sheds light on the evolutionary relationship between baculovirus GP64 and glycoproteins, offering insights into viral evolution and potential biotechnological applications in gene delivery and protein expression.IMPORTANCEBaculoviruses are widely utilized for the biological control of insect pests and as versatile biotechnological tools, with their effectiveness largely dependent on the activity of their envelope fusion proteins (EFPs). Thogotoviruses, in contrast, are emerging vector-borne pathogens of significant concern. In this study, we present the first successful functional substitution of the baculovirus GP64 protein with a thogotovirus EFP, alongside the identification of what appears to be a lepidopteran-associated thogotovirus, Melitaea didyma thogothovirus 1. Our work provides functional and phylogenetic insights into the evolutionary relationship between these distantly related viral groups, particularly the hypothesized horizontal gene transfer event that gave rise to baculoviral gp64 gene. These findings offer a deeper understanding of the determinants underlying the adaptation of baculoviral glycoproteins to novel hosts. Furthermore, the discovery of novel viral genes highlights promising opportunities for biotechnological advancements, including the development of enhanced baculovirus-based gene delivery systems and tools for protein expression.},
}

@article {pmid40556893,
year = {2025},
author = {Di Marcantonio, L and Chiatamone Ranieri, S and Toro, M and Marchegiano, A and Cito, F and Sulli, N and Del Matto, I and Di Lollo, V and Alessiani, A and Foschi, G and Platone, I and Paoletti, M and D'Alterio, N and Garofolo, G and Janowicz, A},
title = {Comprehensive regional study of ESBL Escherichia coli: genomic insights into antimicrobial resistance and inter-source dissemination of ESBL genes.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1595652},
pmid = {40556893},
issn = {1664-302X},
abstract = {INTRODUCTION: The global dissemination of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli (E. coli) poses a significant public health challenge, particularly in regions with high antimicrobial resistance (AMR) occurrence. This study investigated the occurrence, genomic characteristics, and dissemination dynamics of ESBL-producing E. coli in Abruzzo, Italy, by analyzing 956 isolates from humans, livestock, wildlife, and food products.

METHODS: Phenotypic and genomic analyses were performed on the isolates to assess ESBL-E. coli occurrence and characteristics. Multilocus sequence typing (MLST) was used to identify sequence types (STs), and plasmid profiling alongside synteny analysis was conducted to investigate horizontal gene transfer and resistance gene integration. Spatial analysis was also carried out to identify hotspots of ESBL-positive isolates.

RESULTS: An overall ESBL-E. coli occurrence of 14.1% (135/956 samples) was found, with significant variation across hosts: companion animals exhibited the highest occurrence (16.2%), followed by livestock and food matrices (14.6%), and wildlife (7.0%). Spatial analysis identified a hotspot in northeastern Abruzzo, where ESBL-positive isolates were 5.34 times more likely to occur (p < 0.001). MLST identified 58 sequence types (STs), with ST131 dominating human isolates (12/19). In cattle, predominant sequence types were ST16565 (5 isolates) and ST540 (4 isolates); in poultry, ST43 (5 isolates), ST10 (4 isolates), and ST6215 (3 isolates) were most common; ST206 (8 isolates) was predominant in swine; and in dogs, ST10 (4 isolates) and ST3580 (3 isolates) were most prevalent. Genomic analysis revealed host-specific distributions of ESBL genes: bla CTX-M-15 predominated in humans and dogs, while bla CTX-M-1 was most common in pigs. Plasmid profiling revealed IncF and IncI plasmids as key vectors for horizontal gene transfer. Synteny analysis showed identical flanking regions of bla CTX-M-1 and bla CTX-M-15 across phylogenetically distant strains, suggesting chromosomal integration and stable maintenance of resistance genes.

DISCUSSION: These findings underscore the interconnectedness of human, animal, and environmental reservoirs in AMR dissemination. The high genetic diversity observed within farms and the detection of shared clusters across hosts emphasize the need for integrated One Health interventions, including reduced antibiotic use in livestock and enhanced surveillance of high-risk environments. This study provides critical insights into local AMR dynamics, offering a model for regional mitigation strategies.},
}

@article {pmid40556891,
year = {2025},
author = {Chekole, WS and Potgieter, L and Adamu, H and Sternberg-Lewerin, S and Tessema, TS and Magnusson, U},
title = {Genomic insights into antimicrobial resistance and virulence of E. coli in central Ethiopia: a one health approach.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1597580},
pmid = {40556891},
issn = {1664-302X},
abstract = {Antimicrobial resistance is a global threat causing millions of deaths annually. The study aimed to identify antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and virulence genes (VGs) and track their dissemination among E. coli isolates. Seventy-seven isolates from calves, environments, and human sources were studied. The study involved WGS sequencing, bacterial strains characterized; pan genome, multi-locus sequence typing, and serotyping using O-, and H-typing. The ARGs, VGs, and MGEs were identified using ABRicate against selected respective databases. A maximum likelihood SNP (single nucleotide polymorphism) tree was constructed and visualized with an interactive tree of life (IToL). Descriptive statistics were used to analyze the data. Seventy-seven of the isolates were identified as E. coli, later grouped into 5 clades and four known phylogroups. ST10 and O16:H48 were most prevalent in 12 and 42 isolates, respectively. There were about 106 unique ARGs detected between 1.3% and 91.9%, with 57 detected in 40% of isolates. In terms of ARGs, the most common were bla-ampH (90.9%), bla-AmpC1 (89.6%), tet(A) (84.4%), mdf(A) (81.8%), aph(3")-Ib (79%), sul2 (79%), aph(6)-Id (75%), and bla-PBP (70%). It was found that 95 percent (96/106) of ARGs came from at least two sources. The majority of detected ARGs exhibited high concordance between phenotypic resistance and ARGs profiles (JSI ≥ 0.5). In eight isolates, mutations in the gyrA (3) and par-C/E (5) genes led to ciprofloxacin and nalidixic acid resistance. The most common co-occurrences of ARG and MGE were Tn3 with bla-TEM-105 (34), Int1 with sul1 (13), and dhfr7 (11). Meanwhile, the most frequently detected VGs (n ≥ 71 isolates) included elfA-G, fimB-I, hcpA-C, espL, ibeC, entA, fepA-C, ompA, ecpA-E, fepD, fes, and ibeB. Nearly, 88.3% (128/1450) VGs were shared in isolates from at least two sources. ETEC (53.2%), EAEC (22.1%), and STEC (14.3%) were the three most frequently predicted pathotypes. Despite significant ST diversity, ARGs and VGs showed an extensive distribution among the study groups. These findings suggest limited clonal transmission of isolates. In comparison, the wide distribution of ARGs and VGs may be attributed to horizontal gene transfer driven by similar antibiotic selection pressures in the study area.},
}

@article {pmid40556499,
year = {2025},
author = {Yang, Y and Jin, X and Zhao, Z},
title = {Distribution and Evolutionary Trajectories of β-Lactamases in Vibrio: Genomic Insights from CARB-Type Enzymes in the Harveyi and Cholerae Clades.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evaf128},
pmid = {40556499},
issn = {1759-6653},
abstract = {Antibiotic resistance mediated by β-lactamases (BLs), encoded by bla genes, is a significant global health threat, necessitating systematic studies of their diversity and evolution, particularly among pathogenic bacteria lineages. Leveraging over 6,000 quality-filtered Vibrio genomes alongside six newly sequenced marine symbiotic strains representing 128 nominal and 57 unclassified Vibrio species, our study extends taxonomic breadth and resolution for investigating BL diversity. We identified 4,431 BLs across 41 species, encompassing all four Ambler Classes (A∼D). Among these, CARBenicillin-hydrolyzing Class A BLs (CARBs encoded by blaCARB family) were the most prevalent (60.7%) and exhibited a clade-centric distribution particularly in Harveyi clade and V. cholerae, underscoring influence of specific ecological and evolutionary pressures. We refined CARB classification into two subfamilies: CARB-17-like (blaCARB-17-like) confined to Harveyi clade, and CARB-1-like (blaCARB-1-like) found exclusively outside Harveyi clade, based on phylogenetic placement, sequence similarity, and inheritance patterns, providing a clearer framework for delineating their functional and phylogenetic nuances. Notably, blaCARB-17-like genes in non-pathogenic Harveyi Subclade II showed significantly relaxed selection, accompanied by unusual mutations within key conserved motifs especially catalytic serine residues, suggesting evolutionary drift that may compromise canonical enzymatic activity. Furthermore, blaCARB-17-like genes, present as a single copy, emerged as a core gene in Harveyi clade, showing promise as a diagnostic marker for clinically significant Harveyi clade species, despite limited yet significant interspecies genetic exchanges mediated by recombination or mobile genetic elements. Our study advances the understanding of BL evolution and genomic distribution in Vibrio, with broad implications for diagnostic applications and resistance management strategies.},
}

@article {pmid40556036,
year = {2025},
author = {Li, Y and Liu, X and Yang, J and Li, R and Wang, M and Kuang, S},
title = {Characteristics of intracellular/extracellular antibiotic resistance genes and microbial community in sludge compost under sulfadiazine stress.},
journal = {Environmental technology},
volume = {},
number = {},
pages = {1-11},
doi = {10.1080/09593330.2025.2522480},
pmid = {40556036},
issn = {1479-487X},
abstract = {The accumulation of emerging antibiotics in sewage sludge, which serves as a repository for antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs), is raising growing concern. To accurately assess the environmental risks, it is essential to separately investigate intracellular and extracellular ARGs (iARGs and eARGs) due to their distinct roles in resistance persistence and horizontal gene transfer. However, the impact of sulfadiazine (SDZ) on iARGs and eARGs, and the mechanisms involved in the composting process remain under further investigation. In this study, composts with SDZ concentrations of 5 and 50 mg/kg were constructed, and ARGs, microbial community composition and functional pathways were analyzed. The results showed that the abundance of iARGs varied significantly under SDZ selective pressure, while eARGs showed no significant differences. Specifically, i-erm decreased in the 50SDZ group, likely due to competition for ecological niches. The abundance of ermA, ermB and ermF decreased by approximately 97%, 85%, and 84%, respectively. i-sul increased by 127% to 156% in SDZ-added groups but not dose-dependently. Bacillus, Paracoccus, Pseudomonas, and Caproiciproducens were predominant in the SDZ-added groups. The abundance of potential ARG hosts, such as Bacillus and Paracoccus, increased significantly, with Paracoccus showing 2.3-fold and 1.8-fold higher abundance in the 50SDZ and 5SDZ treatments, respectively, compared to the CK. Functional genes related to the ABC-2 type transport system, signal transduction, and genome maintenance decreased with SDZ application. These findings suggested that the dynamics of ARGs should be continuously monitored during sludge composting and land application of compost products to reduce their environmental risks.},
}

@article {pmid40555322,
year = {2025},
author = {Ying, S and Zhang, Z and Xiang, R},
title = {Metagenomic and Whole-Genome Characterization of Carbapenem-Resistant Acinetobacter baumannii Carrying blaOXA-23 Gene within the Tn2006 Transposon Among ICU Patients.},
journal = {Journal of global antimicrobial resistance},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jgar.2025.06.009},
pmid = {40555322},
issn = {2213-7173},
abstract = {PURPOSE: To characterize carbapenem-resistant Acinetobacter baumannii carrying blaOXA-23 genes within the Tn2006 transposon using metagenomic and whole-genome sequencing, focusing on their genetic features, antimicrobial resistance, and potential for clonal spread and horizontal gene transfer among ICU patients.

METHODS: Bronchoalveolar lavage fluid samples from 28 ICU patients were analyzed using mNGS to detect pathogens and resistance genes. A. baumannii isolates underwent whole-genome sequencing for genetic diversity assessment. Antimicrobial susceptibility testing and comparative genomic analysis were performed.

RESULTS: mNGS revealed mixed infections in 71.4% of patients, identifying multiple bacteria, viruses, fungi, and mycoplasma species. A. baumannii was detected in 25 samples, often alongside other pathogens. All isolates harbored blaOXA-23 within Tn2006 on the chromosome and belonged to sequence type ST2, indicating clonal dissemination despite significant genetic diversity (up to 2,969 SNP differences). The isolates were highly resistant to multiple antibiotics but remained susceptible to tigecycline and colistin. Comparative genomic analysis with 238 global CRAB genomes confirmed the prevalence of the Tn2006 transposon carrying blaOXA-23 in ST2 strains, emphasizing the potential for rapid spread of this resistance mechanism.

CONCLUSION: The widespread presence of multidrug-resistant A. baumannii carrying blaOXA-23 within Tn2006 among ICU patients poses a significant public health concern. The high rate of mixed infections and the potential for horizontal gene transfer complicate infection management in critically ill patients. Enhanced infection control measures, continuous surveillance, and targeted interventions are urgently needed to prevent further dissemination of these resistant strains in hospital settings.},
}

@article {pmid40459279,
year = {2025},
author = {Parras-Moltó, M and Lund, D and Ebmeyer, S and Larsson, DGJ and Johnning, A and Kristiansson, E},
title = {The transfer of antibiotic resistance genes between evolutionarily distant bacteria.},
journal = {mSphere},
volume = {10},
number = {6},
pages = {e0011425},
doi = {10.1128/msphere.00114-25},
pmid = {40459279},
issn = {2379-5042},
mesh = {*Gene Transfer, Horizontal ; *Bacteria/genetics/drug effects/classification ; Phylogeny ; *Drug Resistance, Bacterial/genetics ; Genome, Bacterial ; Anti-Bacterial Agents/pharmacology ; Evolution, Molecular ; *Genes, Bacterial ; Humans ; },
abstract = {UNLABELLED: Infections from antibiotic-resistant bacteria threaten human health globally. Resistance is often caused by mobile antibiotic resistance genes (ARGs) shared horizontally between bacterial genomes. Many ARGs originate from environmental and commensal bacteria and are transferred between divergent bacterial hosts before they reach pathogens. This process remains, however, poorly understood, which complicates the development of countermeasures that reduce the spread of ARGs. In this study, we aimed to systematically analyze the ARGs transferred between the most evolutionarily distant bacteria, defined here based on their phylum. We implemented an algorithm that identified inter-phylum transfers (IPTs) by combining ARG-specific phylogenetic trees with the taxonomy of the bacterial hosts. From the analysis of almost 1 million ARGs identified in >400,000 bacterial genomes, we identified 661 IPTs, which included transfers between all major bacterial phyla. The frequency of IPTs varies substantially between ARG classes and was highest for the aminoglycoside resistance gene AAC(3), while the levels for beta-lactamases were generally lower. ARGs involved in IPTs also differed between phyla, where, for example, tetracycline ARGs were commonly transferred between Firmicutes and Proteobacteria, but rarely between Actinobacteria and Proteobacteria. The results, furthermore, show that conjugative systems are seldom shared between bacterial phyla, suggesting that other mechanisms drive the dissemination of ARGs between divergent hosts. We also show that bacterial genomes involved in IPTs of ARGs are either over- or underrepresented in specific environments. These IPTs were also found to be more recent compared to transfers associated with bacteria isolated from water, soil, and sediment. While macrolide and tetracycline ARGs involved in IPTs almost always were >95% identical between phyla, corresponding β-lactamases showed a median identity of <60%. We conclude that inter-phylum transfer is recurrent, and our results offer new insights into how ARGs are disseminated between evolutionarily distant bacteria.

