@article {pmid41313384,
year = {2025},
author = {Pal, R and Poddar, BJ and D Pandit, P and Purohit, HJ and Warke, R and Warke, GM},
title = {Pan-genome analysis of Morganella morganii reveals niche-specific selection of functional traits: friend or foe?.},
journal = {Archives of microbiology},
volume = {208},
number = {1},
pages = {40},
pmid = {41313384},
issn = {1432-072X},
mesh = {*Genome, Bacterial ; *Morganella morganii/genetics/isolation & purification/drug effects/classification ; Gene Transfer, Horizontal ; Anti-Bacterial Agents/pharmacology ; Multigene Family ; Drug Resistance, Bacterial/genetics ; Phylogeny ; Wastewater/microbiology ; Animals ; },
abstract = {Morganella morganii exemplifies a typical case of an open pangenome, where genes move intra- and interspecies via horizontal gene transfer. Through pangenome analysis, the study maps three agriculture isolates; M. morganii with strong plant growth promoting (PGP) activity, along with 78 publicly available genomes from clinical, food, wastewater, and animal sources. The analysis showed 20,860 gene clusters with only 9.99% core genes and a discriminating distribution of 75.20% cloud genes across different niches. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed 33, 36, and 38 genes related to nutrient solubilization in M. morganii isolates HM01, HM02, and HM03, respectively. Chemotaxis genes, crucial for stress response, were most abundant in HM03 (30), followed by HM01 (17) and HM02 (27). Additionally, numerous biosynthetic gene clusters encoding antibacterial and antifungal metabolites were identified. Clinical and wastewater isolates harboured a higher number of mobile genetic element (MGE) linked antimicrobial resistance (AMR) genes that confer resistance to 15 antibiotic classes. These AMR genes were predominantly plasmid-borne and found to transfer in M. morganii from clinical pathogens such as E. coli and A. baumannii. This study indicates that habitat pressure creates the scenario for selection of functional traits which enables the ecosystem specific survival of M. morganii. Together, the present investigation provides important insight into the genomic diversity and remarkable PGP potential of M. morganii strains for sustainable agriculture. The pangenome analysis proposes that detailed investigation is needed to confirm their efficacy as PGP bacteria and to distinguish them from pathogenic strains.},
}

*Genome, Bacterial
*Morganella morganii/genetics/isolation & purification/drug effects/classification
Gene Transfer, Horizontal
Anti-Bacterial Agents/pharmacology
Multigene Family
Drug Resistance, Bacterial/genetics
Phylogeny
Wastewater/microbiology
Animals

@article {pmid41313000,
year = {2025},
author = {Zhang, R and Liu, P and Bai, J and Zhu, K and Liu, Y and Roberts, AP and Pan, Y and Li, J},
title = {Phylogenetic and genomic insights into magnetosome biomineralization in magnetotactic Alphaproteobacteria.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0212125},
doi = {10.1128/aem.02121-25},
pmid = {41313000},
issn = {1098-5336},
abstract = {Magnetotactic bacteria (MTB) biomineralize intracellular, membrane-enclosed magnetite or greigite nanocrystals (magnetosomes). How magnetosome gene clusters (MGCs) control magnetosome morphology and evolve across lineages remains central to reconstructing the history of magnetotaxis. Here, we report five uncultured MTB strains from Yuyuantan Lake (Beijing, China), all within Rhodospirillales order (Alphaproteobacteria class). Using phylogenetics, fluorescence in situ hybridization-scanning electron microscopy, and transmission electron microscopy, we show that magnetosome morphology is more strongly constrained by phylogeny than by cell morphology. Whole-genome comparisons and MGC phylogenies indicate that vertical inheritance predominates at the genus level, whereas topological incongruences reveal additional processes, notably horizontal transfer and gene duplication. In particular, the presence of a canonical mamAB operon together with a duplicated mamAB-2 cluster supports inter-genus horizontal gene transfer between Magnetospirillum and Paramagnetospirillum. These findings refine evolutionary models by showing that conserved MGC architectures provide a stable scaffold for magnetosome biomineralization while permitting diversification within the Alphaproteobacteria class.IMPORTANCEMagnetotactic bacteria (MTB) build intracellular magnetic nanoparticles (magnetosomes) that guide navigation and influence biogeochemical cycling. Yet how the underlying genes map onto ancestry and crystal shape remains unclear. Pairing quantitative crystal-morphology statistics with phylogenomic analysis for MTB from the Rhodospirillales order, we show that magnetosome traits carry a stronger phylogenetic signal than cell shape. Newly recovered uncultured strains broaden Paramagnetospirillum diversity, and a high-quality genome (YYTV-2) represents a novel species within the rarely studied Candidatus Magneticavibrio. Analyses of both the canonical mamAB operon and a duplicated mamAB-2 cluster indicate predominantly vertical inheritance, with horizontal transfer and gene duplication introducing modular variation. These results tighten genotype-mineral phenotype links, improving the interpretation of magnetofossils and MTB as indicators of environmental change.},
}

@article {pmid41312414,
year = {2025},
author = {Temesgen, AB and Shiferaw, SA},
title = {Antimicrobial Multidrug Resistance and Mechanisms of Action: An Overview.},
journal = {BioMed research international},
volume = {2025},
number = {},
pages = {8847267},
pmid = {41312414},
issn = {2314-6141},
mesh = {Humans ; *Anti-Infective Agents/therapeutic use/pharmacology ; *Drug Resistance, Multiple, Bacterial/genetics/drug effects ; *Drug Resistance, Multiple/genetics/drug effects ; Methicillin-Resistant Staphylococcus aureus/drug effects/pathogenicity/genetics ; Animals ; },
abstract = {Antimicrobial multidrug resistance is the ability of microorganisms to withstand the effects of several antimicrobial agents, presenting a major challenge to modern healthcare systems worldwide. Although considerable research has been conducted, the molecular and evolutionary mechanisms underlying resistance are still not completely understood. This review brings together current knowledge to explain how resistance originates, spreads, and persists in different pathogens. Microorganisms may show primary resistance, which arises naturally without prior exposure to drugs, or acquired resistance, which develops after contact with antimicrobial agents. Intrinsic resistance is related to structural or functional traits that are naturally present in specific species. Strains that are extensively resistant demonstrate survival against a wide range of important drugs, while clinical resistance becomes evident when standard treatments fail to control infections effectively. Pathogens employ several mechanisms, including enzymatic inactivation of drugs, modification of target sites, reduced drug uptake, and active efflux systems. Parasitic and fungal pathogens often rely on impaired drug transport and altered molecular targets, whereas viruses adopt multiple strategies to escape the activity of antiviral drugs. The appearance of highly resistant organisms such as methicillin-resistant Staphylococcus aureus reflects the growing threat of so-called superbugs. The rapid spread of resistance, driven by genetic mutations and horizontal gene transfer, highlights its ability to disseminate quickly within microbial populations. A clear understanding of these molecular processes is essential to guide the development of new therapeutic strategies, improve clinical management, and strengthen global efforts to control antimicrobial resistance.},
}

Humans
*Anti-Infective Agents/therapeutic use/pharmacology
*Drug Resistance, Multiple, Bacterial/genetics/drug effects
*Drug Resistance, Multiple/genetics/drug effects
Methicillin-Resistant Staphylococcus aureus/drug effects/pathogenicity/genetics
Animals

@article {pmid41312397,
year = {2025},
author = {Shawa, M and Kamboyi, HK and Chambaro, H and Hayashida, K and Nao, N and Chizimu, J and Nundwe, M and Zorigt, T and Kawai, N and Ogata, S and Ndebe, J and Nsofwa, M and Sinjani, M and Nasilele, SJ and Samutela, M and Simbotwe, M and Changula, K and Sawa, H and Hang'ombe, BM and Suzuki, Y and Kajihara, M and Higashi, H},
title = {Genomic characterization of cefotaxime-resistant Proteobacteria isolated from a bat-harboring cave in Zambia.},
journal = {New microbes and new infections},
volume = {68},
number = {},
pages = {101661},
pmid = {41312397},
issn = {2052-2975},
abstract = {Bats are widely recognized as reservoirs of emerging and re-emerging pathogens, and their ecological interactions with humans and livestock present important opportunities for the transmission of infectious agents and antimicrobial resistance (AMR). However, little is known about the occurrence of resistant bacteria in bat-associated environments in Zambia or their potential role in the maintenance of AMR outside clinical and agricultural settings. This study investigated the genomic characteristics of cefotaxime-resistant Proteobacteria isolated from bat fecal droppings collected at Leopards Hill Cave, an established hotspot for zoonotic pathogens. Four hundred bat fecal samples were cultured on cefotaxime-supplemented MacConkey agar, and those exhibiting bacterial growth were subjected to antimicrobial susceptibility testing and whole-genome analysis. Of the 400 samples processed, four (1 %) yielded growth, resulting in three bacterial species: Pseudomonas aeruginosa (n = 1), Enterobacter mori (n = 1), and Brucella intermedia (formerly Ochrobactrum intermedium) (n = 2). Genomic screening revealed that P. aeruginosa strain CB_234 harbored bla OXA-50, aph(3')-IIb, and catB7, which confer resistance to β-lactams, aminoglycosides, and chloramphenicol, respectively. It also possessed multiple virulence determinants involved in adherence, motility, and secretion systems that enhance host colonization and environmental persistence. Core genome phylogenetic analysis placed CB_234 within a clade exclusively composed of clinical isolates from Nigeria, Thailand, Russia, Kenya, and Ghana, indicating a shared evolutionary lineage among globally dispersed hospital-associated strains. Conversely, environmental isolates from plant and aquatic sources, along with a dog-associated isolate, were phylogenetically distant, highlighting the distinct evolutionary origins. The E. mori isolate carried bla ACT and qnrE resistance genes and plasmid replicons, suggesting potential mobility of resistance traits through horizontal gene transfer. In contrast, the two B. intermedia isolates did not harbor any known AMR genes or plasmid replicons. However, this species is increasingly recognized as an opportunistic pathogen. The detection of AMR-associated bacterial species in a natural bat habitat supports the evidence of resistance determinants circulating in wildlife environments in Zambia. Given that bats are unlikely to encounter clinical antibiotics directly, the persistence of such genes in their environment suggests that natural ecosystems may play an underappreciated role in maintaining AMR reservoirs independent of direct antimicrobial pressure. These findings underscore the importance of incorporating wildlife and environmental niches into national and global AMR surveillance frameworks under a One Health approach to better understand the ecological dimensions of AMR emergence and dissemination.},
}

@article {pmid41309349,
year = {2025},
author = {Yount, TA and Shukla, N and Chang, YW and St Geme, JW},
title = {PilY proteins: bimodular drivers of type IV pilus versatility.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2025.10.016},
pmid = {41309349},
issn = {1878-4380},
abstract = {Type IV pili (T4P) are dynamic surface fibers that mediate diverse bacterial activities, including adhesion, twitching motility, horizontal gene transfer, biofilm formation, and virulence. The PilY family of T4P-associated proteins are found across a wide range of bacterial species and are critical for key T4P functions. PilY proteins are characterized by a shared domain architecture which consists of a variable N-terminal region that mediates adhesion and a conserved C-terminal beta-propeller domain that facilitates pilus biogenesis. Given their surface exposure and roles in virulence, PilY family proteins represent an attractive target for novel therapeutic interventions, including small-molecule antivirulence therapies against pathogenic bacteria and potential as vaccine antigens. This review synthesizes our current understanding of PilY structure, localization, function, and evolutionary relationships across T4P systems.},
}

@article {pmid41308287,
year = {2025},
author = {Díaz-Martínez, C and Bolívar, A and Pérez-Rodríguez, F},
title = {Influence of product type and ripening time on the antibiotic resistance profile of lactic acid bacteria isolated from Spanish fermented pork products.},
journal = {Meat science},
volume = {232},
number = {},
pages = {109998},
doi = {10.1016/j.meatsci.2025.109998},
pmid = {41308287},
issn = {1873-4138},
abstract = {Antibiotic resistance (AR) poses a significant public health threat, particularly in the food chain where lactic acid bacteria (LAB) may act as reservoirs for resistance genes. This study aimed to evaluate the AR profiles of LAB isolated from Spanish fermented pork products, focusing on the effects of product type and ripening time on the AR patterns. A total of 150 samples of various fermented pork products were collected and analyzed for LAB isolates. Antibiotic susceptibility testing was conducted using the Kirby-Bauer method, revealing that most isolates exhibited resistance to multiple antibiotics, with enterococci showing higher resistance levels, particularly to cefotaxime, tetracycline, and erythromycin. Notably, factors such as product type and ripening duration influenced resistance profiles, with long-ripened products demonstrating higher resistance to tetracycline and erythromycin, while short-ripened products showed increased resistance to vancomycin and ciprofloxacin. The findings suggest that Spanish fermented pork products could serve as potential reservoirs of multidrug-resistant LAB, underscoring the importance of continued surveillance of AR dynamics in food products to better understand any potential implications for human health.},
}

@article {pmid41308173,
year = {2025},
author = {Vijayanathan, M and Faryad, A and Abeywickrama, TD and Christensen, JM and Jakobsen Neilson, EH},
title = {The auxin gatekeepers: Evolution and diversification of the YUCCA family.},
journal = {The Plant journal : for cell and molecular biology},
volume = {124},
number = {4},
pages = {e70563},
doi = {10.1111/tpj.70563},
pmid = {41308173},
issn = {1365-313X},
support = {0054890//Novo Nordisk Fonden/ ; 101110417//European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant/ ; 1051-00083B//Danmarks Frie Forskningsfond/ ; 1131-0002B//Danmarks Frie Forskningsfond/ ; },
mesh = {*Indoleacetic Acids/metabolism ; Phylogeny ; Evolution, Molecular ; *Plant Proteins/genetics/metabolism ; *Plant Growth Regulators/metabolism ; *Yucca/genetics/metabolism ; Multigene Family ; Gene Expression Regulation, Plant ; },
abstract = {The critically important YUCCA (YUC) gene family is highly conserved and specific to the plant kingdom, primarily responsible for the final and rate-limiting step for indole-3-acetic acid (IAA) biosynthesis. IAA is an essential phytohormone, involved in virtually all aspects of plant growth and development. In addition, IAA is involved in fine-tuning plant responses to biotic and abiotic interactions and stresses. While the YUC gene family has significantly expanded throughout the plant kingdom, a detailed analysis of the evolutionary patterns driving this diversification has not been performed. Here, we present a comprehensive phylogenetic analysis of the YUC family, combining YUCs from species representing key evolutionary plant lineages. The evolutionary history of YUCs is complex and suggests multiple recruitment events via horizontal gene transfer from bacteria. We identify and hierarchically classify the YUC family into an early diverging grade, five distinct classes and 41 subclasses. Angiosperm YUC diversity and expansion are explained in the context of protein sequence conservation, as well as spatial and gene expression patterns. The presented YUC gene landscape offers new perspectives on the distribution and evolutionary trends of this crucial family, which facilitates further YUC characterization within plant development and response to environmental change.},
}

*Indoleacetic Acids/metabolism
Phylogeny
Evolution, Molecular
*Plant Proteins/genetics/metabolism
*Plant Growth Regulators/metabolism
*Yucca/genetics/metabolism
Multigene Family
Gene Expression Regulation, Plant