IMPORTANCE: Antibiotic-resistant infections pose a growing threat to global health. This study reveals how genes conferring antibiotic resistance can move between bacteria that belong to different phyla lineages previously thought to be too evolutionarily distant for frequent gene exchange. By analyzing nearly 1 million resistance genes from over 400,000 bacterial genomes, the researchers uncovered hundreds of inter-phylum transfer events, exposing surprising patterns in how different classes of resistance genes spread. The findings highlight that conjugative systems are less common than expected in cross-phyla transfers and suggest that alternative mechanisms may play key roles. This new understanding of how resistance genes leap between vastly different bacterial groups can inform strategies to slow the emergence of drug-resistant infections, aiding in the development of more effective public health interventions.},
}

*Gene Transfer, Horizontal
*Bacteria/genetics/drug effects/classification
Phylogeny
*Drug Resistance, Bacterial/genetics
Genome, Bacterial
Anti-Bacterial Agents/pharmacology
Evolution, Molecular
*Genes, Bacterial
Humans

@article {pmid40298963,
year = {2025},
author = {Karki, S and Barth, ZK and Aylward, FO},
title = {Ancient Host-Virus Gene Transfer Hints at a Diverse Pre-LECA Virosphere.},
journal = {Journal of molecular evolution},
volume = {93},
number = {3},
pages = {295-305},
pmid = {40298963},
issn = {1432-1432},
support = {2141862//National Science Foundation/ ; },
mesh = {Phylogeny ; *DNA Viruses/genetics ; Evolution, Molecular ; *Eukaryota/genetics/virology ; *Gene Transfer, Horizontal ; DNA-Directed DNA Polymerase/genetics ; DNA-Directed RNA Polymerases/genetics ; },
abstract = {The details surrounding the early evolution of eukaryotes and their viruses are largely unknown. Several key enzymes involved in DNA synthesis and transcription are shared between eukaryotes and large DNA viruses in the phylum Nucleocytoviricota, but the evolutionary relationships between these genes remain unclear. In particular, previous studies of eukaryotic DNA and RNA polymerases often show deep-branching clades of eukaryotes and viruses indicative of ancient gene exchange. Here, we performed updated phylogenetic analysis of eukaryotic and viral family B DNA polymerases, multimeric RNA polymerases, and mRNA-capping enzymes to explore their evolutionary relationships. Our results show that viral enzymes form clades that are typically adjacent to eukaryotes, suggesting that they originate prior to the emergence of the Last Eukaryotic Common Ancestor (LECA). The machinery for viral DNA replication, transcription, and mRNA capping are all key processes needed for the maintenance of virus factories, which are complex structures formed by many nucleocytoviruses during infection, indicating that viruses capable of making these structures are ancient. These findings hint at a diverse and complex pre-LECA virosphere and indicate that large DNA viruses may encode proteins that are relics of extinct proto-eukaryotic lineages.},
}

Phylogeny
*DNA Viruses/genetics
Evolution, Molecular
*Eukaryota/genetics/virology
*Gene Transfer, Horizontal
DNA-Directed DNA Polymerase/genetics
DNA-Directed RNA Polymerases/genetics

@article {pmid40197024,
year = {2025},
author = {Gillett, DL and Selinidis, M and Seamons, T and George, D and Igwe, AN and Del Valle, I and Egbert, RG and Hofmockel, KS and Johnson, AL and Matthews, KRW and Masiello, CA and Stadler, LB and Chappell, J and Silberg, JJ},
title = {A roadmap to understanding and anticipating microbial gene transfer in soil communities.},
journal = {Microbiology and molecular biology reviews : MMBR},
volume = {89},
number = {2},
pages = {e0022524},
doi = {10.1128/mmbr.00225-24},
pmid = {40197024},
issn = {1098-5557},
mesh = {*Soil Microbiology ; *Microbiota/genetics ; *Gene Transfer, Horizontal ; Soil/chemistry ; Bacteria/genetics ; Synthetic Biology ; Biotechnology ; },
abstract = {SUMMARYEngineered microbes are being programmed using synthetic DNA for applications in soil to overcome global challenges related to climate change, energy, food security, and pollution. However, we cannot yet predict gene transfer processes in soil to assess the frequency of unintentional transfer of engineered DNA to environmental microbes when applying synthetic biology technologies at scale. This challenge exists because of the complex and heterogeneous characteristics of soils, which contribute to the fitness and transport of cells and the exchange of genetic material within communities. Here, we describe knowledge gaps about gene transfer across soil microbiomes. We propose strategies to improve our understanding of gene transfer across soil communities, highlight the need to benchmark the performance of biocontainment measures in situ, and discuss responsibly engaging community stakeholders. We highlight opportunities to address knowledge gaps, such as creating a set of soil standards for studying gene transfer across diverse soil types and measuring gene transfer host range across microbiomes using emerging technologies. By comparing gene transfer rates, host range, and persistence of engineered microbes across different soils, we posit that community-scale, environment-specific models can be built that anticipate biotechnology risks. Such studies will enable the design of safer biotechnologies that allow us to realize the benefits of synthetic biology and mitigate risks associated with the release of such technologies.},
}

*Soil Microbiology
*Microbiota/genetics
*Gene Transfer, Horizontal
Soil/chemistry
Bacteria/genetics
Synthetic Biology
Biotechnology

@article {pmid40553200,
year = {2025},
author = {Xie, X and Ren, Z and Wang, R and Tian, K and Huang, X and Lyu, Y and Cao, G and Fu, J},
title = {Mobile Genomic Island GEI-FN1A in Aeromonas salmonicida FN1 Contributes to the Spread of Antibiotic-Resistance Genes.},
journal = {Current microbiology},
volume = {82},
number = {8},
pages = {345},
pmid = {40553200},
issn = {1432-0991},
support = {ZR2022MH107//Shandong Provincial Natural Science Foundation/ ; M-2023040//TCM science and technology project of Shandong Province/ ; },
mesh = {*Genomic Islands ; Anti-Bacterial Agents/pharmacology ; Animals ; Gene Transfer, Horizontal ; *Aeromonas salmonicida/genetics/drug effects/isolation & purification ; *Drug Resistance, Multiple, Bacterial/genetics ; Chickens ; Whole Genome Sequencing ; Genome, Bacterial ; Feces/microbiology ; Soil Microbiology ; Genes, Bacterial ; Bacterial Proteins/genetics ; Microbial Sensitivity Tests ; },
abstract = {Antibiotics are used to treat severe bacterial infections. However, owing to excessive antibiotic use, bacteria under high selective pressure for antibiotics develop resistance through spontaneous mutation or by acquiring antibiotic-resistance genes (ARGs) through horizontal gene transfer (HGT). Horizontal transfer of ARGs among bacteria in the environment can lead to the emergence of multidrug-resistant (MDR) bacteria that infect animals and humans, thus causing disease outbreaks. In this study, MDR strain FN1 was isolated from a feces-contaminated soil sample from a chicken farm under pressure from the antibiotic florfenicol (16 mg/L) and identified as Aeromonas salmonicida. Whole-genome sequencing and analysis revealed the 86.8-kb antibiotic-resistant genomic island, GEI-FN1A, in the FN1 genome. Genome annotation revealed that GEI-FN1A carried several ARGs, including two tetracycline-resistance genes [tetR and tet(A)], three aminoglycoside-resistance genes [aph(6), aph(3"), and aac(3)], one trimethoprim-resistance gene (dfrB4), two chloramphenicol/florfenicol-resistance genes (catB3 and floR), three macrolide-resistance genes [mphR(A), mrx(A), and mph(A)] and two sul1 genes. GEI-FN1A also contained genes encoding integrase, transposase, and recombinase, which mediate the horizontal transfer of MDR genes. These findings suggest that GEI-FN1A in A. salmonicida FN1 can potentially spread ARGs among environmental bacteria.},
}

*Genomic Islands
Anti-Bacterial Agents/pharmacology
Animals
Gene Transfer, Horizontal
*Aeromonas salmonicida/genetics/drug effects/isolation & purification
*Drug Resistance, Multiple, Bacterial/genetics
Chickens
Whole Genome Sequencing
Genome, Bacterial
Feces/microbiology
Soil Microbiology
Genes, Bacterial
Bacterial Proteins/genetics
Microbial Sensitivity Tests

@article {pmid40553195,
year = {2025},
author = {Sonkar, V and Devtalla, H and Kumar, S},
title = {Pesticide-driven antimicrobial resistance in water bodies: insights on environmental concerns, health implications and mitigation strategies.},
journal = {Environmental geochemistry and health},
volume = {47},
number = {7},
pages = {282},
pmid = {40553195},
issn = {1573-2983},
mesh = {*Pesticides/toxicity/analysis ; *Water Pollutants, Chemical/toxicity/analysis ; *Drug Resistance, Microbial/drug effects ; Humans ; India ; Agriculture ; Water Microbiology ; },
abstract = {Pesticide contamination in water bodies is an emerging driver of antimicrobial resistance (AMR), posing severe environmental and public health risks. Due to excessive agricultural use, pesticides routinely end up in water bodies due to leaching, improper disposal, and agricultural runoff. Pesticides act as selective pressures, promoting resistant microbial strains by providing evolutionary pressure for the strains to thrive. Pesticides facilitate the dissemination of resistance genes through several mechanisms; horizontal gene transfer, bio-film formation, and co-selection with heavy metals. Pathogens carrying antibiotic resistance genes, are emerging as a threat to global populations exposed to contaminated water, as they are increasingly more challenging to treat with traditional antibiotics. Moreover, these issues escalate due to the overlap in disposal of agricultural runoffs and untreated hospital waste into water bodies leading to co-selection pressure facilitating multi drug resistance. Current review examines the critical role of pesticides contamination in driving AMR in Indian aquatic ecosystems, a novel intersection threatening global health and deteriorating aquatic life. However, existing policies are insufficient, necessitating stricter regulations to control the problem. There also needs to be stronger laws in place to limit and monitor pollution in the water bodies. The increasing incidences of health issues linked to resistant strains in Indian population, need to be tackled more comprehensively. Mitigation requires stringent agricultural regulations, improved waste management, and interdisciplinary strategies to curb this growing threat.},
}

*Pesticides/toxicity/analysis
*Water Pollutants, Chemical/toxicity/analysis
*Drug Resistance, Microbial/drug effects
Humans
India
Agriculture
Water Microbiology

@article {pmid40552317,
year = {2025},
author = {Jafari, E and Azizian, R and Tabasi, M and Banakar, M and Bagheri Lankarani, K},
title = {Human Gut Bacteriophageome: Insights Into Drug Resistance Mechanisms in Tuberculosis.},
journal = {Interdisciplinary perspectives on infectious diseases},
volume = {2025},
number = {},
pages = {8811027},
pmid = {40552317},
issn = {1687-708X},
abstract = {Tuberculosis (TB), caused by Mycobacterium tuberculosis, remains a major global health burden. The emergence of drug-resistant strains presents a critical challenge in TB management. The recent research has explored the interaction between TB and the human gut bacteriophage community (phageome). The gut phageome plays a crucial role in regulating microbial diversity and functionality, and its composition and function have been linked to various health conditions. Examining the gut phageome through metagenomic analysis provides insights into its composition, role in health, and interactions with the host immune system. Exploring the interaction between the gut phageome and M. tuberculosis may reveal how phages affect the bacterium's pathogenicity, survival, and mechanisms of drug resistance. Understanding the gut phageome's impact on TB drug resistance could inform novel therapeutic strategies, such as phage therapy, and highlight the importance of microbiome-based interventions in combating drug-resistant TB strains. This review explores the role of the gut phageome in influencing drug resistance in TB, focusing on interaction mechanisms and potential therapeutic implications, synthesizing current research findings, and identifying knowledge gaps in this emerging field. This review also synthesizes the current evidence on the gut phageome's role in TB drug resistance, focusing on phage-mediated horizontal gene transfer (e.g., rpoB, katG), immune modulation, and preclinical efficacy of mycobacteriophage therapies. Key findings highlight phage cocktails (e.g., DS6A, D29 LysB) as promising adjuncts to antibiotics, reducing M. tuberculosis burden in murine models. These insights advocate for phage therapy as a complementary strategy against drug-resistant TB, urging clinical validation to bridge the existing knowledge gaps.},
}

@article {pmid40551445,
year = {2025},
author = {Deshamukhya, C and Das, BJ and Dhar, D and Bhattacharjee, A},
title = {Influence of AHL and Imipenem on blaNDM Conjugation and sRNA Rydb Expression in Escherichia coli.},
journal = {Journal of basic microbiology},
volume = {},
number = {},
pages = {e70074},
doi = {10.1002/jobm.70074},
pmid = {40551445},
issn = {1521-4028},
abstract = {The rise of carbapenem resistance in Escherichia coli is mainly due to the rapid spread of carbapenemase-encoding genes through horizontal gene transfer, particularly via bacterial conjugation. Recent research has highlighted the role of a small RNA molecule known as RydB in bacterial conjugation, specifically through its interaction with the protein SdiA. This study investigated the effects of sub-inhibitory concentrations of imipenem and N-acyl homoserine lactones (AHLs) on the expression of rydB in E. coli strains that overexpress sdiA. Additionally, we examined how AHLs influence the bacterial conjugation of plasmids that contain carbapenem resistance genes. We selected a carbapenem-resistant isolate of E. coli harbouring the blaNDM gene and its corresponding plasmid-cured derivative, based on the overexpression of the sdiA gene in response to AHLs. Conjugation experiments were conducted, both without AHL treatment and with AHL treatments, to assess the transferability of the blaNDM plasmid. The transcriptional response of rydB gene was evaluated in the plasmid-cured derivative, the native type, the transconjugant, and E. coli J53. Our findings indicated that AHLs and imipenem inhibit the expression of the rydB gene. Interestingly, while RydB does not seem to impact bacterial conjugation when suppressed by these agents, the combination of AHLs enhances the conjugation of plasmid that carry the blaNDM gene. This study enhances our understanding of the regulatory roles that quorum sensing signal molecules, including C4 AHL and C12AHL, as well as imipenem, play in bacterial conjugation and sRNA expression.},
}

@article {pmid40548977,
year = {2025},
author = {Bhadra, S and Das, C and Bawali, S and Bhattacharya, A},
title = {Evolutionary analysis of the Leishmania major orthologues for the newly identified cyclic AMP response proteins.},
journal = {Archives of microbiology},
volume = {207},
number = {8},
pages = {184},
pmid = {40548977},
issn = {1432-072X},
mesh = {*Leishmania major/genetics/metabolism ; Phylogeny ; *Evolution, Molecular ; *Protozoan Proteins/genetics/metabolism/chemistry ; *Cyclic AMP/metabolism ; Gene Transfer, Horizontal ; },
abstract = {Cyclic AMP (cAMP) signalling is largely noncanonical in kinetoplastids. With virtual absence of canonical cAMP effectors including cyclic nucleotide sensitive protein kinase A regulatory subunits. Through a number of RNAi screens, a group of novel cAMP-responsive effectors were identified from Trypanosoma with 11 members, assigned as cAMP Response Proteins (CARPs, CARP1 to 11). Four of the CARPs were reported earlier, recently the remaining seven were identified. Except for CARP3 and CARP11, the orthologues for other CARPs can be identified from Leishmania. An intricate evolutionary analysis performed earlier indicated CARP1 and CARP4 from Leishmania major comprise features of horizontally transferred genes. Aiming for comprehensive understanding of the evolution of CARPs, the study further extends the evolutionary analysis to newly annotated CARP orthologues from L. major. The study reveals the phylogenetic relation among kinetoplastid CARP orthologues and functional divergence. A systemic codon adaptation profiling suggested horizontal transfer for some of the CARPs. Alongside, structural analysis highlighted heterogeneity among the T. brucei and L. major orthologues.},
}

*Leishmania major/genetics/metabolism
Phylogeny
*Evolution, Molecular
*Protozoan Proteins/genetics/metabolism/chemistry
*Cyclic AMP/metabolism
Gene Transfer, Horizontal

@article {pmid40548945,
year = {2025},
author = {},
title = {Correction to 'Enhancing insights into diseases through horizontal gene transfer event detection from gut microbiome'.},
journal = {Nucleic acids research},
volume = {53},
number = {12},
pages = {},
doi = {10.1093/nar/gkaf631},
pmid = {40548945},
issn = {1362-4962},
}

@article {pmid40548717,
year = {2025},
author = {Xu, C and Li, X and Zhang, Y and Li, Y and Li, Y and Zhang, R and Dong, N},
title = {Interorder horizontal gene transfer of tet(X3) between Acinetobacter spp. and Enterobacteriaceae.},
journal = {Antimicrobial agents and chemotherapy},
volume = {},
number = {},
pages = {e0194524},
doi = {10.1128/aac.01945-24},
pmid = {40548717},
issn = {1098-6596},
}