@article {pmid41305496,
year = {2025},
author = {Morgese, EA and Ferrell, BD and Toth, SC and Polson, SW and Wommack, KE and Fuhrmann, JJ},
title = {Comparative Analysis Reveals Host Species-Dependent Diversity Among 16 Virulent Bacteriophages Isolated Against Soybean Bradyrhizobium spp.},
journal = {Viruses},
volume = {17},
number = {11},
pages = {},
doi = {10.3390/v17111474},
pmid = {41305496},
issn = {1999-4915},
support = {1736030//U.S. National Science Foundation/ ; P20 GM103446/GM/NIGMS NIH HHS/United States ; 1S10OD028725-01A1/GM/NIGMS NIH HHS/United States ; },
mesh = {*Bradyrhizobium/virology ; *Glycine max/microbiology ; *Bacteriophages/genetics/isolation & purification/classification/physiology/pathogenicity ; Host Specificity ; Symbiosis ; Phylogeny ; Genome, Viral ; },
abstract = {Phages play a role in shaping ecosystems by controlling host abundance via cell lysis, driving host evolution via horizontal gene transfer, and promoting nutrient cycling. The genus Bradyrhizobium includes bacteria able to symbiotically nodulate the roots of soybean (Glycine max), providing the plant with a direct source of biologically fixed nitrogen. Optimizing this symbiosis can minimize the use of nitrogen fertilizers and make soybean production more sustainable. Phages targeting Bradyrhizobium may modify their hosts' genotype, alter phenotypic traits such as symbiotic effectiveness, and mediate competition among strains for nodulation sites. Sixteen phages were isolated against B. diazoefficiens strain USDA110 and B. elkanii strains USDA94 and USDA31. Comparative analyses revealed host species-dependent diversity in morphology, host range, and genome composition, leading to the identification of three previously undescribed phage species. Remarkably, all B. elkanii phages shared a siphophage morphology and formed a single species with >97% nucleotide identity, even when isolated from farms separated by up to ~70 km, suggesting genomic stability across geographic scales. In contrast, phages isolated against B. diazoefficiens had a podophage-like morphology, exhibited greater genetic diversity, and divided into two distinct species. Although no phages were recovered against the B. japonicum strains or native Delaware Bradyrhizobium isolates tested, some Delaware Bradyrhizobium isolates showed susceptibility in a host range assay. The phage genomes demonstrated features predicting phenotypes. The phage terminase genes predicted headful packaging which promotes generalized transduction. The B. elkanii phages all carried tmRNA genes capable of rescuing stalled ribosomes, and all but one of the phages isolated against the two host species carried DNA polymerase A indicating greater phage control of genome replication. State-of-the-art structural annotation of a hypothetical gene shared by the B. diazoefficiens phages, having a mean amino acid identity of ~25% and similarity of ~35%, predicted a putative tail fiber function. Together this work expands the limited knowledge available on soybean Bradyrhizobium phage ecology and genomics.},
}

*Bradyrhizobium/virology
*Glycine max/microbiology
*Bacteriophages/genetics/isolation & purification/classification/physiology/pathogenicity
Host Specificity
Symbiosis
Phylogeny
Genome, Viral

@article {pmid41305371,
year = {2025},
author = {Zhang, Q and Zwe, YH and Sano, D and Li, D},
title = {Antimicrobial Resistance Transmission of Multidrug-Resistant Bacteria in Hydroponic Farming Components.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {11},
pages = {},
doi = {10.3390/pathogens14111134},
pmid = {41305371},
issn = {2076-0817},
support = {W22W3D0001//Singapore Food Agency/ ; A-8000216-00-00 and JPJSBP120229002//JSPS-NUS Joint Research Grant/ ; },
mesh = {*Drug Resistance, Multiple, Bacterial ; *Hydroponics/methods ; Plasmids/genetics ; *Escherichia coli/drug effects/genetics ; *Salmonella/drug effects/genetics ; Anti-Bacterial Agents/pharmacology ; Conjugation, Genetic ; *Gene Transfer, Horizontal ; Humans ; },
abstract = {Hydroponic farming offers sustainability benefits, but its microbial safety remains a concern, particularly regarding antimicrobial resistance (AMR) transmission. This study evaluated the potential for conjugative plasmid transfer of multidrug-resistant bacteria in hydroponic systems, using Salmonella Saintpaul B23 as a donor and various Escherichia coli strains and a self-isolated Salmonella strain from a hydroponic system as recipients. The tested bacteria are human enteric bacteria and may have a chance of being introduced into hydroponic systems. The transconjugation assay was conducted in hydroponic solutions and on different hydroponic components. Results revealed that hydroponic solutions and plant substrates could support significant transconjugation (>4 log CFU transconjugants detected in per mL hydroponic solution and >4 log CFU transconjugants detected in per g plant substrates), while facility surfaces showed minimal transfer (<1 log CFU transconjugants detected on per cm[2] surface). UV irradiation reduced plasmid transfer rates significantly (p < 0.05), suggesting its potential as a mitigation strategy, though proper implementation is critical. Antibiotic residues at sub-minimum inhibitory concentrations exhibited varying effects on AMR propagation, with gentamicin and chloramphenicol unexpectedly reducing transconjugants. These findings highlight the complex dynamics of AMR transmission in hydroponics and underscore the importance of monitoring, UV application, and cautious use of recycled waste to ensure microbial safety and mitigate AMR risks in agricultural production.},
}

*Drug Resistance, Multiple, Bacterial
*Hydroponics/methods
Plasmids/genetics
*Escherichia coli/drug effects/genetics
*Salmonella/drug effects/genetics
Anti-Bacterial Agents/pharmacology
Conjugation, Genetic
*Gene Transfer, Horizontal
Humans

@article {pmid41304237,
year = {2025},
author = {Zhang, L and Wang, M and Sheng, J and Yu, L and Zhao, Y and Liao, W and Liu, Z and Yu, J and Zhang, X},
title = {Analysis of Antimicrobial Resistance and Virulence Factors in Multidrug-Resistant Streptococcus suis Serotype 2 Isolates Using Whole-Genome Sequencing.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112552},
pmid = {41304237},
issn = {2076-2607},
support = {ZR2022QC118//Natural Science Foundation of Shandong Province/ ; 32202810//National Natural Science Foundation of China/ ; },
abstract = {Multidrug-resistant (MDR) Streptococcus suis (S. suis) is a zoonotic pathogen capable of infecting pigs across all age groups, leading to conditions such as meningitis, arthritis, and endocarditis. In humans, infections can result in septic arthritis, meningitis, necrotizing fasciitis, and septicemia, which may be fatal. The absence of a complete genome sequence hinders comprehensive bioinformatic studies of MDR S. suis derived from pigs. In this study, we present the whole-genome sequence of MDR S. suis serotype 2 ST01 isolated from joint fluid samples obtained from pigs. Whole-genome analysis revealed that the ST01 chromosome carries 19 antibiotic resistance genes that confer resistance to major classes of antibiotic including aminoglycosides, tetracyclines, fluoroquinolones, lincosamides, polypeptide, and nitrofurans. Additionally, it contains 15 virulence factors associated with immune modulation, bacterial adherence, and stress survival. Whole-genome analysis identified 84 horizontal gene transfer elements in ST01 (comprising 28 genomic islands, 52 transposons, and 4 prophages), alongside mutations resulting in reduced virulence (302 instances) and loss of pathogenicity (34 instances). Furthermore, 18 antibiotic targets along with 21 lethal mutations were identified as potential targets for preventing, controlling, and treating infection caused by MDR S. suis serotype 2 ST01. In vivo infection experiments demonstrated that intraperitoneal inoculation with ST01 resulted in mortality among Kunming mice, with a median lethal dose (LD50) of 5.62 × 10[9] CFU/mL. Histopathological analysis revealed varying degrees of lesions in the infected organs of the mice. This study thus provides valuable insights into strategies aimed at combating S. suis infections and their transmission within swine populations.},
}

@article {pmid41304231,
year = {2025},
author = {Fadiji, AE and Adeniji, A and Lanrewaju, AA and Adedayo, AA and Chukwuneme, CF and Nwachukwu, BC and Aderibigbe, J and Omomowo, IO},
title = {Key Challenges in Plant Microbiome Research in the Next Decade.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112546},
pmid = {41304231},
issn = {2076-2607},
abstract = {The plant microbiome is pivotal to sustainable agriculture and global food security, yet some challenges hinder fully harnessing it for field-scale impact. These challenges span measurement and integration, ecological predictability and translation across environments and seasons. Key obstacles include technical challenges, notably overcoming the limits of current sequencing for low-abundance taxa and whole-community coverage, integrating multi-omics data to uncover functional traits, addressing spatiotemporal variability in microbial dynamics, deciphering the interplay between plant genotypes and microbial communities, and enforcing standardized controls, metadata, depth targets and reproducible workflows. The rise of synthetic biology, omics tools, and artificial intelligence offers promising avenues for engineering plant-microbe interactions, yet their adoption requires regulatory, ethical, and scalability issues alongside clear economic viability for end-users and explicit accounting for evolutionary dynamics, including microbial adaptation and horizontal gene transfer to ensure durability. Furthermore, there is a need to translate research findings into field-ready applications that are validated across various soils, genotypes, and climates, while ensuring that advances benefit diverse regions through global, interdisciplinary collaboration, fair access, and benefit-sharing. Therefore, this review synthesizes current barriers and promising experimental and computational strategies to advance plant microbiome research. Consequently, a roadmap for fostering resilient, climate-smart, and resource-efficient agricultural systems focused on benchmarked, field-validated workflows is proposed.},
}