@article {pmid40544776,
year = {2025},
author = {Huang, W and Wang, F and Su, Y and Huang, H and Luo, J},
title = {Underestimated roles of phages in biological wastewater treatment systems: Recent advances and challenges.},
journal = {Journal of hazardous materials},
volume = {495},
number = {},
pages = {139007},
doi = {10.1016/j.jhazmat.2025.139007},
pmid = {40544776},
issn = {1873-3336},
abstract = {Bacteriophages (phages) are vital components in biological wastewater ecosystems, whose concentrations are far exceeding those bacteria. Despite their importance, they are often overlooked and regarded as the "dark matter" in biological treatment processes. Phages play a pivotal role in shaping the dynamic evolution of host microbial communities within wastewater treatment plants (WWTPs), driving their functional evolution through interactions with host microorganisms. Phages are crucial in driving microbial ecological dynamics and regulating metabolic functions. At the macroscopic scale, the organic matters released through viral shunting demonstrate enhanced bioavailability and facilitated organic element cycling based on viral shuttle-mediated bio-pump. Additionally, at the micro-scale, gene transfer mediated by phages can assist functional microorganisms in enhancing metabolic efficiency and adapting to environmental stress. However, this process also introduces environmental risks, particularly the dissemination of antibiotic resistance genes through horizontal gene transfer and plasmids. Phages offer distinct advantages over conventional chemical and physical methods, including superior efficiency and environmental sustainability. Nonetheless, the development of phage-based biocontrol strategies is constrained by phage specificity and the complexity of biological treatment systems. Recent advances in artificial intelligence and genetic technologies provide promising avenues for optimizing phage applications. Further research into phage ecology is essential to lay a theoretical foundation for enhancing operational stability, treatment efficiency, and targeted biocontrol strategies.},
}

@article {pmid40544537,
year = {2025},
author = {Sinha, S and Upadhyay, LSB},
title = {Understanding antimicrobial resistance (AMR) mechanisms and advancements in AMR diagnostics.},
journal = {Diagnostic microbiology and infectious disease},
volume = {113},
number = {2},
pages = {116949},
doi = {10.1016/j.diagmicrobio.2025.116949},
pmid = {40544537},
issn = {1879-0070},
abstract = {The overuse and abuse of antibiotics, which results in the evolution of resistant microorganisms, is the primary cause of the global health catastrophe known as antimicrobial resistance (AMR). The enzymatic breakdown of antibiotics, target site modification, efflux pump overexpression, and the formation of biofilm are some of the mechanisms responsible for acquiring antimicrobial resistance (AMR). These mechanisms enable bacteria to evade or neutralize the effects of antimicrobial agents, complicating treatment options and increasing mortality rates. The rapid dissemination of resistance genes via horizontal gene transfer further exacerbates the problem, necessitating urgent intervention. Advanced AMR diagnostics are transforming the fight against antimicrobial resistance. Biosensors enable rapid, point-of-care detection; Cluster regularly interspaced short palindromic repeat (CRISPR) technologies offer precise identification of resistance genes; and mass spectrometry provides fast, accurate profiling. Automated systems streamline workflows and boost throughput, while flow cytometry delivers real-time, single-cell analysis of phenotypic resistance. Together, these innovations accelerate detection and support targeted antimicrobial stewardship, essential for combating the global AMR threat. This review covers the mechanisms underlying antimicrobial resistance (AMR) and recent advancements in AMR diagnostic technologies.},
}

@article {pmid40542629,
year = {2025},
author = {Aristova, EO and Volkhin, IA and Denisova, AA and Nikitin, PA and Petrukhin, ER},
title = {[De Novo Gene Birth].},
journal = {Molekuliarnaia biologiia},
volume = {59},
number = {1},
pages = {22-31},
pmid = {40542629},
issn = {0026-8984},
mesh = {*Evolution, Molecular ; Humans ; *Gene Duplication ; *Gene Transfer, Horizontal ; Animals ; },
abstract = {According to classic ideas, new genes emerge from old genes by duplication or horizontal transfer. Analyses of a large number of genomes in recent decades have shown that some genes have no visible homologs and have presumably emerged de novo from previously noncoding sequences. The review considers possible mechanisms of de novo gene formation, the properties of protein sequences encoded by such genes, and features of their expression and selection. The problem of identification of de novo arising gene is discussed separately.},
}

*Evolution, Molecular
Humans
*Gene Duplication
*Gene Transfer, Horizontal
Animals

@article {pmid40540566,
year = {2025},
author = {Woods, PH and Speth, DR and Laso-Pérez, R and Utter, DR and Ruff, SE and Orphan, VJ},
title = {Identification of key steps in the evolution of anaerobic methanotrophy in Candidatus Methanovorans (ANME-3) archaea.},
journal = {Science advances},
volume = {11},
number = {25},
pages = {eadq5232},
pmid = {40540566},
issn = {2375-2548},
mesh = {*Methane/metabolism ; Anaerobiosis ; Phylogeny ; *Evolution, Molecular ; Genome, Archaeal ; *Archaea/genetics/metabolism ; Metagenomics ; Gene Transfer, Horizontal ; },
abstract = {Despite their large environmental impact and multiple independent emergences, the processes leading to the evolution of anaerobic methanotrophic archaea (ANME) remain unclear. This work uses comparative metagenomics of a recently evolved but understudied ANME group, "Candidatus Methanovorans" (ANME-3), to identify evolutionary processes and innovations at work in ANME, which may be obscured in earlier evolved lineages. We identified horizontal transfer of hdrA homologs and convergent evolution in carbon and energy metabolic genes as potential early steps in Methanovorans evolution. We also identified the erosion of genes required for methylotrophic methanogenesis along with horizontal acquisition of multiheme cytochromes and other loci uniquely associated with ANME. The assembly and comparative analysis of multiple Methanovorans genomes offers important functional context for understanding the niche-defining metabolic differences between methane-oxidizing ANME and their methanogen relatives. Furthermore, this work illustrates the multiple evolutionary modes at play in the transition to a globally important metabolic niche.},
}

*Methane/metabolism
Anaerobiosis
Phylogeny
*Evolution, Molecular
Genome, Archaeal
*Archaea/genetics/metabolism
Metagenomics
Gene Transfer, Horizontal

@article {pmid40379877,
year = {2025},
author = {Gonzalez-Duran, E and Kroop, X and Schadach, A and Bock, R},
title = {Suppression of plastid-to-nucleus gene transfer by DNA double-strand break repair.},
journal = {Nature plants},
volume = {11},
number = {6},
pages = {1154-1164},
pmid = {40379877},
issn = {2055-0278},
mesh = {*DNA Breaks, Double-Stranded ; *Plastids/genetics ; *DNA Repair ; *Nicotiana/genetics ; *Cell Nucleus/genetics ; *Gene Transfer, Horizontal ; Symbiosis/genetics ; },
abstract = {Plant nuclear genomes contain thousands of genes of mitochondrial and plastid origin as the result of endosymbiotic gene transfer (EGT). EGT is a still-ongoing process, but the molecular mechanisms determining its frequency remain largely unknown. Here we demonstrate that nuclear double-strand break (DSB) repair is a strong suppressor of EGT. Through large-scale genetic screens in tobacco plants, we found that EGT from plastids to the nucleus occurs more frequently in somatic cells when individual DSB repair pathways are inactive. This effect is explained by the expected increase in the number and residence time of DSBs available as integration sites for organellar DNA. We also show that impaired DSB repair causes EGT to increase 5- to 20-fold in the male gametophyte. Together, our data (1) uncover DSB levels as a key determinant of EGT frequency, (2) reveal the strong mutagenic potential of organellar DNA and (3) suggest that changes in DNA repair capacity can impact EGT across evolutionary timescales.},
}

*DNA Breaks, Double-Stranded
*Plastids/genetics
*DNA Repair
*Nicotiana/genetics
*Cell Nucleus/genetics
*Gene Transfer, Horizontal
Symbiosis/genetics

@article {pmid40544427,
year = {2025},
author = {Lamberte, LE and Darby, EM and Kiu, R and Moran, RA and Acuna-Gonzalez, A and Sim, K and Shaw, AG and Kroll, JS and Belteki, G and Clarke, P and Felgate, H and Webber, MA and Rowe, W and Hall, LJ and Van Schaik, W},
title = {Staphylococcus haemolyticus is a reservoir of antibiotic resistance genes in the preterm infant gut.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2519700},
doi = {10.1080/19490976.2025.2519700},
pmid = {40544427},
issn = {1949-0984},
abstract = {Staphylococcus haemolyticus is an important cause of sepsis in preterm infants, with gut colonization being recognized as a risk factor for infection. To better understand the diversity of S. haemolyticus among preterm infants, we generated genome sequences of S. haemolyticus strains (n = 140) from 44 stool samples of 22 preterm infants from four hospitals in England. Core genome phylogenetic analyses, incorporating 126 publicly available S. haemolyticus genome sequences, showed that 85/140 (60.1%) of the isolates, from three different hospitals, formed a clonal group with 78/85 (91.7%) strains having Multi-Locus Sequence Type (ST) 49. Antibiotic resistance genes were prevalent in the genomes. There was a strong association between the presence of mecA and phenotypic resistance to oxacillin, and the aacA-aphD gene and phenotypic resistance to gentamicin. While mecA was near-ubiquitous, none of the strains from the preterm infant cohort had a complete Staphylococcal Cassette Chromosome mec (SCCmec) element. The aacA-aphD gene was associated with the transposon Tn4001 in multiple chromosomal and plasmid contexts. Our data suggest the existence of a distinct sub-population of S. haemolyticus that has adapted to colonize the gut of preterm infants, and widespread horizontal gene transfer and recombination among this frequent colonizer of the preterm infant gut.},
}

@article {pmid40544087,
year = {2025},
author = {Bhattacharya, D and Van Etten, J and Panayotakis, G and McDermott, T and Stephens, TG},
title = {Gene transfer drives community cooperation in geothermal habitats.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2025.06.004},
pmid = {40544087},
issn = {1878-4380},
abstract = {Cyanidiophyceae red algae dominate many geothermal habitats and provide important tools for investigating the evolution of extremophilic eukaryotes and associated microbial communities. We propose that resource sharing drove genome reduction in Cyanidiophyceae and enabled the neofunctionalization of genes in multi-enzyme pathways. Utilizing arsenic detoxification as a model, we discuss how the sharing of gene functions by other members of the microbial assemblage weakened selection on homologs in the Cyanidiophyceae, allowing long-term gene persistence via the putative gain of novel functions. This hypothesis, referred to as the Integrated Horizontal Gene Transfer (HGT) Model (IHM), attempts more generally to explain how extremophilic eukaryotes may have transitioned from 'hot start' milieus by functional innovations driven by the duplication and divergence of HGT-derived genes.},
}

@article {pmid40543345,
year = {2025},
author = {Li, S and Jiang, Y and Wang, J and Bartlam, M and Wang, Y},
title = {Chiral naproxen enhances horizontal transfer of antibiotic resistance genes in biofilms: Molecular docking reveals stereoselective mechanisms.},
journal = {Journal of hazardous materials},
volume = {495},
number = {},
pages = {138980},
doi = {10.1016/j.jhazmat.2025.138980},
pmid = {40543345},
issn = {1873-3336},
abstract = {The dissemination of antibiotic resistance genes (ARGs) is a growing global health concern. This study investigates how the chiral enantiomers of the non-antibiotic drug naproxen (NAP) influence ARG dissemination in biofilms. Metagenomic sequencing and binning analyses revealed that NAP enantiomers selectively enriched ARGs and their bacterial hosts, enhancing resistance to specific antibiotics. Notably, the stereoselective effects of NAP enantiomers not only shaped microbial community composition but also affected the potential for ARG spread. Mechanistically, exposure to R-NAP, in comparison to S-NAP, resulted in a 1.53-fold increase in reactive oxygen species (ROS) production, an 18.20 % enhancement in cell membrane permeability, and a 1.93-fold rise in the abundance of genes associated with the type IV secretion system (T4SS). These physiological and genetic changes promoted microbial aggregation and DNA conjugation, particularly enhancing the transfer of the sul1 gene within the Aquabacter genus through the coordinated action of T4SS, two-component systems (TCS), and quorum sensing (QS). Molecular docking and qRT-PCR analyses further revealed that the stereoselectivity of NAP enantiomers stemmed from their distinct binding interactions with proteins involved in horizontal gene transfer, shedding light on the molecular mechanisms underlying ARG dissemination under chiral NAP exposure.},
}

@article {pmid40541684,
year = {2025},
author = {Sies, AN and Nowlan, JP and Schnell, LJ and Lumsden, JS and Russell, S and Cameron, ADS},
title = {Discovery and assembly of plasmids in the fish pathogen Tenacibaculum.},
journal = {Plasmid},
volume = {},
number = {},
pages = {102753},
doi = {10.1016/j.plasmid.2025.102753},
pmid = {40541684},
issn = {1095-9890},
abstract = {Members of the marine bacterial genus Tenacibaculum cause disease in finfish and outbreaks result in significant animal harm and losses in aquaculture around the globe. Plasmids have not been previously identified in Tenacibaculum, but long-read DNA sequencing of genomes from disease-associated Tenacibaculum isolates collected between 2017 and 2020 in British Columbia, Canada, revealed circular putative plasmids in three Tenacibaculum species. In addition to high-quality circular assembly, the putative plasmids contained genes encoding plasmid replication, mobility, and partitioning proteins. Genes for type B conjugation machinery and type 6iii secretion system components were also identified on each of the two largest plasmid sequences. Several protocols were tested to visualize and enrich Tenacibaculum plasmid DNA. Rolling-circle replication with Phi29 DNA polymerase amplified putative plasmids smaller than 100 kb. Alkaline lysis extraction provided weak enrichment of putative plasmid DNA, and plasmids could not be confidently resolved by Eckhardt extraction and electrophoresis in agarose gels. The newly assembled plasmids matched previously sequenced Tenacibaculum contigs, highlighting that publicly available Tenacibaculum genomes contain unrecognized plasmids. The discovery of putative plasmids in Tenacibaculum is significant because plasmids often confer important functions to host cells and serve as vehicles for horizontal gene transfer within and beyond the host species.},
}

@article {pmid40539803,
year = {2025},
author = {Mapiki, P and Laiser, E and Mufungwe, J and Shawa, M and Siamujompa, M and Johnson, T and Namukonde, N and Mwaanga, P and Hang'ombe, BM},
title = {Bacteriological quality of fresh and processed black soldier fly Hermetia illucens larvae reared on chicken manure in Kitwe, Zambia.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0057024},
doi = {10.1128/spectrum.00570-24},
pmid = {40539803},
issn = {2165-0497},
abstract = {UNLABELLED: Black soldier fly larvae (BSFL) have high nutrient content and are rapidly becoming an alternative protein source for animal feed. However, microbial contamination is a potential risk due to the environment in which they are reared. This study assessed the bacteriological quality of fresh and processed BSFL by comparing the processed BSFL using two traditional methods (oven-dried and sun-dried), on their effectiveness at reducing the bacterial load and further elucidated bacterial composition. PCR was used to identify extended-spectrum β-lactamase (ESBL) and mecA genes in Escherichia coli and Staphylococcus spp., respectively. A total of 51 fresh BSFL samples were collected from a commercial poultry farm in Kitwe, Zambia. The results showed various bacterial genera, with a higher diversity among gram-positive isolates. The comparison of the effectiveness of two traditional processing methods for BSFL, sun-drying and oven-drying, showed that both methods significantly reduced the bacterial load, with oven-drying causing a larger reduction. While various genera were identified, we focused on E. coli and Staphylococcus spp. This is because some E. coli harbor ESBLs that hydrolyze β-lactam antibiotics like cephalosporins and penicillin, leading to resistance. Similarly, the genus Staphylococcus was selected since some strains are potentially pathogenic and contain the mecA gene that encodes resistance to β-lactam antibiotics. Molecular characterization of the isolated strains revealed blaCTX-M and blaTEM genes among E. coli, but the mecA gene was not detected among Staphylococcus. This study revealed that BSFL harbor bacteria of zoonotic significance, emphasizing the need for good processing methods to eliminate potential risks.