@article {pmid41304121,
year = {2025},
author = {Ramirez-Plascencia, HHF and Colima-Fausto, AG and Licona-Lasteros, KC and Díaz-Zaragoza, M and Cazarez-Navarro, G and Macias-Barragan, JG and Rodriguez-Preciado, SY},
title = {Presence of Microorganisms in the Environment: One Health Approach.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112435},
pmid = {41304121},
issn = {2076-2607},
abstract = {The One Health approach offers an integrative framework to understand infectious threats, environmental factors, antimicrobial resistance (AMR) and how their interactions affect the human-animal-environment interface. This review examines the epidemiology, transmission pathways, and mechanisms of microorganisms of public health importance (bacteria, fungi, parasites, and viruses). It highlights the interconnectedness of ecosystems, where the environment plays a central role in the dissemination of pathogens, driven by climate change, globalization, agricultural intensification, and habitat degradation. AMR is a major concern, driven by the indiscriminate use of pharmaceuticals in human, veterinary, and agricultural settings, horizontal gene transfer through mobile genetic elements, and microbial evolution. The study of different pathogens is of great importance due to their high prevalence in different ecosystems, their virulence, clinical interest, and mortality rates produced. Some of them are ESKAPE bacteria, Candida auris, Plasmodium falciparum, and emerging viruses such as SARS-CoV-2, which present complex transmission dynamics influenced by ecological and health determinants. The review also addresses the effects of climate change on the persistence and geographic spread of pathogens. Successful implementation of the One Health program requires intersectoral policies, integrated surveillance systems, prudent use of antimicrobials and investment in translational science. Coordinating these strategies is essential to limit the spread of pathogens, protect biodiversity, and save global health in the face of the growing threat of infectious diseases.},
}

@article {pmid41303648,
year = {2025},
author = {Hammerl, JA and Hertwig, S},
title = {The Gene Ail for the Attachment-Invasion Locus Protein of Yersinia enterocolitica Biotype 1A Strains Is Located on the Genomes of Novel Prophages.},
journal = {International journal of molecular sciences},
volume = {26},
number = {22},
pages = {},
doi = {10.3390/ijms262211166},
pmid = {41303648},
issn = {1422-0067},
mesh = {*Yersinia enterocolitica/genetics/virology/classification/isolation & purification/pathogenicity ; *Prophages/genetics ; Phylogeny ; *Bacterial Outer Membrane Proteins/genetics ; Animals ; Genome, Bacterial ; *Virulence Factors/genetics ; *Genome, Viral ; },
abstract = {The attachment-invasion locus protein Ail of pathogenic Yersinia strains is an important virulence factor, both for invasion of eucaryotic cells and for serum resistance. In other Yersinia strains, e.g., those belonging to biotype (BT) 1A of Yersinia enterocolitica, ail has only occasionally been described. Sequence analysis of 370 BT 1A isolates in our laboratory revealed 41 (11.1%) which were ail-positive. Most of these isolates were recovered from minced meat and tonsils of wild boars, and belonged to 17 MLST allele profiles. A closer look at DNA sequences surrounding ail disclosed that the gene in most isolates is embedded in DNA regions encoding phage proteins. The genomes of four prophages belonging to four different phylogenetic clusters were determined and analyzed by in silico studies. These have sizes of 34.9 and 50.7 kb, and are closely related to each other but not to known phages. Unlike other regions of the prophages, the integrases and attachment sites of some of them diverge, leading to different integration sites in the isolates. In a fifth cluster, ail is relocated at a position on the Y. enterocolitica chromosome that is several hundred kilobases apart from those of the other clusters, but surrounded by prophage-related sequences. In addition, highly pathogenic 1B/O:8 strains contain a DNA segment which includes ail and is 65 to 94% identical to the prophage sequences determined in this study.},
}

*Yersinia enterocolitica/genetics/virology/classification/isolation & purification/pathogenicity
*Prophages/genetics
Phylogeny
*Bacterial Outer Membrane Proteins/genetics
Animals
Genome, Bacterial
*Virulence Factors/genetics
*Genome, Viral

@article {pmid41301669,
year = {2025},
author = {Mlynarcik, P and Zdarska, V and Kolar, M},
title = {Are Putative Beta-Lactamases Posing a Potential Future Threat?.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {11},
pages = {},
doi = {10.3390/antibiotics14111174},
pmid = {41301669},
issn = {2079-6382},
support = {LX22NPO5103//Ministry of Education, Youth and Sports of the Czech Republic (MŠMT)/ ; IGA_LF_2025_022//Palacký University Olomouc/ ; },
abstract = {BACKGROUND: Antimicrobial resistance is a growing global health threat, with beta-lactamases playing a central role in resistance to beta-lactam antibiotics. Building on our previous survey of 2340 putative beta-lactamases, we conducted an in-depth analysis of 129 prioritized candidates (70-98.5% amino acid identity to characterized enzymes) detected in 102 bacterial genera across 13 phylogenetic classes from environmental, animal, and human sources worldwide.

METHODS: We applied a motif-centric assessment of class-defining catalytic residues, evaluated the genomic context using a heuristic Index of Proximal Mobility (IPM) derived from the two immediately adjacent open reading frames, and examined the phylogenetic placement. AI-based substrate predictions were generated at a restricted scope as exploratory evidence.

RESULTS: Candidates spanned all Ambler classes (A-D); preservation of catalytic motifs was common and consistent with potential catalytic activity. Twelve of 129 (9.3%) loci had nearby mobile-element types (e.g., insertion sequences, integrases, transposases) and scored High IPM, indicating genomic contexts compatible with horizontal gene transfer. We also observed near-identical class A enzymes across multiple genera and continents, frequently adjacent to mobilization proteins.

CONCLUSIONS: We propose a reproducible, bias-aware, early warning framework that prioritizes candidates based on motif integrity and mobility context. The framework complements existing surveillance (GLASS/EARS-Net) and aligns with a One Health approach integrating human, animal, and environmental reservoirs. Identity thresholds and IPM are used for inclusion and contextual prioritization, rather than as proof of function or mobility; AI-based predictions serve as hypothesis-generating tools. Experimental studies will be essential to confirm enzymatic activity, mobility, and clinical relevance.},
}

@article {pmid41301664,
year = {2025},
author = {Osei Duah Junior, I and Ampong, J and Danquah, CA},
title = {Mechanisms and Evolution of Antimicrobial Resistance in Ophthalmology: Surveillance, Clinical Implications, and Future Therapies.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {11},
pages = {},
doi = {10.3390/antibiotics14111167},
pmid = {41301664},
issn = {2079-6382},
abstract = {Antimicrobial resistance (AMR) is a growing global health concern with profound implications for ophthalmology, where it compromises the management of ocular infections such as bacterial keratitis, conjunctivitis, endophthalmitis, and postoperative complications. Resistance in common ocular pathogens, including Staphylococcus aureus (S. aureus), Streptococcus pneumoniae (S. pneumoniae), Pseudomonas aeruginosa (P. aeruginosa), and coagulase-negative staphylococci (CoNS) emerge through genetic mutations, horizontal gene transfer, and biochemical mechanisms such as enzymatic degradation, target modification, efflux pumps, and reduced membrane permeability. Biofilm formation further complicates eradication on the ocular surface and interior. The key drivers of resistance include inappropriate or prolonged topical antibiotic use, routine prophylaxis in ocular surgery, subtherapeutic dosing, and cross-resistance with systemic antimicrobials. The rise in multidrug-resistant strains, particularly methicillin-resistant S. aureus, fluoroquinolone-resistant P. aeruginosa, and drug-resistant S. pneumoniae has been linked to delayed treatment response, increased healthcare costs, and sight-threatening outcomes. Recent advances in rapid diagnostics, molecular assays, and point-of-care testing support earlier and more precise detection of resistance, enabling timely therapeutic decisions. Promising strategies to address AMR in ophthalmology include antimicrobial stewardship, novel drug delivery platforms, and alternative approaches such as bacteriophage therapy and antimicrobial peptides. Emerging tools, including genomic surveillance, artificial intelligence (AI)-driven resistance prediction, and personalized antimicrobial regimens, further expand opportunities for innovation. Collectively, this review synthesizes current evidence on AMR in ocular disease, summarizing patterns of resistance, underlying mechanisms, and clinical consequences, while highlighting strategies for mitigation and underscoring the need for global awareness and collaboration among clinicians, researchers, and policymakers to safeguard vision.},
}

@article {pmid41301640,
year = {2025},
author = {Akhwale, JK and Mutai, IJ and Nale, JY},
title = {The Potential Roles of Prophages in the Pathogenicity of Klebsiella pneumoniae Strains from Kenya.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {11},
pages = {},
doi = {10.3390/antibiotics14111145},
pmid = {41301640},
issn = {2079-6382},
abstract = {Background/Objectives: Antimicrobial resistance (AMR) in Klebsiella pneumoniae poses a serious threat to healthcare, especially in sub-Saharan Africa (SSA). To complement AMR infection control in Kenya, here, clinical and environmental genomes were investigated to determine the potential roles prophages play in K. pneumoniae pathogenicity. Methods: Prophages were extracted from 89 Kenyan K. pneumoniae genomes. The intact prophages were examined for virulence genes carriage, and their phylogenetic relationships were established. Results: Eighty-eight (~99%) of the genomes encode at least a single prophage, and there is an average of four prophages and 2.8% contributory genomes per bacterial strain. From the 364 prophages identified, 250 (68.7%) were intact, while 58 (15.9%) and 57 (15.7%) were questionable and incomplete, respectively. Approximately, 30% of the intact prophages encode 38 virulence genes that are linked to iron uptake (8), regulation (6), adherence (5), secretion system (4), antiphagocytosis (4), autotransporter (4), immune modulation (3), invasion (2), toxin (1) and cell surface/capsule (1). Phylogenetic analyses revealed three distinct clades of the intact prophages irrespective of their hosts, sources and locations, which support the plasticity of the genomes and potential to mediate horizontal gene transfer. Conclusions: This study provides first evidence showing the diverse prophages that are encoded in K. pneumoniae from SSA with particular focus on Kenyan strains. This also shows the potential roles these prophages play in the pathogenicity and success of K. pneumoniae and could improve knowledge and complement control strategies in the region and across the globe. Further work is needed to show the expression of these genes through lysogenisation.},
}

@article {pmid41301601,
year = {2025},
author = {Rossi, F and Santonicola, S and Colavita, G},
title = {Enrichment of Antibiotic Resistance Genes on Plastic Waste in Aquatic Ecosystems, Aquatic Animals, and Fishery Products.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {11},
pages = {},
doi = {10.3390/antibiotics14111106},
pmid = {41301601},
issn = {2079-6382},
abstract = {This comprehensive review compiles current knowledge about the connection between plastic waste and the selection and transmission of antibiotic resistance genes (ARGs) in aquatic ecosystems, which can result in ARG contamination of fishery products-a significant source of microplastic (MP) introduction into the food chain. Plastic debris in aquatic environments is covered by a biofilm (the plastisphere) in which antibiotic-resistant bacteria (ARB) are selected and horizontal gene transfer (HGT) of ARGs is facilitated. The types of plastic waste considered in this study for their role in ARG enrichment are mainly microplastics (MPs), and also nanoplastics (NPs) and macroplastics. Studies regarding freshwaters, seawaters, aquaculture farms, and ARG accumulation favored by MPs in aquatic animals were considered. Most studies focused on the identification of the microbiota and its correlation with ARGs in plastic biofilms, while a few evaluated the effect of MPs on ARG selection in aquatic animals. A higher abundance of ARGs in the plastisphere than in the surrounding water or natural solid substrates such as sand, rocks, and wood was repeatedly reported. Studies regarding aquatic animals showed that MPs alone, or in association with antibiotics, favored the increase in ARGs in exposed organisms, with the risk of their introduction into the food chain. Therefore, reducing plastic pollution in water bodies and aquaculture waters could mitigate the ARG threat. Further investigations focused on ARG selection in aquatic animals should be conducted to better assess health risks and increase awareness of this ARG transmission route, enabling the adoption of appropriate countermeasures.},
}

@article {pmid41299763,
year = {2025},
author = {Manrique-de-la-Cuba, MF and López-Rodríguez, M and Abades, S and Trefault, N},
title = {Cold adaptation and horizontal gene transfer shape Antarctic sponge microbiomes.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02262-z},
pmid = {41299763},
issn = {2049-2618},
support = {Fondecyt 1230758//Agencia Nacional de Investigación y Desarrollo/ ; DG_02-22//Instituto Antartico Chileno/ ; },
abstract = {BACKGROUND: Marine sponges exhibit wide distribution in tropical, temperate, and polar environments. They host diverse microbiomes important to their survival and ecological roles. Antarctic sponges, thriving in extreme cold environments, harbor unique microbial communities. However, functional differences distinguishing Antarctic sponge microbiomes have been poorly investigated. In this study, we investigated how the functional composition of the microbiomes of Antarctic sponges differs from that of their counterparts in other environments, with a particular focus on functions related to cold adaptation. We also assessed the role of horizontal gene transfer (HGT) in driving these functional adaptations.

RESULTS: Antarctic sponge microbiomes displayed a unique functional signature characterized by significantly higher proportions of genes related to cold adaptation, such as cold shock proteins, chaperones, heat shock proteins, and osmoprotectants, compared to their tropical and temperate counterparts, and antioxidants compared to the surrounding seawater. HGT was prevalent in Antarctic sponge symbionts, particularly in the dominant Gammaproteobacteria, Alphaproteobacteria, and Bacteroidia, contributing equally to metabolic functions and cold adaptation, with an important fraction of the latter exhibiting long-distance horizontal gene transfer (HGT). Conjugation, primarily mediated by integrative and conjugative elements (ICE), is a proposed crucial mechanism driving horizontal gene transfer (HGT) in Antarctic sponge symbionts. The cold shock protein C (CspC), linked to cold adaptation, was restricted to Proteobacteria and identified as a potential horizontally acquired gene exclusive to sponge symbionts compared to free-living bacteria in the Antarctic marine ecosystem.

CONCLUSIONS: Antarctic sponge microbiomes exhibit higher proportions of functional adaptations for cold environments facilitated by horizontal gene transfer (HGT). These findings highlight the evolutionary importance of HGT mechanisms in shaping microbial symbioses in extreme environments. Further exploration of HGT dynamics and the role of specific symbionts in cold adaptation could reveal novel insights into microbial evolution and host-symbiont interactions in polar ecosystems. Video Abstract.},
}

@article {pmid41299176,
year = {2025},
author = {Wirbel, J and Hickey, AS and Chang, D and Enright, NJ and Dvorak, M and Chanin, RB and Schmidtke, DT and Bhatt, AS},
title = {Long-read metagenomics reveals phage dynamics in the human gut microbiome.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {41299176},
issn = {1476-4687},
abstract = {Gut bacteriophages profoundly impact microbial ecology and health[1-3]; yet, they are understudied. Using deep long-read bulk metagenomic sequencing, we tracked prophage integration dynamics in stool samples from six healthy individuals, spanning a 2-year timescale. Although most prophages remained stably integrated into their hosts, approximately 5% of phages were dynamically gained or lost from persistent bacterial hosts. Within a sample, we found that bacterial hosts with and without a given prophage coexisted simultaneously. Furthermore, phage induction, when detected, occurred predominantly at low levels (1-3× coverage compared to the host region), in line with theoretical expectations[4]. We identified multiple instances of integration of the same phage into bacteria of different taxonomic families, challenging the dogma that phages are specific to a host of a given species or strain[5]. Finally, we describe a new class of 'IScream phages', which co-opt bacterial IS30 transposases to mediate their mobilization, representing a previously unrecognized form of phage domestication of selfish bacterial elements. Taken together, these findings illuminate fundamental aspects of phage-bacterial dynamics in the human gut microbiome and expand our understanding of the evolutionary mechanisms that drive horizontal gene transfer and microbial genome plasticity.},
}