IMPORTANCE: Isolation and identification of Escherichia coli and Staphylococcus spp. in processed black soldier fly larvae (BSFL) samples meant for animal feed indicate insufficient processing methods and pose a public health risk. For instance, some E. coli harbor extended-spectrum β-lactamases (ESBLs) that hydrolyze β-lactam antibiotics like cephalosporins and penicillin, leading to resistance. In addition, some E. coli commensals can transfer antimicrobial resistance genes to pathogenic bacteria through horizontal gene transfer using various mobile genetic elements, leading to resistance. Similarly, for Staphylococcus spp., some strains of the genus Staphylococcus are potentially pathogenic and contain the mecA gene that encodes resistance to β-lactam antibiotics. In this study, we used PCR to screen E. coli isolates for the two commonly reported ESBL genes in Zambia, blaCTX-M and blaTEM, and Sanger sequencing was used to reveal blaCTX-M gene alleles. Our results highlight the importance of using adequate processing methods for BSFL to eliminate potential health risks to animal feed.},
}

@article {pmid40535478,
year = {2025},
author = {Zhang, Y and Su, Z and Qiu, X and Liu, H and Wen, D and Chen, L},
title = {Distinct ARG profiles associated with class 1 integrons in municipal and industrial wastewater treatment plants.},
journal = {Environmental science and ecotechnology},
volume = {26},
number = {},
pages = {100586},
pmid = {40535478},
issn = {2666-4984},
abstract = {Class 1 integrons facilitate horizontal gene transfer, significantly influencing antibiotic resistance gene (ARG) dissemination within microbial communities. Wastewater treatment plants (WWTPs) are critical reservoirs of ARGs and integrons, yet the integron-mediated dynamics of ARG transfer across different WWTP types remain poorly understood. Here we show distinct ARG profiles associated with class 1 integrons in municipal and industrial WWTPs using a novel approach combining nested-like high-throughput qPCR and PacBio sequencing. Although industrial WWTPs contained higher absolute integron abundances, their relative ARG content was lower (1.27 × 10[7]-9.59 × 10[7] copies/ng integron) compared to municipal WWTPs (3.72 × 10[7]-1.98 × 10[8] copies/ng integron). Of the 132,084 coding sequences detected from integrons, 56.8 % encoded antibiotic resistance, with industrial plants showing lower ARG proportions, reduced ARG array diversity, and greater incorporation of non-ARG sequences. These findings suggest industrial WWTP integrons integrate a broader array of exogenous genes, reflecting adaptation to complex wastewater compositions. This work enhances our understanding of integron-driven ARG dynamics in wastewater and offers a robust strategy for environmental integron analysis.},
}

@article {pmid40533044,
year = {2025},
author = {Tian, Y and Li, J and Meng, J and Li, J},
title = {Deciphering antibiotic resistance gene transfer in activated sludge systems for piggery wastewater: behaviors, hosts and drivers.},
journal = {Environmental research},
volume = {},
number = {},
pages = {122166},
doi = {10.1016/j.envres.2025.122166},
pmid = {40533044},
issn = {1096-0953},
abstract = {Understanding the transfer and driving mechanisms of antibiotic resistance genes (ARGs) in activated sludge is essential for mitigating environmental risks, particularly during real wastewater treatment where these processes remain poorly characterized. This study investigated the prevalence of ARGs in a sequencing batch reactor (SBR) - up-flow microaerobic sludge reactor (UMSR) system treating high-risk piggery wastewater and revealed critical pathways for resistance propagation. Ten prevalent ARG subtypes, categorized into three types, were selected as target genes, exhibiting a total relative abundance of 0.52 copies per 16S rRNA in raw wastewater. The SBR-UMSR system reduced total ARGs by 0.04 log in wastewater, with half of subtypes decreasing 0.14-1.30 log, despite 0.23-0.58 log enrichment in sludge. By integrating correlation analysis with partial least-squares path modeling, this study identified Burkholderiaceae as the primary potential host of ARGs and pinpointed other high-risk hosts. It further revealed two crucial mechanisms: (1) conjugation-mediated horizontal gene transfer dominated ARG propagation, and (2) bacterial community succession served as the main driving force for ARG transfer. This study advances mechanistic understanding of ARG transmission in real wastewater systems, providing critical insights for optimizing sludge management to mitigate antibiotic resistance risks.},
}

@article {pmid40530826,
year = {2025},
author = {Carolak, E and Czajkowska, J and Stypułkowska, A and Waszczuk, W and Dutkiewicz, A and Grzymajlo, K},
title = {Being a better version of yourself: genetically engineered probiotic bacteria as host defense enhancers in the control of intestinal pathogens.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2519696},
doi = {10.1080/19490976.2025.2519696},
pmid = {40530826},
issn = {1949-0984},
mesh = {*Probiotics ; Humans ; *Gastrointestinal Microbiome ; Genetic Engineering ; Animals ; *Microorganisms, Genetically-Modified/genetics ; *Bacteria/genetics ; },
abstract = {Intestinal pathogens pose a significant global health burden, and traditional antibiotic treatments often disrupt the beneficial gut microbiota that plays a crucial role in maintaining host health through pathogen prevention and immune regulation. Although probiotics have emerged as promising therapeutic agents, their efficacy is limited by strain-dependent variations, survival challenges in the gastrointestinal tract, and inconsistent immune responses. Recent advances in genetic engineering, particularly CRISPR-Cas systems and their combinations with complementary technologies, such as Cre-lox and RecE/T, have enabled the precise modification of probiotic strains to enhance their therapeutic potential. These enhanced probiotics demonstrate improved functionality through multiple mechanisms, including increased adhesion via the expression of specific proteins (InlA, FnBPA, and LAP), targeted antimicrobial activity through engineered sensing systems (Lactococcus lactis detecting Vibrio cholerae CAI-1), and enhanced immunomodulation through cytokine production. Results have demonstrated the potential of genetically modified probiotics in preventing and treating gastrointestinal infections through mechanisms that include competitive exclusion, bacteriocin production, intestinal barrier reinforcement, and immune modulation. However, challenges remain in ensuring genetic stability and preventing horizontal gene transfer. Future research should focus on optimizing probiotic strains for targeted applications while addressing biosafety concerns. By understanding the complex interplay between probiotics, pathogens, and host immunity, innovative strategies can be developed to harness the full therapeutic potential of probiotic interventions in maintaining gut health.},
}

*Probiotics
Humans
*Gastrointestinal Microbiome
Genetic Engineering
Animals
*Microorganisms, Genetically-Modified/genetics
*Bacteria/genetics

@article {pmid40529306,
year = {2025},
author = {Xu, J and Zhang, M and Yan, Y and Li, Z and Lu, X},
title = {Intestinal flora metabolites indole-3-butyric acid and disodium succinate promote IncI2 mcr-1-carrying plasmid transfer.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1564810},
pmid = {40529306},
issn = {2235-2988},
mesh = {*Plasmids/genetics ; Reactive Oxygen Species/metabolism ; *Indoles/metabolism/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Escherichia coli/genetics/drug effects ; *Gene Transfer, Horizontal/drug effects ; Conjugation, Genetic/drug effects ; *Succinic Acid/metabolism ; Cell Membrane Permeability/drug effects ; Drug Resistance, Bacterial/genetics ; },
abstract = {INTRODUCTION: Plasmid-driven horizontal transfer of resistance genes in bacterial communities is a major factor in the spread of resistance worldwide. The gut microbiome, teeming with billions of microorganisms, serves as a reservoir for resistance genes. The metabolites of gut microorganisms strongly influence the physiology of their microbial community, but the role of the metabolites in the transfer of resistance genes remains unclear.

METHODS: A dual-fluorescence conjugation model was established. We assessed the effects of different concentrations of indole-3-butyric acid (IBA) and disodium succinate (DS) on plasmid transfer using conjugation assays. The growth of bacteria (donors, recipients, and transconjugants), the reactive oxygen species (ROS) levels and membrane permeability were measured under IBA and DS exposure. The plasmid copy number, and transcriptional levels of conjugation-related genes (including the related genes of the regulation of ROS production, the SOS response, cell membrane permeability, pilus generation, ATP synthesis, and the type IV secretion system (T4SS)) were evaluated by qPCR.

RESULTS: In this study, we demonstrated that IBA and DS at low concentrations, which can also be ingested through diet, enhance the interspecies transfer ratio of IncI2 mcr-1-carrying plasmid in Escherichia coli. At 20 mg/L, the transfer ratios in the presence of IBA or DS increased by 2.5- and 2.7-fold compared to that of the control, respectively. Exposure to this concentration of IBA or DS increased the production of reactive oxygen species (ROS), the SOS response, cell membrane permeability, and plasmid copy number. The transcription of genes of the related pathways and of pilus, ATP, and the T4SS was upregulated.

DISCUSSION: Our findings revealed that low-dose gut microbiota metabolites-particularly those with dietary origins-promote plasmid-mediated resistance gene dissemination through multifaceted mechanisms involving oxidative stress, SOS activation, and conjugation machinery enhancement. This highlights potential public health risks associated with microbiota metabolites, especially those utilized in food production.},
}

*Plasmids/genetics
Reactive Oxygen Species/metabolism
*Indoles/metabolism/pharmacology
*Gastrointestinal Microbiome/drug effects
Escherichia coli/genetics/drug effects
*Gene Transfer, Horizontal/drug effects
Conjugation, Genetic/drug effects
*Succinic Acid/metabolism
Cell Membrane Permeability/drug effects
Drug Resistance, Bacterial/genetics

@article {pmid40528005,
year = {2025},
author = {Baker, BA and McCarthy, CGP and López-García, P and Leroy, RB and Susko, E and Roger, AJ and Eme, L and Moreira, D},
title = {Phylogenomic analyses indicate the archaeal superphylum DPANN originated from free-living euryarchaeal-like ancestors.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {40528005},
issn = {2058-5276},
support = {787904//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 101141745//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 803151//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 101141745//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 803151//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 812811//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; 812811//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; },
abstract = {The episymbiotic DPANN archaea are thought to be one of the four major archaeal clades. However, the monophyly and placement of DPANN within the archaeal tree remain debated, and their fast-evolving reduced genomes render phylogenetic reconstructions challenging. Here we used 126 highly conserved protein markers, extensive taxon sampling representing the 11 known DPANN phyla and in-depth phylogenomic analyses to reassess DPANN monophyly and their relationships to other archaea. Our analyses robustly support the monophyly and placement within Euryarchaeota, and we identify the probably free-living Altiarchaeota as the earliest diverging DPANN branch. Our phylogenies suggest DPANN probably acquired several hallmark proteins through ancient horizontal gene transfer events from different bacterial donors, notably Patescibacteria and Omnitrophota, two bacterial phyla that also exhibit episymbiotic lifestyles. Overall, the monophyletic DPANN archaea probably evolved from a free-living, euryarchaeal-like ancestor, with proteins of bacterial origin playing a role in the emergence of their episymbiotic lifestyle.},
}

@article {pmid40527192,
year = {2025},
author = {Yin, Y and Xiao, K and Wang, YF and Cao, JM and Dong, JP and Zhu, D and Zhu, YG},
title = {Nanoplastics released from textile washing enrich antibiotic resistance and virulence genes in sewage sludge microbiomes.},
journal = {Environment international},
volume = {202},
number = {},
pages = {109611},
doi = {10.1016/j.envint.2025.109611},
pmid = {40527192},
issn = {1873-6750},
abstract = {The washing of synthetic textiles is a major source of microplastic pollution, contributing to the widespread presence of nanoplastics (NPs) in wastewater treatment plants (WWTPs). However, the role of laundry-released NPs in shaping microbial communities and facilitating the spread of antibiotic resistance genes (ARGs) and virulence factor genes (VFGs) in sludge remains unclear. Here, we quantified the concentration and size distribution of NPs released during the washing of polyamide (PA), polypropylene (PP), and polyethylene terephthalate (PET) textiles using nanoparticle tracking analysis. Substantial NP release was observed, with concentrations ranging from 3.4 × 10[7] to 1.7 × 10[8] particles mL[-1], and sizes between 130 and 240 nm. We then evaluated their impact on ARG and VFG profiles, as well as bacterial communities in anaerobic sludge through metagenomic and 16S rRNA gene sequencing. Laundry-released NPs significantly increased the abundance of ARGs, VFGs, and mobile genetic elements (MGEs) in sludge, with D8A-2 and Halomonas identified as potential ARG and VFG hosts. Notably, the mechanisms driving ARG enrichment varied by NP type. PA-released NPs elevated reactive oxygen species levels in bacterial communities, facilitating horizontal gene transfer via MGEs, while PP- and PET-released NPs enhanced ARG enrichment through both horizontal gene transfer and shifts in bacterial community composition. These findings highlight the risks posed by laundry-released NPs accumulating in WWTPs, emphasizing the urgent need for improved wastewater management strategies to mitigate their environmental and public health impacts.},
}

@article {pmid40520376,
year = {2025},
author = {Cao, H and Shen, Y and Ma, K and Zheng, D and Xu, Y and Qiao, X},
title = {Molecular characterization of clinical non-typhoidal Salmonella isolates shows high antimicrobial resistance burden in Jiangsu, China.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1587421},
pmid = {40520376},
issn = {1664-302X},
abstract = {Non-typhoidal Salmonella (NTS) poses a significant global health burden due to its association with gastroenteritis and rising antimicrobial resistance (AMR). This study conducted a genomic analysis of 62 Salmonella isolates from outpatient cases in Jiangsu, China, to monitor the epidemiological characteristics of NTS, including genetic diversity, AMR profiles, and resistance transmission mechanisms 18 serovars and 21 sequence types (STs) were identified by whole genome sequencing, with S. enteritidis (27.42%) and S. typhimurium (19.35%) predominating. 61 resistance genes from ten different antimicrobial categories were found by genotypic AMR screening. 90.32% of isolates had β-lactam resistance genes, indicating a high frequency of extended-spectrum β-lactamases (ESBL). Serovar-dependent resistance patterns were highlighted by the most varied AMR profile (40/61 genes) found in S. typhimurium. The co-occurrence of genes for aminoglycoside resistance, sul2, and blaTEM indicated clustering driven by mobile genetic elements. A plasmid in a S. Stanley isolate harbored 12 AMR genes, which showed structural changes suggestive of horizontal gene transfer and active recombination. These findings underscore the role of plasmids in disseminating MDR and the urgent need for enhanced antimicrobial stewardship, food safety protocols, and One Health interventions to mitigate the spread of resistant Salmonella clones.},
}

@article {pmid40517254,
year = {2025},
author = {Gozashti, L and Corbett-Detig, R},
title = {Double-stranded DNA viruses may serve as vectors for horizontal transfer of intron-generating transposons.},
journal = {Mobile DNA},
volume = {16},
number = {1},
pages = {25},
pmid = {40517254},
issn = {1759-8753},
support = {R35GM128932/GM/NIGMS NIH HHS/United States ; },
abstract = {Specialized transposable elements capable of generating introns, termed introners, are one of the major drivers of intron gain in eukaryotes. Horizontal transfer of transposable elements (HTT) is thought to play an important role in shaping introner distributions. Viruses could function as vehicles of introner HTT since they often integrate into host genomes and have been implicated in widespread HTT in eukaryotes. We annotated integrated viral elements in diverse dinoflagellate genomes with active introners and queried viral elements for introner sequences. We find that 25% of viral elements contain introners. The vast majority of viral elements represent maverick-polinton-like double-stranded DNA (dsDNA) viruses in the family eupolintoviridae as well as giant dsDNA viruses. By querying a previously annotated set of eupolintoviral proviruses, we show that introners populate full-length elements with machinery required for transposition as well as viral infection. Introners in the vast majority of viral elements are younger than or similar in age to others in their host genome, suggesting that most viral elements acquired introners after integration. However, a subset of viral elements shows the opposite pattern wherein viral introners are significantly older than other introners, possibly consistent with virus-to-host horizontal transfer. Together, our results suggest that dsDNA viruses may serve as vectors for HTT of introners between individuals and species, resulting in the introduction of intron-generating transposons to new lineages.},
}

@article {pmid40069292,
year = {2025},
author = {Lang, AS and Buchan, A and Burrus, V},
title = {Interactions and evolutionary relationships among bacterial mobile genetic elements.},
journal = {Nature reviews. Microbiology},
volume = {23},
number = {7},
pages = {423-438},
pmid = {40069292},
issn = {1740-1534},
mesh = {*Interspersed Repetitive Sequences/genetics ; *Bacteria/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genome, Bacterial ; },
abstract = {Mobile genetic elements (MGEs) have profound influence on the ecology and evolution of organisms, including bacteria. During the past two decades, a great number of new types of MGEs have been discovered that now seem to be prevalent in diverse bacterial lineages. With the rapid discovery of new categories of MGEs comes an array of new acronyms that present a challenge to grasp. Moreover, it is now clear that there are complex evolutionary connections and molecular interactions among MGEs, and that these entities are not discrete, independent genetic elements acting in isolation. Different types of MGEs share and exchange genes, and coresident MGEs interact with each other within cells, in both cooperative and antagonistic ways. This all greatly affects the end results that are felt by the host organism. In this Review, we strive to clarify emerging bacterial MGE terms and elements while also presenting a comprehensive overview of the current knowledge landscape regarding MGEs in bacteria, their evolutionary relationships and interactions with their host and with one another.},
}

*Interspersed Repetitive Sequences/genetics
*Bacteria/genetics
*Evolution, Molecular
Gene Transfer, Horizontal
Genome, Bacterial

@article {pmid40516885,
year = {2025},
author = {Cunha da Silva, G and Rossi, CC},
title = {Defense systems and mobile elements in Staphylococcus haemolyticus: a genomic view of resistance dissemination.},
journal = {Microbial pathogenesis},
volume = {206},
number = {},
pages = {107808},
doi = {10.1016/j.micpath.2025.107808},
pmid = {40516885},
issn = {1096-1208},
abstract = {Staphylococcus haemolyticus is a multidrug-resistant opportunistic pathogen and a major reservoir of antimicrobial resistance (AMR) genes within the Staphylococcaceae family. Its high genomic plasticity, frequent association with mobile genetic elements (MGEs), and prevalence in clinical settings underscore its relevance as both a threat and a conduit for resistance dissemination. In this study, we performed a comprehensive pan-genomic analysis of the S. haemolyticus defensome - including restriction-modification (RM), abortive infection (Abi), and CRISPR-Cas systems - across 692 high-quality genomes. Our results reveal a highly diverse and modular repertoire of immune systems, often organized in physical clusters and frequently associated with MGEs. We identified evidence of antagonistic interactions, with both defense and anti-defense elements encoded on plasmids and prophages. CRISPR spacer analysis showed a predominant targeting of phages, and genomes encoding CRISPR-Cas systems exhibited a lower abundance of MGEs and AMR genes, suggesting a trade-off between defense and gene acquisition. RNA-seq data from one reference strain indicate that only a fraction of the defensome is actively transcribed under standard conditions, hinting at environment-responsive regulation. Together, these findings provide new insights into the genomic strategies sustaining the persistence and adaptability of S. haemolyticus in clinical environments. The interplay between its immune systems and mobilome likely contributes not only to its evolutionary trajectory, but also to its role in the horizontal transfer of resistance determinants among pathogenic staphylococci. A deeper understanding of this immune-mobilome interface may help inform future strategies to limit the spread of resistance.},
}

@article {pmid40516407,
year = {2025},
author = {Fang, C and Liu, H and Chen, X and Lu, H and Ren, C and Hu, Z and Wang, Y and Zhang, J},
title = {Thioredoxin-mediated sulfur cycling and biogenic sulfur encapsulation synergistically enhance co-removal of nitrogen, sulfamethoxazole, and resistance genes in constructed wetlands.},
journal = {Water research},
volume = {284},
number = {},
pages = {123939},
doi = {10.1016/j.watres.2025.123939},
pmid = {40516407},
issn = {1879-2448},
abstract = {The interplay between sulfur-driven denitrification and antibiotic resistance genes (ARGs) proliferation remains unresolved in constructed wetlands (CWs), where sulfide accumulation and reactive oxygen species generation paradoxically enhance nitrogen removal while compromising microbial integrity. To resolve this conflict, this study engineered a FeS2@S° composite filler that synergized thioredoxin (Trx)-mediated sulfur cycling and biogenic sulfur (bio-S[0]) encapsulation. Upregulation of trxA/B genes (2.3-fold increase) enabled Trx to convert toxic sulfide into adhesive bio-S[0], exhibiting higher microbial adhesion that shielded functional denitrifiers like Thiomonas (84.03 % viability under SMX stress). Concurrently, sulfur vacancies (SVs) at FeS2 {210}
crystal facets generated hydroxyl radicals (•OH) and singlet oxygen ([1]O2) via vacancy-activated pathways, selectively degrading about 73.00 % of extracellular polymeric substance (EPS)-bound ARGs while suppressing horizontal gene transfer (tolC downregulation). The 6:4 FeS2@S[0] system achieved 68.66 % total nitrogen removal and 50.17 % sulfamethoxazole degradation, outperforming conventional substrates by 28.00-39.00 %, alongside a 61.24-67.31 % reduction in ARG abundance. A self-sustaining sulfur cycle recycled about 89.00 % of sulfides into bio-S[0] or FeS2, minimizing H2S emissions (0.045 mg·m[-2]·h[-1]) and maintaining electron flux. By bridging Trx-driven redox homeostasis and bio-S[0]'s physical protection, this work redefines CWs as robust systems capable of simultaneous nitrogen retention, antibiotic degradation, and ARGs suppression, establishing a transformative paradigm for sustainable wastewater treatment.},
}

@article {pmid40513520,
year = {2025},
author = {Wu, K and Yang, J and Zhang, T and Zuo, J and Lin, H and Wang, J and Zhang, A and Lei, C and Wang, H},
title = {Emergence and traceability of Salmonella enterica serotype Mbandaka harboring blaOXA-10 from chickens in China.},
journal = {Veterinary microbiology},
volume = {307},
number = {},
pages = {110593},
doi = {10.1016/j.vetmic.2025.110593},
pmid = {40513520},
issn = {1873-2542},
abstract = {Salmonella enterica serotype Mbandaka (S. Mbandaka), a multi-host adapted non-typhoidal Salmonella, has emerged as a significant public health concern in recent years. In this study, we isolated S. Mbandaka strains carrying a multidrug-resistant IncHI2A/IncHI2 plasmid from deceased chickens in China and performed whole-genome sequencing and comparative genomic analyses to investigate their global dissemination and evolutionary adaptation. The multidrug-resistant IncHI2A/IncHI2 plasmid in isolate YK35 harbored multiple antibiotic resistance genes (ARGs) including blaOXA-10, which was firstly observed in S. Mbandaka in China. It exhibited high sequence identity with IncHI2A/IncHI2 plasmids identified in other bacterial species, including S. Typhimurium, Klebsiella aerogenes, and E. coli, which suggested the cross-species dissemination of IncHI2A/IncHI2 plasmids and ARGs. Global genomic epidemiology classified S. Mbandaka strains into seven distinct clades, with the majority originating from the USA and the UK. The pan-genomic analysis indicated an open pan-genome structure, with continuous expansion of accessory genes, particularly those associated with replication, recombination, repair, and defense mechanisms, underscoring the evolutionary adaptation of S. Mbandaka to external environments. Evolutionary analysis further traced the international transmission routes of S. Mbandaka, revealing potential cross-regional spread, particularly from the USA and the UK to other countries, including China. The findings emphasize the global spread and evolutionary adaptation of S. Mbandaka, likely driven by international trade and horizontal gene transfer, including the acquisition of ARGs, which have contributed to its increasing public health risks. This study underscores the urgent need for enhanced surveillance and control measures to mitigate the spread of S. Mbandaka and its antibiotic resistance, particularly in the context of global food supply chains and international trade.},
}

@article {pmid40506592,
year = {2025},
author = {Singh, H and Pandya, S and Jasani, S and Patel, M and Kaur, T and Rustagi, S and Shreaz, S and Yadav, AN},
title = {Integrons: the hidden architects of bacterial adaptation, evolution, and the challenges of antimicrobial resistance.},
journal = {Antonie van Leeuwenhoek},
volume = {118},
number = {7},
pages = {90},
pmid = {40506592},
issn = {1572-9699},
mesh = {*Integrons/genetics ; *Bacteria/genetics/drug effects ; *Evolution, Molecular ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; *Adaptation, Physiological ; },
abstract = {Integrons, a diverse group of genetic elements, have emerged as key players in bacterial adaptation and evolution. These elements, commonly found in both environmental as well as clinical settings, facilitate the acquisition, exchange, and expression of integron cassettes, allowing bacteria to rapidly adapt to changing environments and acquire antibiotic resistance. This review provides an in-depth exploration of the various classes of clinical integrons, including class 1, 2, and 3, highlighting their origins, distribution, and associated mobile elements. We delve into the astonishing success of "class 1 integrons", emphasizing their ability to recognize diverse attachment sites known as "attC sites" and getting integrated within many different integron cassettes from diverse sources. Class 1 integrons are able to propagate widely among bacterial hosts due to their lack of host specificity, interaction with transposons, and broad host range plasmids. Moreover, we discuss the substantial impact of class 1 integrons in antimicrobial resistance, as they accumulate an array of resistance genes through strong positive selection. Additionally, we address the challenging issue regarding the evolution and function of integrons and integron cassettes, including the role of promoters, origins of integron cassettes, and the abundance of unknown proteins encoded within them. The future prospects of integron research are also explored, highlighting the need to understand cassette expression patterns, assess the contribution of chromosomal/superintegron arrays to host fitness, unravel the mechanisms of cassette generation, and investigate the connection between the SOS induction and horizontal gene transfer. Overall, this review underlines the significance of integrons as hidden architects driving bacterial adaptation and evolution, providing valuable insights into their ecological and evolutionary dynamics, and shaping the future direction of research in this field.},
}

*Integrons/genetics
*Bacteria/genetics/drug effects
*Evolution, Molecular
*Drug Resistance, Bacterial/genetics
Anti-Bacterial Agents/pharmacology
*Adaptation, Physiological

@article {pmid40505955,
year = {2025},
author = {Kaneko, S and Fukushima, H and Nakahama, M and Tsuge, K and Ishii, J and Aizawa, Y and Itaya, M and Kondo, A},
title = {Versatile Methodology for Efficient Large-sized DNA Delivery between Microorganisms without in vitro purification.},
journal = {Journal of molecular biology},
volume = {},
number = {},
pages = {169289},
doi = {10.1016/j.jmb.2025.169289},
pmid = {40505955},
issn = {1089-8638},
abstract = {Purified DNA plasmids traditionally used for microbial transformation have been supplanted by extracellular plasmids released via host bacterial lysis, offering an alternative approach for DNA-plasmid delivery. Specifically, shuttle vector plasmids liberated from host Bacillus subtilis were directly employed for the transformation of chemically competent cells Escherichia coli, eliminating the need for biochemical purification. This unconventional DNA delivery technique, referred to as 'Cell Lysis Technology to provide Transformable Extra-cellular DNA; CELyTED', has been successfully adapted for the transformation of microorganism Saccharomyces cerevisiae as well. The protocol includes optimized conditions for efficient cell lysis of the donor host cells. Notably, ' CELyTED ' enables the introduction of large-sized DNA plasmids exceeding 50 kb into target microorganisms mitigating the potential adverse effects of physical shearing during the purification process. This simplicity in the delivery protocol makes it versatile for both prokaryotic and eukaryotic microorganisms, establishing a fundamental platform in the synthetic genome field. Our study demonstrates the feasibility of introducing large DNA plasmids into cells E. coli and S. cerevisiae using the lysate of donor host cells, showcasing the potential of 'CELyTED ' as a streamlined approach in genetic transformation methodologies.},
}

@article {pmid40505265,
year = {2025},
author = {Chen, M and Wang, G and Ma, B and Musat, N and Shen, P and Wei, Z and Wei, Y and Richnow, HH and Zhang, J},
title = {Deciphering the transfer of antimicrobial resistance genes in the urban water cycle from water source to reuse: a review.},
journal = {Environment international},
volume = {201},
number = {},
pages = {109584},
doi = {10.1016/j.envint.2025.109584},
pmid = {40505265},
issn = {1873-6750},
abstract = {Antimicrobial resistance genes (ARGs) threaten ecosystems and human health, impacting United Nations Sustainable Development Goal 3 (Good Health and Well-being). This review examines ARG occurrence and transfer within the urban water cycle (UWC) from drinking water source to wastewater reuse, highlighting molecular mechanisms and research gaps. Quantitative and metagenomic data reveal that UWC amplifies ARG spread, with plasmid-mediated ARGs rising from ∼ 2.23 % to ∼ 49.51 % and high-risk ARGs increasing from ∼ 0.25 % to ∼ 5.07 %, enhancing horizontal gene transfer in receiving waters. The primary sources of ARGs in UWC are wastewater treatment plants and combined sewage overflows. Multidrug-resistant Pseudomonas aeruginosa in drinking water treatment plant and multidrug-resistant fecal coliforms in wastewater treatment plants should be emphasized. These pose significant risks to both the environment and human health and underscore the urgent need for targeted monitoring and mitigation strategies within the UWC to safeguard public health and aquatic ecosystems. Future research should: (1) map ARG dynamics across the entire UWC, (2) identify hosts of high-risk ARGs and key pathogens, (3) elucidate HGT mechanisms and risk transmission, and (4) develop targeted control technologies for high-risk ARGs at critical UWC points. These insights will inform strategies to ensure water security and curb ARG proliferation in aquatic environments.},
}

@article {pmid40503823,
year = {2025},
author = {Karlsson, PA and Zhang, T and Järhult, JD and Joffré, E and Wang, H},
title = {Heterogeneity and metabolic diversity among Enterococcus species during long-term colonization.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0316024},
doi = {10.1128/spectrum.03160-24},
pmid = {40503823},
issn = {2165-0497},
abstract = {Urinary tract infections (UTIs), traditionally dominated by Gram-negative pathogens, are increasingly complicated by antimicrobial-resistant Enterococcus spp. in hospital settings, particularly during the use of indwelling catheters. This study screened urine samples from 210 catheterized intensive care unit patients at Uppsala University Hospital (June 2020-September 2021), identifying 39 unique PhenePlate™-RF types across E. faecium, E. faecalis, and E. durans. E. faecium isolates showed considerable diversity, primarily within clonal complex 17 (CC17), known for its virulence and antibiotic resistance. We identified multiple lineages and sequence types (STs), such as in patient HWP143, who had isolates from both ST80 and ST22 (an ancestral CC17 lineage). Notably, metabolic adaptations, such as increased L-arabinose metabolism, and shifts in antibiotic resistance were observed. Variations and similarities in plasmid content between individual lineages suggest horizontal gene transfer. E. faecalis isolates exhibited less diversity, but still significant metabolic variability across patients and mixed infections, as seen in patient HWP051, colonized by both ST16 (CC58) and ST287. E. durans, though less common, shared important metabolic traits with E. faecium and displayed polyclonal characteristics, highlighting its potential role in UTIs and the complexity of enterococcal infections. E. durans was sometimes misidentified, underlining the need for accurate identification methods. This research underscores the importance of understanding genetic and metabolic diversity, plasmid variations, and horizontal gene transfer (HGT) in Enterococcus spp., which influence antibiotic resistance, virulence, and ultimately, treatment outcomes.IMPORTANCEOur study, performed in Uppsala University Hospital, Sweden, uncovers novel insights into the genetic and metabolic diversity of Enterococcus species, focusing on E. faecium, E. faecalis, and E. durans. Unlike prior studies, which often have focused on single lineages, we reveal multiple clones and lineages within individual catheterized intensive care unit patients, including clones from clonal complex 17 and the emerging sequence type (ST) 192, highlighting notable metabolic adaptations and shifts in antibiotic resistance. The detection of mixed colonization with varied ST types and E. durans misidentification by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry further emphasizes the challenges in Enterococcus species identification. Our findings have significant implications for understanding the complexity of Enterococcus infections, stressing the need to consider genetic and metabolic diversity to improve disease management and treatment outcomes.},
}