@article {pmid41298298,
year = {2025},
author = {Liu, YY and Liao, M and Li, YJ and Lin, CY and Qian, RR and Liu, JH and Chen, JK and Yue, HY and Lian, XL and Huang, Y and Liu, JH},
title = {Flavomycin inhibits plasmid-mediated conjugative transfer of antibiotic resistance genes by disrupting energy metabolism and pilus assembly.},
journal = {Zoological research},
volume = {46},
number = {6},
pages = {1438-1446},
doi = {10.24272/j.issn.2095-8137.2025.125},
pmid = {41298298},
issn = {2095-8137},
mesh = {*Plasmids/genetics ; *Anti-Bacterial Agents/pharmacology ; *Energy Metabolism/drug effects ; *Conjugation, Genetic/drug effects ; *Fimbriae, Bacterial/drug effects ; *Gene Transfer, Horizontal/drug effects ; Gene Expression Regulation, Bacterial/drug effects ; *Drug Resistance, Bacterial/genetics ; },
abstract = {The rapid global dissemination of multidrug-resistant (MDR) bacteria, primarily driven by horizontal gene transfer through conjugative plasmids, poses a significant challenge to modern medicine. Conjugation enables the efficient spread of antibiotic resistance genes across bacterial populations, severely compromising the efficacy of existing therapies. This study examined the inhibitory potential of flavomycin against plasmid-mediated transmission of clinically relevant resistance genes and elucidated the underlying molecular mechanisms. Results showed that flavomycin markedly reduced the conjugative transfer of plasmids carrying bla CTX-M, bla NDM, and mcr-1 genes in a dose-dependent manner, decreasing conjugation frequencies by approximately 14- to 100-fold. Mechanistic analysis indicated that inhibition of plasmid transfer resulted from intracellular depletion of ATP and L-arginine, both essential for the energy-dependent conjugation process. Transcriptomic analyses revealed broad suppression of genes involved in energy metabolism, while supplementation with exogenous L-arginine restored conjugation frequencies. Additionally, flavomycin down-regulated the expression of mating pair formation (MPF) genes and disrupted pilus biogenesis, as confirmed by scanning electron microscopy. These findings identify flavomycin as a potent inhibitor of horizontal gene transfer, acting through disruption of bacterial energy metabolism and impairment of pilus assembly, and highlight its potential as a promising strategy to limit the propagation of MDR bacteria.},
}

*Plasmids/genetics
*Anti-Bacterial Agents/pharmacology
*Energy Metabolism/drug effects
*Conjugation, Genetic/drug effects
*Fimbriae, Bacterial/drug effects
*Gene Transfer, Horizontal/drug effects
Gene Expression Regulation, Bacterial/drug effects
*Drug Resistance, Bacterial/genetics

@article {pmid41296881,
year = {2025},
author = {Mayer, MJ and Sayavedra, L and Gotts, K and Wong, N and Whiley, H and Barham, M and Narbad, A},
title = {Human gut strains of Desulfovibrio piger exhibit spontaneous induction of multiple prophages.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0191725},
doi = {10.1128/aem.01917-25},
pmid = {41296881},
issn = {1098-5336},
abstract = {UNLABELLED: Sulfate-reducing bacterium Desulfovibrio piger is a common member of the human gastrointestinal microbiome, associated with inflammatory conditions but also prevalent in healthy individuals. This suggests that lifestyle factors may shape its ecological role. We investigated prophage carriage and release in three new D. piger strains from healthy donors and strain FI11049 from a patient with ulcerative colitis. Sequencing revealed a larger genome in strain FI11455 (3.096 Mb) compared to FI11311 (2.985 Mb) and FI11458 (2.838 Mb), including a 154 kb megaplasmid which contained an 87 kb section with high similarity to the chromosome of strain FI11311, suggesting horizontal gene transfer between chromosomes and plasmids. This section encoded genes involved in DNA replication, transcription, and recombination, as well as protein folding and modification, defense, and phage proteins. Strain FI11049 showed less than 95% similarity to other D. piger strains but shared similar prophages with them. Each strain carried four to five predicted prophages, ranging from 30 to 60 kb, which clustered into four groups, with at least three groups per strain. Although the prophages had no nucleotide similarity to known phages, genes for lysis, integration, regulation, and structural proteins were identified, and three groups contained Mu-like proteins. Electron microscopy and PCR of mitomycin C-induced supernatants confirmed the release of tailed bacteriophage particles and capsids of multiple prophages. Similar results were demonstrated from uninduced samples, indicating spontaneous prophage release. Host defense systems were widespread, and cross-infections failed to identify suitable hosts in related strains and species. This is the first evidence of prophage release in gut-associated Desulfovibrio, with implications for gene transfer in the gut.

IMPORTANCE: Gastrointestinal health has a significant impact on quality of life, and increasing profiling of the gut microbiome is identifying key players involved in disease states. However, evidence of the association of sulfate-reducing bacteria with pathologies, such as inflammatory bowel disease and colorectal cancer, conflicts with their prevalence in healthy subjects. Investigating the ecology of D. piger in the gut may be key to answering if and why it can be harmful and could inform future interventions. Here, we show that gut-associated D. piger strains carry multiple prophages, some of which are spontaneously released as bacteriophage particles in culture. Our results pave the way for future work to understand prophage release in gut conditions and its effects on D. piger populations.},
}

@article {pmid41295723,
year = {2025},
author = {Lei, X and Che, M and Zhou, Y and Pan, S and Yang, X and Liu, S and Laghari, I and Wu, M and Han, R and Li, X and Zhou, L and Peng, G and Liu, H and Zhou, Z and Zhang, K and Zhong, Z},
title = {ESBL-Producing E. coli in Captive Black Bears: Molecular Characteristics and Risk of Dissemination.},
journal = {Veterinary sciences},
volume = {12},
number = {11},
pages = {},
doi = {10.3390/vetsci12111085},
pmid = {41295723},
issn = {2306-7381},
support = {(2024YFD1800202)//the National Key Research and Development Program of China/ ; (CGF2024001)//the Study on Key Technologies for Conservation of Wild Giant Panda Populations and Its Habitats within Giant Panda National Park System/ ; },
abstract = {The emergence and global dissemination of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli (ESBL-E. coli) represent a major public health concern. However, the characterization and capacity for horizontal gene transfer (HGT) of ESBL-E. coli in captive black bears remain substantially understudied. In the present study, 19 ESBL-E. coli strains were successfully identified (13.38%, 19/142). A total of 11 sequence types (STs) were identified from 19 ESBL-E. coli strains using MLST. This included eight known types (ST10, ST2690, ST208, ST695, ST4160, ST540, ST3865 and ST2792) and three new STs. Antimicrobial susceptibility testing demonstrated that all 19 ESBL-E. coli exhibited high resistance to KZ (100.00%), CRO (78.95%), and CTX (73.68%). Polymerase chain reaction (PCR) screening for 14 β-lactam antibiotic resistance genes (ARGs) and their variants revealed that blaCTX-M was the most prevalent, followed by blaSHV, blaTEM, and blaDHA. Furthermore, eight β-lactamase variants were detected, including five blaCTX-M variants (blaCTX-M-15, blaCTX-M-3, blaCTX-M-14, blaCTX-M-55, and blaCTX-M-27) and one variant each of blaSHV-1, blaTEM-1, and blaDHA-14. Conjugation assays revealed that eight ESBL-E. coli strains were capable of conjugative transfer. Five plasmid types (IncFII, IncW, IncFrepB, IncY, and IncHI1) and three mobile genetic elements (MGEs) (IS26, ISEcp1, and trbC) were identified as co-transferred with blaCTX-M. ESBL-E. coli poses a potential threat to captive black bears and may lead to further transmission. Consequently, the implementation of continuous surveillance and targeted interventions is imperative to prevent the transmission of ESBL-E. coli.},
}

@article {pmid41293994,
year = {2025},
author = {Tabatabaee, Y and Zhang, C and Arasti, S and Mirarab, S},
title = {Species Tree Branch Length Estimation despite Incomplete Lineage Sorting, Duplication, and Loss.},
journal = {Genome biology and evolution},
volume = {17},
number = {11},
pages = {},
doi = {10.1093/gbe/evaf200},
pmid = {41293994},
issn = {1759-6653},
support = {1R35GM142725/NH/NIH HHS/United States ; #2138259//U.S. National Science Foundation/ ; #2138286//U.S. National Science Foundation/ ; #2138307//U.S. National Science Foundation/ ; #2137603//U.S. National Science Foundation/ ; #2138296//U.S. National Science Foundation/ ; },
mesh = {*Phylogeny ; *Gene Duplication ; Algorithms ; *Models, Genetic ; *Evolution, Molecular ; Computer Simulation ; },
abstract = {Phylogenetic branch lengths are essential for many analyses, such as estimating divergence times, analyzing rate changes, and studying adaptation. However, true gene tree heterogeneity due to incomplete lineage sorting, gene duplication and loss, and horizontal gene transfer can complicate the estimation of species tree branch lengths. While several tools exist for estimating the topology of a species tree addressing various causes of gene tree discordance, much less attention has been paid to branch length estimation on multi-locus datasets. For single-copy gene trees, some methods are available that summarize gene tree branch lengths onto a species tree, including coalescent-based methods that account for heterogeneity due to incomplete lineage sorting. However, no such branch length estimation method exists for multi-copy gene family trees that have evolved with gene duplication and loss. To address this gap, we introduce the CASTLES-Pro algorithm for estimating species tree branch lengths while accounting for both gene duplication and loss and incomplete lineage sorting. CASTLES-Pro improves on the existing coalescent-based branch length estimation method CASTLES by increasing its accuracy for single-copy gene trees and extending it to handle multi-copy ones. Our simulation studies show that CASTLES-Pro is generally more accurate than alternatives, eliminating the systematic bias toward overestimating terminal branch lengths often observed when using concatenation. Moreover, while not theoretically designed for horizontal gene transfer, we show that CASTLES-Pro is relatively robust to random horizontal gene transfer, though its accuracy can degrade at the highest levels of horizontal gene transfer.},
}

*Phylogeny
*Gene Duplication
Algorithms
*Models, Genetic
*Evolution, Molecular
Computer Simulation

@article {pmid41292866,
year = {2025},
author = {Liu, Z and Good, BH},
title = {Dynamics of dN/dS within recombining bacterial populations.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.09.09.675256},
pmid = {41292866},
issn = {2692-8205},
abstract = {The ratio of nonsynonymous to synonymous substitutions (dN/dS) encodes important information about the selection pressures acting on protein-coding genes. In bacterial populations, dN/dS often declines with the sequence divergence between strains, but the mechanisms responsible for this broad empirical trend are still debated. Existing models have primarily focused on de novo mutations, overlooking the older genetic variants that are continually introduced through horizontal gene transfer and recombination. Here we introduce a phenomenological model of dN/dS in recombining populations of bacteria, which allows us to disentangle the effects of recombination among pairs of closely related strains. We find that clonally inherited regions of the genome exhibit consistently higher dN/dS ratios, and that the accumulation of recombined segments can quantitatively explain the majority of the decline in dN/dS. We use these observations to re-examine models of purifying selection and adaptive reversion in human gut bacteria, and uncover evidence for widespread weak selection at a large fraction of protein coding sites. Our findings show that horizontal gene transfer can be an important factor in shaping genome-wide patterns of selective constraint, and raise new questions about the effectiveness of natural selection in complex bacterial populations.},
}

@article {pmid41292681,
year = {2025},
author = {Bradshaw, A},
title = {Mobile genetic elements and wastewater treatment: contaminants of emerging concern, climate change, and trophic transmission.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1699325},
pmid = {41292681},
issn = {1664-302X},
abstract = {This minireview focuses on recent developments regarding mobile genetic elements (MGEs) and horizontal gene transfer (HGT) in wastewater treatment plants (WWTPs) and proximal environments. WWTPs are often discussed as hotspots and bioreactors for the evolution of MGEs and ARGs and their horizontal transfer. Firstly, the article reviews the effects of emerging contaminants on HGT and MGEs with a specific focus on microplastics and per- and polyfluoroalkyl substances (PFAS). Secondly, the review focuses on how extreme weather and climate change can overwhelm WWTPs, increase the input of diverse genetic elements, and alter the dynamics of HGT. Finally, the trophic connections between the WWTP microbiota and external ecosystems underscore the potential for wider transmission of MGEs. Here, the focus is on transfer of MGEs to larger organisms in the vicinity of WWTPs. In sum, the review focuses on emerging areas of research that refine our understanding of the WWTP environment as a hotspot for HGT and dissemination of MGEs with potentially deleterious implications for human and wider ecosystem health.},
}

@article {pmid41291654,
year = {2025},
author = {Okuda, M and Suehiro, Y and Lapirattanakul, J and Naka, S and Matsumoto-Nakano, M and Nomura, R and Okawa, R and Nakano, K},
title = {Evaluation of Streptococcus mutans strains possessing genes encoding collagen-binding proteins in the Japanese population.},
journal = {BMC oral health},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12903-025-07276-5},
pmid = {41291654},
issn = {1472-6831},
abstract = {BACKGROUND: Streptococcus mutans harbors collagen-binding protein genes, namely cnm and cbm, which are implicated in its virulence and pathogenicity in both oral and extraoral infections. Although both genes were initially identified in S. mutans isolated from Japanese populations, their geographical prevalence, distribution, and genetic relatedness within Japan remain largely unexplored. This study investigates the prevalence of S. mutans strains carrying cnm and cbm genes across Japan, correlates these findings with clinical data, and analyzes the genetic relatedness of cnm-positive and cnm-negative strains using multilocus sequence typing (MLST).

METHODS: Dental plaque specimens were collected from 1248 individuals from eight Japanese cities (Hiroshima, Fukuoka, Nagasaki, Niigata, Okayama, Osaka, Tokushima, and Tokyo) and plated on selective medium for S. mutans isolation. S. mutans was confirmed in 523 subjects by colony morphology and PCR using species-specific primers, and the presence of the cnm and cbm genes was determined by PCR with gene-specific primers. Demographic (age, sex) and oral examination (caries prevalence, caries experience, number of teeth) data were recorded. MLST was employed to genotype selected cnm-positive and cnm-negative S. mutans strains to assess their clonal relationships.

RESULTS: Among 523 subjects possessing S. mutans (aged 3-90 years), we detected cnm-positive strains in all cities; specifically, the prevalence ranged from 5.5% in Okayama to 25.0% in Tokushima. In contrast, cbm-positive strains were less common and undetectable in some regions. Furthermore, subjects harboring cnm-positive S. mutans were significantly older (p = 0.002) and had higher caries prevalence and experience (p < 0.001). MLST revealed evolutionary relationships among cnm-positive strains across the cities but no discernible region-specific clustering. Clonal relationships partially reflected cnm gene distribution, particularly for exclusively cnm-positive or cnm-negative clonal complexes, but inconsistencies involving serotypes and cnm presence within some clonal complexes and sequence types were also noted.

CONCLUSIONS: The cnm-positive S. mutans strains are widely distributed throughout Japan and are associated with increased age and caries burden. Although core genome analysis revealed some clonal patterns, the non-uniform distribution of the non-core cnm gene is likely influenced by horizontal gene transfer, providing S. mutans with adaptive advantages irrespective of its core genetic background or serotype.},
}

@article {pmid40846035,
year = {2025},
author = {Liu, S and Fang, L and Zhu, W and Xu, H and Guo, X and Gu, S and Li, S and Shen, Y and Zhang, L and Zheng, B},
title = {Emergence of a novel transferable megaplasmid driving blaVIM-24 and tmexCD3-toprJ3 dissemination in clinical Pseudomonas fulva isolates.},
journal = {International journal of antimicrobial agents},
volume = {66},
number = {6},
pages = {107594},
doi = {10.1016/j.ijantimicag.2025.107594},
pmid = {40846035},
issn = {1872-7913},
mesh = {*Plasmids/genetics ; *Pseudomonas/genetics/drug effects/isolation & purification/classification ; Humans ; *Pseudomonas Infections/microbiology ; Phylogeny ; Microbial Sensitivity Tests ; *beta-Lactamases/genetics ; *Drug Resistance, Multiple, Bacterial/genetics ; Whole Genome Sequencing ; Anti-Bacterial Agents/pharmacology ; Gene Transfer, Horizontal ; Electrophoresis, Gel, Pulsed-Field ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; },
abstract = {OBJECTIVE: To investigate the genetic characteristics and transmission mechanism of clinical Pseudomonasfulva isolates with transferable megaplasmid co-carrying blaVIM-24 and tmexCD3-toprJ3.

METHODS: Bacterial identification was performed using MALDI-TOF/MS, and antimicrobial susceptibility testing was carried out using agar dilution and broth microdilution. The genetic context of drug resistance genes and plasmid characteristics was analyzed by S1-PFGE, Southern blotting, conjugation experiments, and whole-genome sequencing analysis. Comparative genomics analysis of the plasmids and genetic context was conducted by using BLAST Ring Image Generator (BRIG) and Easyfig 2.3. Phylogenetic analysis of P. fulva strains and pJBCL41-like megaplasmids was performed by Snipy and Mega, respectively.