@article {pmid40501780,
year = {2025},
author = {Dubinkina, V and Smith, B and Zhao, C and Pino, C and Pollard, KS},
title = {Linkage of nucleotide and functional diversity varies across gut bacteria.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.06.06.658399},
pmid = {40501780},
issn = {2692-8205},
abstract = {Understanding the forces shaping genomic diversity within bacterial species is essential for interpreting microbiome evolution, ecology, and host associations. Here, we analyze over one hundred prevalent gut bacterial species using the Unified Human Gut Genome (UHGG) collection to characterize patterns of intra-specific genomic variability. Gene content divergence scales predictably with divergence in core genome single nucleotide polymorphisms (SNPs), though there is substantial variability in evolutionary dynamics across species. Overall, accessory genes exhibit consistently faster linkage decay compared to core SNPs, highlighting the fluidity of functional repertoires within species boundaries. This signal is strongest for mobile genetic elements, which show minimal linkage to core genome SNPs. Together, our findings reveal species-specific recombination regimes in the gut microbiome, underscoring the importance of accounting for horizontal gene transfer and genome plasticity in microbiome-wide association studies and evolutionary models.},
}

@article {pmid40501577,
year = {2025},
author = {Babajanyan, SG and Garushyants, SK and Wolf, YI and Koonin, EV},
title = {Evolution of antivirus defense in prokaryotes depending on the environmental virus prevalence and virome dynamics.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.27.656525},
pmid = {40501577},
issn = {2692-8205},
abstract = {UNLABELLED: Prokaryotes can acquire antivirus immunity via two fundamentally distinct types of processes: direct interaction with the virus as in CRISPR-Cas adaptive immunity systems and horizontal gene transfer (HGT) which is the main route of transmission of innate immunity systems. These routes of defense evolution are not mutually exclusive and can operate simultaneously, but empirical observations suggest that at least in some bacterial and archaeal species, one or the other route dominates the defense landscape. We hypothesized that the observed dichotomy stems from different life-history tradeoffs characteristic of these organisms. To test this hypothesis, we analyzed a mathematical model of a well-mixed prokaryote population under a stochastically changing viral prevalence. Optimization of the long-term population growth rate reveals two contrasting modes of defense evolution. In stable, predictable and fluctuating, unpredictable environments with a moderate viral prevalence, direct interaction with the virus and horizontal transfer of defense genes become the optimal routes of immunity acquisition, respectively. In the HGT-dominant mode, we observed a universal distribution of the fraction of microbes with different immune repertoires. Under very low virus prevalence, the cost of immunity exceeds the benefits such that the optimal state of a prokaryote is complete defense systems. By contrast, under very high virus prevalence, horizontal spread of defense systems dominates regardless of the stability of the virome. These findings might explain consistent but enigmatic patterns in the spread of antivirus defense systems among prokaryotes such as the ubiquity of adaptive immunity in hyperthermophiles contrasting their patchy distribution among mesophiles.

IMPORTANCE: The virus-host arms race is a major component of the evolutionary process in all organisms that drove the evolution of a broad variety of immune mechanisms. In the last few years, over 200 distinct antivirus defense systems have been discovered in prokaryotes. There are two major modes of immunity acquisition: innate immune systems spread through microbial populations via horizontal gene transfer (HGT) whereas adaptive-type immune systems acquire immunity via direct interaction with the virus. We developed a mathematical model to explore the short term evolution of prokaryotic immunity and show that in stable environments with predictable viral repertoires, adaptive-type immunity is the optimal defense strategy whereas in fluctuating environments with unpredictable virus composition, HGT dominates the immune landscape.},
}

@article {pmid40500700,
year = {2025},
author = {Salem, S and Osama, D and Abdelsalam, NA and Shata, AH and Mouftah, SF and Elhadidy, M},
title = {Comparative genomics of Acinetobacter baumannii from Egyptian healthcare settings reveals high-risk clones and resistance gene mobilization.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {803},
pmid = {40500700},
issn = {1471-2334},
mesh = {*Acinetobacter baumannii/genetics/drug effects/isolation & purification/classification ; Egypt/epidemiology ; Humans ; *Acinetobacter Infections/microbiology/epidemiology ; Anti-Bacterial Agents/pharmacology ; Pilot Projects ; Microbial Sensitivity Tests ; *Drug Resistance, Multiple, Bacterial/genetics ; Genomics ; Whole Genome Sequencing ; Virulence Factors/genetics ; Genome, Bacterial ; Gene Transfer, Horizontal ; Multilocus Sequence Typing ; beta-Lactamases/genetics ; Health Facilities ; Bacterial Proteins/genetics ; },
abstract = {BACKGROUND: Acinetobacter baumannii (A. baumannii) has emerged as a major public health threat in low- and middle-income countries (LMICs), particularly in Egypt, due to its remarkable ability to acquire and transfer resistance genes, as highlighted in the WHO bacterial Priority Pathogens List 2024 classification. This pilot study aimed to characterize 18 A. baumannii isolates from Egyptian healthcare settings, focusing on clonal lineages, antibiotic resistance determinants, horizontal gene transfer potential, and the presence of virulence factors and chromosomal mutations.

METHODS: Antimicrobial susceptibility testing was performed to determine resistance profiles using minimum inhibitory concentrations. Whole-genome sequencing was used to identify β-lactamase, carbapenemase, and other antibiotic resistance genes (ARGs), as well as mobile genetic elements (MGEs). Clonal relationships among isolates were assessed via core genome multilocus sequence typing (cgMLST).

RESULTS: Phenotypic analysis revealed that 72% of the isolates were extensively drug-resistant (XDR), exhibiting resistance to all tested antibiotics except colistin. Clonal diversity analysis identified 11 Oxford sequence types (STs), including two novel STs (ST3309[OXF] and ST3321[OXF]), and six international clonal (IC) groups, with IC2 being the most prevalent. Additionally, eight Pasteur STs were detected, with ST570[PAS] being the most frequent. The cgMLST analysis showed that two Egyptian ST570[PAS] isolates clustered with a strain from Saudi Arabia, suggesting potential regional transmission. Genomic analysis revealed the widespread dissemination of ARGs via MGEs, particularly rep plasmids and insertion sequence elements, which contributed significantly to genomic diversity and antibiotic resistance.

CONCLUSIONS: This pilot study highlights the clonal diversity of A. baumannii in Egypt and underscores the critical role of MGEs in the spread of resistance genes. Targeted genomic surveillance and infection control are essential to curb the spread of high-risk resistant A. baumannii clones in Egyptian clinical settings.},
}

*Acinetobacter baumannii/genetics/drug effects/isolation & purification/classification
Egypt/epidemiology
Humans
*Acinetobacter Infections/microbiology/epidemiology
Anti-Bacterial Agents/pharmacology
Pilot Projects
Microbial Sensitivity Tests
*Drug Resistance, Multiple, Bacterial/genetics
Genomics
Whole Genome Sequencing
Virulence Factors/genetics
Genome, Bacterial
Gene Transfer, Horizontal
Multilocus Sequence Typing
beta-Lactamases/genetics
Health Facilities
Bacterial Proteins/genetics

@article {pmid40500303,
year = {2025},
author = {Shang, KM and Ma, H and Elsheikha, HM and Wei, YJ and Zhao, JX and Qin, Y and Li, JM and Zhao, ZY and Zhang, XX},
title = {Comprehensive genome catalog analysis of the resistome, virulome and mobilome in the wild rodent gut microbiota.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {101},
pmid = {40500303},
issn = {2055-5008},
support = {No.32170538//the National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Genome, Bacterial ; Virulence Factors/genetics ; *Rodentia/microbiology ; *Bacteria/genetics/drug effects/classification/pathogenicity/isolation & purification ; Interspersed Repetitive Sequences ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; Animals, Wild/microbiology ; },
abstract = {Wild rodent's gut microbiota serves as a crucial reservoir of antibiotic resistance genes (ARGs), where antimicrobial-resistant bacteria interact with mobile genetic elements (MGEs) to facilitate horizontal gene transfer. This study analyzed 12,255 gut-derived bacterial genomes from wild rodents to characterize the distribution of ARGs and virulence factor genes (VFGs), and to identify their bacterial hosts. A total of 8119 ARGs and 7626 VFGs were identified. The most prevalent ARGs conferred resistance to elfamycin, followed by those associated with multi-class antibiotic resistance. Enterobacteriaceae, particularly Escherichia coli, harbored the highest numbers of ARGs and VFGs. A strong correlation between the presence of MGEs, ARGs, and VFGs was observed, highlighting the potential for co-selection and mobilization of resistance and virulence traits. These findings underscore the importance of expanded surveillance to monitor and mitigate the risk of transmission of resistant and potentially pathogenic bacteria from wild rodents to human and animal populations.},
}

Animals
*Gastrointestinal Microbiome/genetics
*Genome, Bacterial
Virulence Factors/genetics
*Rodentia/microbiology
*Bacteria/genetics/drug effects/classification/pathogenicity/isolation & purification
Interspersed Repetitive Sequences
Anti-Bacterial Agents/pharmacology
*Drug Resistance, Bacterial/genetics
Gene Transfer, Horizontal
Animals, Wild/microbiology

@article {pmid40499773,
year = {2025},
author = {Ma, Y and Dong, X and Sun, Y and Li, B and Ma, H and Li, H and Zhao, X and Ran, S and Zhang, J and Ye, Y and Li, J},
title = {Diversity and Functional Roles of Viral Communities in Gene Transfer and Antibiotic Resistance in Aquaculture Waters and Microplastic Biofilms.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {126636},
doi = {10.1016/j.envpol.2025.126636},
pmid = {40499773},
issn = {1873-6424},
abstract = {This study presents a comprehensive metagenomic analysis of viral communities in seawater and microplastic biofilms, uncovering their diversity, functional roles, and ecological significance. We identified 4,999 DNA and 22 RNA viral operational taxonomic units. Seawater samples exhibited greater viral diversity, while microplastic biofilms harbored specialized viral assemblages with enriched metabolic functions, particularly in carbohydrate and amino acid metabolism. Auxiliary metabolic genes were detected, suggesting viral involvement in microbial metabolism and nutrient cycling. The dominance of lytic viruses (98 and 100%) indicates a significant role in microbial regulation. Moreover, antibiotic resistance genes and virulence factors were found, highlighting microplastic biofilms as potential re2servoirs for gene transfer, raising concerns about antibiotic resistance dissemination. The detection of Klebsiella pneumoniae OmpK37 in viruses further underscores the risk of horizontal gene transfer. These findings emphasize the ecological implications of virus-host interactions in marine environments and the urgent need for continued monitoring of viral dynamics in anthropogenically influenced ecosystems.},
}

@article {pmid40498454,
year = {2025},
author = {Brezner, S and Garushyants, SK and Wolf, YI and Koonin, EV and Snir, S},
title = {Evolution of gene order in prokaryotes is driven primarily by gene gain and loss.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {24},
pages = {e2502752122},
doi = {10.1073/pnas.2502752122},
pmid = {40498454},
issn = {1091-6490},
support = {Intramural Research Program//HHS | NIH (NIH)/ ; 2021139.//US-Israel Binational Science Foundation/ ; },
mesh = {*Evolution, Molecular ; *Archaea/genetics ; *Gene Order ; Genome, Archaeal ; Genome, Bacterial ; Models, Genetic ; *Bacteria/genetics ; *Prokaryotic Cells/metabolism ; Gene Transfer, Horizontal ; *Gene Deletion ; },
abstract = {Evolution of bacterial and archaeal genomes is highly dynamic, including extensive gene gain via horizontal gene transfer (HGT) and gene loss as well as different types of genome rearrangements, such as inversions and translocations, so that gene order is not highly conserved even among closely related organisms. We sought to quantify the contributions of different genome dynamics processes to the evolution of the gene order in prokaryote genomes, relying on the recently developed, simple, stochastic model of genome rearrangement through single gene translocations ("jump" model). The jump model was completely solved analytically in our previous work and provides the exact distribution of syntenic gene block lengths (SBL) in compared genomes based on gene translocations alone. Comparing the SBL distribution predicted by the jump model with the distributions empirically observed for multiple groups of closely related bacterial and archaeal genomes, we obtained robust estimates of the genome rearrangement to gene flux (gain and loss) ratio. In most groups of bacteria and archaea, this ratio was found to be on the order of 0.1 indicating that the loss of synteny in the evolution of bacteria and archaea is driven primarily by gene gain and loss rather than by gene translocation.},
}

*Evolution, Molecular
*Archaea/genetics
*Gene Order
Genome, Archaeal
Genome, Bacterial
Models, Genetic
*Bacteria/genetics
*Prokaryotic Cells/metabolism
Gene Transfer, Horizontal
*Gene Deletion

@article {pmid40497057,
year = {2025},
author = {Mediouni, M and Diallo, AB and Makarenkov, V},
title = {Quantifying antimicrobial resistance in food-producing animals in North America.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1542472},
pmid = {40497057},
issn = {1664-302X},
abstract = {The global misuse of antimicrobial medication has further exacerbated the problem of antimicrobial resistance (AMR), enriching the pool of genetic mechanisms previously adopted by bacteria to evade antimicrobial drugs. AMR can be either intrinsic or acquired. It can be acquired either by selective genetic modification or by horizontal gene transfer that allows microorganisms to incorporate novel genes from other organisms or environments into their genomes. To avoid an eventual antimicrobial mistreatment, the use of antimicrobials in farm animal has been recently reconsidered in many countries. We present a systematic review of the literature discussing the cases of AMR and the related restrictions applied in North American countries (including Canada, Mexico, and the USA). The Google Scholar, PubMed, Embase, Web of Science, and Cochrane databases were searched to find plausible information on antimicrobial use and resistance in food-producing animals, covering the time period from 2015 to 2024. A total of 580 articles addressing the issue of antibiotic resistance in food-producing animals in North America met our inclusion criteria. Different AMR rates, depending on the bacterium being observed, the antibiotic class being used, and the farm animal being considered, have been identified. We determined that the highest average AMR rates have been observed for pigs (60.63% on average), the medium for cattle (48.94% on average), and the lowest for poultry (28.43% on average). We also found that Cephalosporines, Penicillins, and Tetracyclines are the antibiotic classes with the highest average AMR rates (65.86%, 61.32%, and 58.82%, respectively), whereas the use of Sulfonamides and Quinolones leads to the lowest average AMR (21.59% and 28.07%, respectively). Moreover, our analysis of antibiotic-resistant bacteria shows that Streptococcus suis (S. suis) and S. auerus provide the highest average AMR rates (71.81% and 69.48%, respectively), whereas Campylobacter spp. provides the lowest one (29.75%). The highest average AMR percentage, 57.46%, was observed in Mexico, followed by Canada at 45.22%, and the USA at 42.25%, which is most probably due to the presence of various AMR control strategies, such as stewardship programs and AMR surveillance bodies, existing in Canada and the USA. Our review highlights the need for better strategies and regulations to control the spread of AMR in North America.},
}

@article {pmid40495475,
year = {2025},
author = {Wang, JY and Dunon, V and Ardevol, VN and Béguet, J and Jechalke, S and Pauwelyn, E and Lavigne, R and Smalla, K and Martin-Laurent, F and Springael, D},
title = {Dynamics of IS1071 and Its Accessory Gene Functions During Start-Up of an On-Farm Biopurification System.},
journal = {Environmental microbiology},
volume = {27},
number = {6},
pages = {e70120},
doi = {10.1111/1462-2920.70120},
pmid = {40495475},
issn = {1462-2920},
support = {222625//European Union's 7th Framework Programme (FP7) for Research and Technological Development/ ; RUN/19/001//KU Leuven/ ; C14/20/063//KU Leuven/ ; G0E8122N//the Research Foundation - Flanders (FWO) and the National Natural Science Foundation of China (NSFC)/ ; 202107650033//China Scholarship Council Fellowship/ ; },
mesh = {*DNA Transposable Elements/genetics ; *Microbiota/genetics ; *Pesticides/metabolism ; *Bacteria/genetics/metabolism/classification ; Wastewater/microbiology ; Farms ; Biodegradation, Environmental ; Betaproteobacteria/genetics/metabolism ; },
abstract = {Insertion sequences (IS) are drivers of bacterial diversification by facilitating recruitment and horizontal transfer of adaptive genes involving composite transposon structures, but their evolutionary role at the community level is rarely addressed. This study explores the dynamics of IS1071 and the cargo of IS1071-associated putative composite transposons in the establishment of a pesticide-degrading microbiome in an on-farm biopurification system (BPS)-which treats pesticide-contaminated wastewater and is considered a hotspot of microbial evolution-during the crucial start-up phase. Pesticide mineralisation assays and quantitative PCR targeting pesticide catabolic genes showed that the microbial community, upon feeding on the pesticide-contaminated wastewater, rapidly evolved into a pesticide-degrading microbiome. Concomitantly, an increase in the relative abundances of several mobile genetic elements, including IS1071, was observed, as well as a striking enrichment of xenobiotic catabolic genes in the cargo of putative IS1071-flanked composite transposons. The IS1071 cargo catabolic genes diversified over time and were mainly of Betaproteobacterial origin. Clear changes in community composition were observed both in the total bacterial community and the Betaproteobacterial community. We conclude that IS1071 supports the rapid establishment of pesticide catabolism in the BPS microbiome, highlighting the contribution of IS elements to microbial community adaptation to environmental changes.},
}

*DNA Transposable Elements/genetics
*Microbiota/genetics
*Pesticides/metabolism
*Bacteria/genetics/metabolism/classification
Wastewater/microbiology
Farms
Biodegradation, Environmental
Betaproteobacteria/genetics/metabolism

@article {pmid40494306,
year = {2025},
author = {Slot, J and Hoffmeister, D},
title = {Psychedelic fungi.},
journal = {Current biology : CB},
volume = {35},
number = {11},
pages = {R513-R518},
doi = {10.1016/j.cub.2025.02.026},
pmid = {40494306},
issn = {1879-0445},
mesh = {*Hallucinogens/metabolism ; *Fungi/metabolism/genetics ; Humans ; Psilocybin/metabolism ; Animals ; },
abstract = {Several species of fungi, collectively known as 'psychedelic fungi', produce a range of psychoactive substances, such as psilocybin, ibotenic acid, muscimol and lysergic acid amides. These substances interact with neurotransmitter receptors in the human brain to induce profound psychological effects. These substances are found across multiple fungal phyla, in the mushroom-forming genera Psilocybe, Amanita, and others, and also the ergot-producing Claviceps and insect-pathogenic Massospora. The ecological roles of these psychedelics may include deterring predators or facilitating spore dispersal. Enzymes for psychedelic compound biosynthesis are encoded in metabolic gene clusters that are sometimes dispersed by horizontal gene transfer, resulting in a patchy distribution of psychedelics among species. The (re-)emerging science of these strange substances creates new opportunities and challenges for science and humanity at large.},
}

*Hallucinogens/metabolism
*Fungi/metabolism/genetics
Humans
Psilocybin/metabolism
Animals

@article {pmid40493666,
year = {2025},
author = {Gumustop, I and Genel, I and Kurt, IC and Ortakci, F},
title = {Comparative genomics of Lentilactobacillus buchneri reveals strain-level hyperdiversity and broad-spectrum CRISPR immunity against human and livestock gut phages.},
journal = {PloS one},
volume = {20},
number = {6},
pages = {e0325832},
pmid = {40493666},
issn = {1932-6203},
mesh = {Animals ; Humans ; *Bacteriophages/genetics/immunology ; *Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; Genomics ; Livestock/microbiology/virology ; Cattle ; Genome, Bacterial ; Plasmids/genetics ; Prophages/genetics ; },
abstract = {This study conducted a comparative genomic investigation of 40 strains of Lentilactobacillus buchneri isolated from various environments-including fermented foods, silage, cattle rumen, and the nasopharynx-to identify species-level diversity and assess their CRISPR immunity. An average genome size of 2.55 ± 0.07 Mb, a GC content of 44.18 ± 0.15%, and 2444 ± 83 coding sequences were identified. Prophages were found in all strains except for two, while 17 strains contained plasmids. No genes associated with bacteriocins were identified. CRISPR analysis revealed the presence of 42 Type II-A and 45 Type I-E systems, with each strain having at least one Type II-A system (~ 2 systems per strain). Among the 33 tested strains, 29 encoded complete LbCas9 proteins, consisting of 1371 amino acids. In-silico analysis of PAM in Type II-A systems revealed a 5'-DNAWDHV-3' motif, with a noted preference for 5'-AAAA-3' at positions 3-6. The spacers found in CRISPR arrays targeted proteins involved in plasmid mobilization as well as components of phage tails, indicating their roles in inhibiting horizontal gene transfer and providing defense against phages. Remarkably, 27 spacers from 24 strains were found to match phages associated with human gut microbiomes, with several showing the ability to cross-target phages from livestock, kefir, and wastewater. This research expands the genomic understanding of L. buchneri from 10 to 40 genomes, uncovering the dynamics of CRISPR-phage co-evolution. The defined PAM preferences of the identified CRISPR systems, together with the broad predicted target range of their spacers, highlight their potential for biotechnological applications-most notably targeted CRISPRization of L. buchneri strains and in-silico-guided phage control during fermentation. These findings deepen our understanding of the ecological adaptability of L. buchneri and provide a foundation for future industrial exploitation of its native CRISPR immunity.},
}

Animals
Humans
*Bacteriophages/genetics/immunology
*Clustered Regularly Interspaced Short Palindromic Repeats/genetics
Genomics
Livestock/microbiology/virology
Cattle
Genome, Bacterial
Plasmids/genetics
Prophages/genetics

@article {pmid40353659,
year = {2025},
author = {Sobkowiak, A and Schwierzeck, V and van Almsick, V and Scherff, N and Schuler, F and Bessonov, K and Robertson, J and Harmsen, D and Mellmann, A},
title = {The dark matter of bacterial genomic surveillance-antimicrobial resistance plasmid transmissions in the hospital setting.},
journal = {Journal of clinical microbiology},
volume = {63},
number = {6},
pages = {e0012125},
doi = {10.1128/jcm.00121-25},
pmid = {40353659},
issn = {1098-660X},
support = {SEED 019/23//Interdisciplinary Center of Clinical Research, University Muenster/ ; NUM 2.0 Grant No. 01KX2121 Project: Collateral Effects of Pandemics - CollPan//German Federal Ministry of Education and Research (BMBF) Network of University Medicine 2.0/ ; },
mesh = {*Plasmids/genetics ; Humans ; Multilocus Sequence Typing ; *Drug Resistance, Multiple, Bacterial/genetics ; Whole Genome Sequencing ; Tertiary Care Centers ; Anti-Bacterial Agents/pharmacology ; *Cross Infection/microbiology/epidemiology/transmission ; *Gram-Negative Bacteria/genetics/drug effects/isolation & purification ; Genome, Bacterial ; *Gram-Negative Bacterial Infections/microbiology/epidemiology/transmission ; Gene Transfer, Horizontal ; Hospitals ; Molecular Epidemiology ; Microbial Sensitivity Tests ; },
abstract = {UNLABELLED: Dissemination of antimicrobial resistance (AMR) is a growing global public health burden. The aim of this study was to characterize AMR plasmid transmissions within a tertiary care hospital and identify relevant AMR plasmid transmission pathways. During an 18-month observation period, 540 clinical gram-negative multidrug-resistant bacterial (MDRB) isolates were collected during routine hospital surveillance and subjected to Pacific Biosciences long-read whole genome sequencing. Potential clonal transmissions were determined based on core genome multilocus sequence typing (cgMLST), and plasmid transmissions were detected using a novel real-time applicable tool for plasmid transmission detection. Potential transmissions were validated using epidemiological data. Among the 471 eligible MDRB isolates, we detected 1,539 plasmids; 84.41% of these were circularized. We identified 38 potential clonal transmissions in 24 clusters based on cgMLST and 121 potential plasmid transmissions in 24 clusters containing genetically related AMR plasmids. Among the latter clusters, 10 contained different multilocus sequence types (involving 2-38 isolates, median: 3 isolates), and nine contained multiple species (2-18 isolates, median: 4). Epidemiological data confirmed 19 clonal transmissions (in seven clusters) and an additional 12 plasmid transmissions (within eight plasmid clusters). Among these, we identified seven cases of intra-host and five patient-to-patient plasmid transmissions. We demonstrate that intra-host and patient-to-patient transmissions of AMR plasmids can be identified by combining long-read sequencing with real-time applicable tools during routine molecular surveillance. In addition, our study highlights that more than a decade of bacterial genomic surveillance missed at least one-third of all AMR transmission events due to plasmids.

IMPORTANCE: Antimicrobial resistance (AMR) poses a significant threat to human health. Most AMR determinants are encoded extra-chromosomally on plasmids. Although current infection control strategies primarily focus on clonal transmission of multidrug-resistant bacteria, until today, AMR plasmid transmission routes are neither understood nor analyzed in the hospital setting. In our study, we simultaneously determined both clonal, that is, based on chromosomes, and AMR plasmid transmissions during routine molecular surveillance by combining long-read sequencing with a novel real-time applicable software tool and validated all potential transmission events with epidemiological data. Our analysis determined not only the yet unknown plasmid transmissions within healthcare facilities or within the community but also resulted, in addition to the clonal transmissions, in at least a third more transmissions due to AMR plasmids.},
}

*Plasmids/genetics
Humans
Multilocus Sequence Typing
*Drug Resistance, Multiple, Bacterial/genetics
Whole Genome Sequencing
Tertiary Care Centers
Anti-Bacterial Agents/pharmacology
*Cross Infection/microbiology/epidemiology/transmission
*Gram-Negative Bacteria/genetics/drug effects/isolation & purification
Genome, Bacterial
*Gram-Negative Bacterial Infections/microbiology/epidemiology/transmission
Gene Transfer, Horizontal
Hospitals
Molecular Epidemiology
Microbial Sensitivity Tests

@article {pmid40315481,
year = {2025},
author = {Ottenbrite, M and Yilmaz, G and Chan, M and Devenish, J and Kang, M and Dan, H and Lau, C and Capitani, S and Carrillo, C and Bessonov, K and Nash, J and Topp, E and Guan, J},
title = {Food-borne microbes influence conjugative transfer of antimicrobial resistance plasmids in pre-disturbed gut microbiome.},
journal = {Canadian journal of microbiology},
volume = {71},
number = {},
pages = {1-11},
doi = {10.1139/cjm-2024-0168},
pmid = {40315481},
issn = {1480-3275},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects/genetics ; Mice ; *Conjugation, Genetic ; *Plasmids/genetics ; Anti-Bacterial Agents/pharmacology ; Salmonella typhimurium/genetics/drug effects ; *Gene Transfer, Horizontal ; Feces/microbiology ; Bacteria/genetics/drug effects ; Female ; Food Microbiology ; Streptomycin/pharmacology ; Drug Resistance, Multiple, Bacterial/genetics ; Drug Resistance, Bacterial ; },
abstract = {Ingestion of antibiotic-resistant bacteria following antibiotic treatments may lead to the transfer of antimicrobial resistance genes (ARGs) within a disturbed gut microbiota. However, it remains unclear whether and how microbes present in food matrices influence ARG transfer. Thus, a previously established mouse model, which demonstrated the conjugative transfer of a multi-drug resistance plasmid (pIncA/C) from Salmonella Heidelberg (donor) to Salmonella Typhimurium (recipient), was used to assess the effects of food-borne microbes derived from fresh carrots on pIncA/C transfer. Mice were pre-treated with ampicillin, streptomycin, sulfamethazine, or left untreated as a control to facilitate bacterial colonization. Contrary to previous findings where high-density colonization of the donor and recipient bacteria occurred in the absence of food-borne microbes, the presence of these microbes resulted in a low abundance of S. Typhimurium and no detection of S. Typhimurium transconjugants in the fecal samples from any of the mice. However, in mice pre-treated with streptomycin, a significant reduction in microbial species richness allowed for the significant enrichment of Enterobacteriaceae and pIncA/C transfer to bacteria from the genera Escherichia, Enterobacter, Citrobacter, and Proteus. These findings suggest that food-borne microbes may enhance ARG dissemination by influencing the population dynamics of bacterial hosts within a pre-disturbed gut microbiome.},
}

Animals
*Gastrointestinal Microbiome/drug effects/genetics
Mice
*Conjugation, Genetic
*Plasmids/genetics
Anti-Bacterial Agents/pharmacology
Salmonella typhimurium/genetics/drug effects
*Gene Transfer, Horizontal
Feces/microbiology
Bacteria/genetics/drug effects
Female
Food Microbiology
Streptomycin/pharmacology
Drug Resistance, Multiple, Bacterial/genetics
Drug Resistance, Bacterial

@article {pmid40492734,
year = {2025},
author = {Samadi, ZF and Hodroj, ZR and Jabbour, ZC and Hussein, HM and Kurdi, A and Shoukair, D and Bitar, RF and Chebaro, HH and Al Semaani, JMJ and Al Hajjar, MT and Zeaiter, HH and Hamadeh, L and Mahfouz, R and Noueihed, LH and Hachem, JH and Khalil, MI and El Hajj, R and Matar, GM and Abou Fayad, AG},
title = {Nationwide surveillance of carbapenem-resistant Gram-negative pathogens in the Lebanese environment.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0193224},
doi = {10.1128/aem.01932-24},
pmid = {40492734},
issn = {1098-5336},
abstract = {UNLABELLED: Gram-negative ESKAPE pathogens with carbapenem resistance pose a significant health threat. Despite extensive research on the spread of these pathogens within Lebanese hospital settings, their emergence in environmental settings remains understudied. This study aimed to explore the environmental spread of carbapenem resistance among Gram-negative bacteria isolated from environmental samples in nine districts across Lebanon. A total of 250 samples were collected from wild animals, sewage, water, and soil between June 2022 and September 2023. Samples were streaked on MacConkey agar plates supplemented with 2 mg/L meropenem. Bacterial species were identified primarily using API20E. Antimicrobial susceptibility profiles were determined by the disk diffusion method and the Vitek 2 compact system. Meropenem-resistant Gram-negative bacteria were further characterized by whole-genome sequencing, and each of the bacterial species, sequence types, resistance genes, and plasmids was detected by sequence data analysis. We successfully isolated 130 carbapenem-resistant isolates from various samples, 67 of which belonged to the ESKAPE pathogens list and showed a multidrug-resistant (MDR) profile. The distribution of the latter was as follows: Escherichia coli (65.67%), Acinetobacter baumannii (16.42%), Pseudomonas aeruginosa (11.94%), and Klebsiella pneumoniae (5.97%). Several carbapenem resistance genes were detected, with a prevalence of blaNDM-5 in Escherichia coli and Klebsiella pneumoniae, blaIMP-1 and mexAB-OprM efflux pumps in Pseudomonas aeruginosa, and blaOXA-23 in Acinetobacter baumannii. Our findings revealed a widespread distribution of carbapenem-resistant ESKAPE bacteria in Lebanon, underscoring the significant public health risk posed by these pathogens. This highlights the urgent need to address the dissemination of antibiotic resistance in Lebanese environmental settings.

IMPORTANCE: The emergence of antimicrobial resistance (AMR) extremely burdens public health and increases morbid and mortal threats in Lebanon. While the majority of the studies in our country target antimicrobial resistance in clinical settings, fewer studies focus on antimicrobial resistance dissemination in the environment. The significance of our research is that it sheds light on the environment as a less explored yet equally crucial sector in the spread of AMR. Here, we isolated carbapenemase-producing bacteria (Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Acinetobacter baumannii) that were categorized as multidrug resistant (MDR) from diverse environmental sources in multiple provinces across Lebanon. The finding of carbapenem-resistant bacteria carrying plasmids represents a potential risk due to the possible spread of resistance genes via horizontal gene transfer across the environment and hospital settings. This highly recommends the implementation of regular surveillance to monitor the spread of antimicrobial resistance among environmental bacteria, which consequently leads to its spread within communities and thus poses a great threat to human health.},
}

@article {pmid40492084,
year = {2025},
author = {Vezina, B and Morampalli, BR and Nguyen, HA and Gomez-Simmonds, A and Peleg, AY and Macesic, N},
title = {The rise and global spread of IMP carbapenemases (1996-2023): a genomic epidemiology study.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.25.25328332},
pmid = {40492084},
abstract = {BACKGROUND: IMP carbapenemases confer extensive drug resistance and are increasingly noted worldwide. Despite this, little is known regarding the global epidemiology of IMP carbapenemases.

METHODS: We comprehensively identified bla IMP genes in all publicly available bacterial genomes, then systematically analysed the distribution of variants across species, lineages, plasmids and mobile elements, examining patterns over time, across geographic regions and by source. Structural analysis of IMP variants was performed.

FINDINGS: 4,556 bla IMP -containing genomes were identified from 1996-2023, including 52 bla IMP variants across 93 bacterial species. Key variants (bla IMP-1 , bla IMP-4 , bla IMP-7 , bla IMP-8 and bla IMP-13) achieved global endemicity, while bla IMP-26 and bla IMP-27 were regionally endemic in Southeast Asia and North America, respectively. bla IMP dissemination was driven by horizontal gene transfer, facilitating inter-species spread. Proliferation of multidrug-resistant Enterobacter hormaechei , Pseudomonas aeruginosa and Klebsiella pneumoniae lineages led to local outbreaks. Dereplication removed 3,175/4,556 (69.9%) genomes, indicating that most bla IMP -containing genomes were highly related. bla IMP variants were associated with mobile genetic element combinations including class 1 integrons and insertion sequences (99.7%), aiding mobilisation into ≥52 plasmid clusters, predominantly IncHI2A, IncN, IncL/M and IncC. Genomes of environmental and animal origin accounted for 10.0% and 1.1% of the dataset, respectively. Evidence of cross-source transmission was limited, with most spillover occurring between genomes of human and environmental origin. Structural analysis revealed a conserved carbapenemase structure (mean lDDT 0.977), with convergent missense mutations at seven catalytically relevant sites.

INTERPRETATION: Global analysis enabled us to historically reconstruct the emergence and variant-specific epidemiologies of bla IMP carbapenemase genes. Intersecting mobile elements enabled bla IMP genes to spread across multiple plasmids and bacterial genera, facilitating global and multi-source spread within a One Health framework. Additionally, convergent evolutionary patterns indicate that IMP variants may continue evolving, potentially evading novel beta-lactam antimicrobial agents.

FUNDING: NHMRC EL1 (APP1176324) to N.M.; NHMRC PF (APP1117940) to A.Y.P.; NIH/NIAID R01AI175414 to A.G-S.

RESEARCH IN CONTEXT PANEL: Evidence before this study: Despite being a major cause of carbapenem resistance in Gram negative infections, little is known about the global epidemiology of IMP carbapenemases. IMP carbapenemases are metallo-beta-lactamases that were first identified in 1991 and have evolved into 96 different IMP variants. On May 21 2025, we searched all published reports available in PubMed using the terms "'IMP' and 'carbapenemase' genomics NOT (Review[Publication Type]) NOT (Case Reports[Publication Type]) NOT PCR" with no language restrictions and no publication date restrictions. We identified 223 articles, 62 and 121 of which reported single species or a single study centre/country, respectively. Only 6 articles employed genomics to examine multi-species and multi-geographical isolates, though this was in the context of carbapenem resistance more broadly rather than IMP carbapenemases specifically. The most relevant study included 38 globally distributed genomes across four species and tracked seven blaIMP variants across mobile genetic elements.Added value of this study: To our knowledge, this global characterisation provides the most comprehensive account of bla IMP carbapenemase gene epidemiology. To analyse the global distribution and diversity of bla IMP genes, we compiled all available public genome data resulting in a dataset of 4,646 genomes. This has allowed us to identify local, regional and international spread of bla IMP variants and determine the contributions of clonal expansion, plasmid proliferation and co-localised mobile genetic elements. We demonstrated that key bla IMP variants display global (IMP-1, IMP-4, IMP-7, IMP-8 and IMP-13) and regional (IMP-26 within Southeast Asia and IMP-27 within North America) endemicity and that these patterns have been previously unacknowledged, reframing the previous understanding that IMP carbapenemases were largely confined to the Asia-Pacific region. Our observation of convergent evolutionary patterns raise concern that IMP variants may continue to evolve, potentially evading new β-lactam antimicrobials. This analysis has revealed the under-recognised contribution IMP carbapenemases make to global carbapenem resistance. Implications of all the available evidence: These findings provide the first comprehensive atlas of bla IMP carbapenemase gene dissemination and underscore the silent global spread of IMP carbapenemases. We note the critical need for enhanced surveillance systems, particularly in low- and middle-income countries, that can detect complex plasmid-mediated and mobile genetic element-associated spread, as we noted with bla IMP carbapenemase genes. Moreover, our analyses show that systematic sampling across human, animal, and environmental reservoirs is crucial to address the One Health dimensions of emerging antimicrobial resistance threats. The study provides a framework for future interventions aimed at tracking and stopping the spread of IMP carbapenemases and calls for co-ordinated, real-time public health responses to this growing challenge.},
}

@article {pmid40490413,
year = {2025},
author = {Gang, D and Li, Z and Yu, H and Hu, C and Qu, J},
title = {PFAS Stress on Functional Expression of Periphyton Communities and Trade-off Strategies for Horizontal/Vertical Transfer of Resistance Genes.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c02692},
pmid = {40490413},
issn = {1520-5851},
abstract = {The dissemination of antibiotic resistance genes (ARGs) induced by perfluoroalkyl and polyfluoroalkyl substances (PFAS) and their ecological impacts have gained significant attention. Periphyton communities on sediments play crucial hydroecological roles and serve as bioindicators of PFAS contamination. However, research on their microbial structure and ARG dissemination in response to PFAS remains limited. This study explored how PFAS stress influences periphyton communities' ecological functions and ARGs dynamics. PFAS varying exposure inhibited communities' formation by decreasing biomass (3.0-26.2%) and significantly reducing protein and polysaccharides (p < 0.05) of periphyton communities. Methanogenic archaea abundance increased by 4.79-159290 times, while Variovorax and Nitrospira decreased by 1266.1-2303.5 and 36.1-140.4 times, respectively. Notably, PFAS enhanced ARGs families (multidrug, aminoglycoside, and glycopeptide) and subtypes (macB, evgS, tetA58, and bcrA), strengthening correlations between the mobile genetic elements (MGEs) and antibiotic efflux (R[2] = 0.941) or target alteration (R[2] = 0.961). Horizontal gene transfer (HGT) mediated by MGEs played a dominant role in ARGs dissemination compared to vertical gene transfer in periphyton communities. Mechanistic insights revealed that PFAS-induced reactive oxygen species elevation, increased membrane permeability, enhanced energy provision, and overexpression of adherent molecular genes collectively facilitated HGT-driven ARGs spread. This study provides new insights into the complex interactions between PFAS and ARGs and its potential risks in microbial habitats.},
}

@article {pmid40488491,
year = {2025},
author = {Franco, MEE and Nickerson, MN and Bowen, BP and Louie, K and Northen, TR and U'Ren, JM},
title = {Hyperdiverse, bioactive, and interaction-specific metabolites produced only in co-culture suggest diverse competitors may fuel secondary metabolism of xylarialean fungi.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0046825},
doi = {10.1128/msystems.00468-25},
pmid = {40488491},
issn = {2379-5077},
abstract = {Xylariales is one of the largest and most ecologically diverse fungal orders that is well-known for its chemical diversity. Enhanced secondary metabolism of Xylariales taxa is associated with increased gene duplication and horizontal gene transfer (HGT) of biosynthetic gene clusters (BGCs), especially in generalist taxa with both greater saprotrophic abilities and broader host ranges as foliar endophytic symbionts. Thus, one hypothesis for BGC diversification among more generalist fungi is that diverse competitive interactions-in both their free-living and symbiotic life stages with many hosts-may exert selective pressure for HGT and a diverse metabolic repertoire. Here, we used untargeted metabolomics to examine how competition (pairwise co-cultures) between seven xylarialean fungi influenced their metabolite production. Of the >9,000 total features detected, 6,115 and 2,071 were over-represented in co-cultures vs monocultures, respectively. For each strain, each additional co-culture interaction resulted in an 11- to 14-fold increase in metabolite richness compared to monocultures, reflecting the limited amount of metabolite overlap among different co-culture combinations. Phylogenetic relatedness and BGC content did not impact the diversity of metabolites produced in co-culture; however, co-cultures between more ecologically distinct fungi elicited the strongest metabolic response. Overall, the diversity, specificity, and putative bioactivity of metabolites over-represented in co-culture support the role of widespread and diverse competitive fungal interactions to drive xylarialean metabolic diversification. Additionally, as fungal-produced plant hormones were only detected in co-culture, our results reveal the potential for in planta interactions among fungal endophytes to influence the host plant.IMPORTANCESaprotrophic and endophytic xylarialean fungi are among the most prolific producers of bioactive secondary metabolites, with numerous industrial uses as antibiotics, pharmaceuticals, and insecticidal toxins. Fungal secondary metabolites are typically encoded in biosynthetic gene clusters (sets of physically clustered genes), but the products of most clusters are unknown as the genes are not active in typical culture conditions. Co-cultures can help to "turn on" fungal secondary metabolite production, yet factors that can influence co-culture outcomes are largely unknown. Here, we used untargeted metabolomics to assess how differences in genomic content, ecology, and phylogenetic relatedness among seven diverse xylarialean fungal strains impact metabolic production in co-culture. As expected, co-culturing significantly increased metabolite diversity, as well as the abundance of putatively bioactive metabolites. Each new pairwise combination produced different metabolites, indicative of strain-specific responses to competitors. This new information will enable further characterization of the immense biotechnological potential of xylarialean fungi.},
}

@article {pmid40485081,
year = {2025},
author = {Tran, V and Langschied, F and Muelbaier, H and Dosch, J and Arthen, F and Balint, M and Ebersberger, I},
title = {Feature architecture-aware ortholog search with fDOG reveals the distribution of plant cell wall-degrading enzymes across life.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msaf120},
pmid = {40485081},
issn = {1537-1719},
abstract = {The decomposition of plant material is a key driver of the global carbon cycle, traditionally attributed to fungi and bacteria. However, some invertebrates also possess orthologs to bacterial or fungal cellulolytic enzymes, likely acquired via horizontal gene transfer. This reticulated mode of evolution necessitates ortholog searches in large taxon sets to comprehensively map the repertoire of plant cell wall degrading enzymes (PCDs) across the tree of life, a task surpassing capacities of current software. Here, we use fDOG, a novel profile-based ortholog search tool to trace 235 potential PCDs across more than 18,000 taxa. fDOG allows to start the ortholog search from a single protein sequence as a seed, it performs on par with state-of-the-art software that require the comparison of entire proteomes, and it is unique in routinely scoring protein feature architecture differences between the seed protein and its orthologs. Visualizing the presence-absence patterns of PCD orthologs using a UMAP highlights taxa where recent changes in the enzyme repertoire indicate a change in lifestyle. Three invertebrates have a particularly rich set of PCD orthologs encoded in their genome. Only few of the orthologs show differing protein feature architectures relative to the seed that suggest functional modifications. Thus, the corresponding species represent lineages within the invertebrates that may contribute to the global carbon cycle. This study shows how fDOG can be used to create a multi-scale view on the taxonomic distribution of a metabolic capacity that ranges from tree of life-wide surveys to individual feature architecture changes within a species.},
}

@article {pmid40473141,
year = {2025},
author = {Luo, Y and Liao, H and Wu, L and Wu, M and Luo, Y and Yao, Y and Ji, W and Gao, L and Xia, X},
title = {Temperature adaptability drives functional diversity and horizontal gene transfer within microbial communities in Daqu solid-state fermentation.},
journal = {Bioresource technology},
volume = {433},
number = {},
pages = {132770},
doi = {10.1016/j.biortech.2025.132770},
pmid = {40473141},
issn = {1873-2976},
abstract = {The spontaneous solid-state fermentation of high-temperature Daqu (HTD) is a temperature-dependent stacking bioprocessing for enriching microbiota and enzymes to guarantee efficient substrate utilization and fermentation. However, there is a lack of clarity regarding how temperature adaptability affects HTD microbial assembly, domestication direction, and metabolic profile. Here, the flavor substances, microbial assembly, metabolic network, and horizontal gene transfer (HGT) events of three HTDs from Renshu (RS), Jiushang (JS), and Maoyuan (MY) were analyzed. 125 volatile compounds were identified, tetramethylpyrazine, 3-methyl-butanoic acid, phenylethyl alcohol, and trimethylpyrazine were clarified as the typical flavor substances. Bacillus and Kroppenstedtia were the shared dominant bacterial genera. Paecilomyces, Aspergillus, Rasamsonia, and Lichtheimia were dominant fungal genera. Differences in flavor metabolism, microbial structure, and key enzyme metabolism are strongly correlated with sample distance. As proximity decreases, the microbial structural and functional metabolic traits tend to exhibit greater similarity. The frequency of HGT events was analyzed using MetaCHIP, 49, 9 and 69 groups of HGT events occurred in RS, JS, and MY, respectively. HGT events occurred most abundantly in Bacillaceae, and the microbial taxa with a closer phylogenetic relationship possessed the highest incidence of HGT. Specifically, the occurrence of HGT was mainly associated with high-temperature adaptability. It was also linked to characteristic flavor metabolism. Our results revealed the effects of temperature stress on microbial regulation of HTD and adaptive transfer of relevant genes in stacked fermented HTDs. This work provides important insights into HTD quality classification and regulation of solid-state fermentation quality and efficiency through microbial domestication.},
}

@article {pmid40473138,
year = {2025},
author = {Wang, F and Li, Y and Zhang, L and Su, Y and Zhang, Y and Hong, S and Zhan, M and Xie, B},
title = {Biochar alleviates adverse effects of polystyrene microplastics on anaerobic digestion performance of food waste and antibiotic resistance gene propagation.},
journal = {Bioresource technology},
volume = {434},
number = {},
pages = {132771},
doi = {10.1016/j.biortech.2025.132771},
pmid = {40473138},
issn = {1873-2976},
abstract = {This study systematically evaluated the efficacy of feedstock-derived biochars (maize straw, rice husk, bamboo) in mitigating polystyrene microplastic (PSMP)-induced inhibition of food waste anaerobic digestion performance and antibiotic resistance gene (ARG) dissemination. Biochar addition increased cumulative methane production by 4.3%-8.3% and reduced total ARG absolute abundance by 35.5%-72.1%. Maize straw-derived biochar demonstrated superior mitigation capacity, attributed to its elevated specific surface area, functional group density, and electrical conductivity compared to other biochar. Mechanistically, biochar alleviated PSMP-induced inhibition of organic conversion and acid accumulation through metabolic pathway enhancement. Biochar enhanced methanogenesis by facilitating direct interspecies electron transfer and enriching diverse methanogenic archaea, thereby promoting metabolic pathway diversification. Additionally, biochar reduced ARG abundance through direct adsorption, reactive oxygen species suppression, selective inhibition of potential host bacteria, and horizontal gene transfer interference. This study confirmed that biochar addition simultaneously mitigates PSMP-induced suppression of methanogenesis and ARG propagation while elucidating the underlying mechanisms.},
}

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

*Gene Transfer, Horizontal
Humans

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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