RESULTS: Clinical P. fulva strains, ZDHY316 and ZDHY414, with transferable megaplasmids co-carrying blaVIM-24 and tmexCD3-toprJ3. The megaplasmids pVIM-24-ZDHY316 and pVIM-24-ZDHY414 carry multiple drug-resistant genes and integrate numerous integrons and transposon truncations from different origins. ΔTn6855-ΔTn6758 is the new discoovered co-transfer module carrying nfxB-mexCD-oprJ, which only exists in chromosomes and megaplasmids. Phylogenetic analysis of pJBCL41-like megaplasmids showed their evolution towards carrying more drug-resistance genes and mobile genetic elements. Additionally, ZDHY316 has another transferable plasmid, pVIM-1-ZDHY316, which carries the novel integron In2008 with the GCA of 5'CS- blaVIM-1-aac(6')-Ib-3'CS. Phylogenetic analysis of P. fulva strains showed that China is the country with the most P. fulva isolated clinically, with strains prevalent and evolving in hospitals.

CONCLUSIONS: The mosaic structure of the megaplasmid, characterized by integrons and transposons, underscores its role in resistance gene dissemination and highlights the adaptability of non-standard pathogens like P. fulva. The horizontal transfer potential of this megaplasmid poses a significant challenge to clinical infection control. Enhanced surveillance of non-standard pathogens and their plasmids is essential.},
}

*Plasmids/genetics
*Pseudomonas/genetics/drug effects/isolation & purification/classification
Humans
*Pseudomonas Infections/microbiology
Phylogeny
Microbial Sensitivity Tests
*beta-Lactamases/genetics
*Drug Resistance, Multiple, Bacterial/genetics
Whole Genome Sequencing
Anti-Bacterial Agents/pharmacology
Gene Transfer, Horizontal
Electrophoresis, Gel, Pulsed-Field
Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization

@article {pmid41291089,
year = {2025},
author = {Calbet, A},
title = {Pelagic Shuttles of Antibiotic Resistance Genes: Zooplankton as Overlooked Vectors Across Space and Food Webs.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02669-z},
pmid = {41291089},
issn = {1432-184X},
abstract = {Antibiotic resistance genes (ARGs) accumulate in aquatic environments, where they create reservoirs and transmission pathways that can undermine antimicrobial treatments and alter the microbial community structure in ways that ultimately affect human and animal health. However, the contribution of zooplankton in these pathways remains critically overlooked. Emerging evidence shows that compared with surrounding water, copepods and cladocerans accumulate ARG loads that are one to two orders of magnitude greater, acting as microbial hotspots that disperse resistant bacteria across seasons and depths. Inside protistan vacuoles, densely packed prey cells undergo conjugation, rapidly accelerating horizontal ARG transfer. Long-term archives reveal persistent ocean-wide dissemination of the class-1 integron integrase (intI1) and sul2 genes since at least the 1970s. Here, I synthesize mechanistic and field evidence, pinpoint knowledge gaps, and recommend priorities: integrate zooplankton into routine ARG surveillance, quantify biofilm-mediated exchanges, and mitigate contamination from coselective pollutants to curb zooplankton-driven ARG propagation. By framing zooplankton-associated ARG dynamics within the broader community ecology of antimicrobial resistance, this mini-review highlights how aquatic food-web processes feed back into the emergence, evolution, and transmission of resistance that concerns for One Health outcomes beyond the clinic.},
}

@article {pmid41291062,
year = {2025},
author = {Gervason, S and Zecchin, P and Shelton, EB and He, N and Pecqueur, L and Garcia, PS and Akinyemi, T and Touati, N and Bimai, O and Velours, C and Ravanat, JL and Faivre, B and Whitman, WB and Fontecave, M and Golinelli-Pimpaneau, B},
title = {Evolution, structure and function of L-cysteine desulfidase, an enzyme involved in sulfur metabolism in the methanogenic archeon Methanococcus maripaludis.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {1667},
pmid = {41291062},
issn = {2399-3642},
support = {ANR-22CE44-0012//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-11-LABX-0011//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-10-LABX-62-IBEID//Agence Nationale de la Recherche (French National Research Agency)/ ; Marie Skłodowska-Curie grant agreement No 101034407//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; },
abstract = {The biosynthesis of sulfur-containing molecules, which play essential roles in cell metabolism, often relies on enzymes that mobilize sulfur from cysteine. The function of such enzyme, L-cysteine desulfidase CyuA, which catalyzes L-cysteine decomposition to pyruvate, ammonia, and hydrogen sulfide, remains incompletely understood. Here, we used phylogenetic, genetic, biochemical, spectroscopic, and structural approaches to connect molecular structure to cellular physiology and evolutionary history and elucidate CyuA's role in sulfur metabolism. We found that Methanococcales and several other archaeal lineages acquired CyuA via horizontal gene transfer from bacteria. In Methanococcus maripaludis, CyuA (MmCyuA) stimulates growth in sulfide-rich conditions and enables slow growth with cysteine as the sole sulfur source. Crystallographic and biochemical data reveal that MmCyuA binds a [4Fe-4S] cluster coordinated by three conserved cysteines; the fourth ligand is a nonconserved cysteine in the wild-type enzyme but is replaced by glycerol or ethylene glycol in a variant. These results enabled modeling of the enzyme-substrate complex, allowing us to propose a detailed mechanism for L-cysteine desulfuration by CyuA, potentially involving a transient [4Fe-5S] species to transfer sulfur from cysteine to various [4Fe-4S]-dependent tRNA sulfuration enzymes. These findings advance understanding of sulfur activation and trafficking related to biosynthetic pathways leading to sulfur-containing compounds.},
}

@article {pmid41289037,
year = {2025},
author = {Seçkin, E and Colinet, D and Sarti, E and Danchin, EGJ},
title = {Orphan and de novo Genes in Fungi and Animals: Identification, Origins and Functions.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evaf220},
pmid = {41289037},
issn = {1759-6653},
abstract = {Genes that lack identifiable homologs in other species have been an intriguing and interesting topic of research for many years. These so-called orphan genes were first studied in yeast and since then, they have been found in many other species. This has fostered a whole field of research aiming at tracing back their evolutionary origin and functional significance. Orphan genes represent an important part of protein-coding genes in many species. Their presence was initially mainly hypothesized to result from high divergence from a pre-existing gene, with duplications or horizontal gene transfer facilitating their accelerated evolution. More recently, their possible de novo emergence from non-genic regions has gained particular interest. Several orphan genes are predicted to be involved in reproduction, while others are involved in specific developmental stages, in adaptation mechanisms such as freeze protection or even human disease. However, there is currently no unified resource or synthesis that brings together existing knowledge about how prevalent orphan genes are across different species and what their roles might be. In this review, we focus on orphan genes in animals and fungi. We provide a detailed summary of discoveries over time in terms of orphan gene prevalence in genomes, their origins as well as their roles in different biological contexts.},
}

@article {pmid41288358,
year = {2025},
author = {Zhao, M and Maclellan, MP and Lamichhane, A and Paudel, S and Gitaitis, R and Kvitko, B and Dutta, B},
title = {Characterization of Pseudomonas alliivorans strains isolated from Georgia, USA: insights into genomic diversity and pathogenicity in onions.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0164325},
doi = {10.1128/aem.01643-25},
pmid = {41288358},
issn = {1098-5336},
abstract = {Pseudomonas alliivorans is an important emerging pathogen affecting numerous crops. The species is closely related to Pseudomonas viridiflava, with which P. alliivorans strains were often misidentified in the past. Here, we investigated the genetic and pathogenic characteristics of P. alliivorans strains isolated primarily from onions and weeds in Georgia, USA, using whole-genome sequencing, comparative genomics, and functional assays. We delineated the core genome and genetic diversity of these isolates, assessed their pathogenicity on onion foliage and red onion scales, and examined the roles of key virulence determinants (Hrp1-type III secretion system [T3SS], rhizobium-T3SS, type II secretion systems [T2SSs], and thiosulfinate [allicin]-tolerance alt cluster). Our results showed that the Hrp1-T3SS is pivotal for pathogenicity in P. alliivorans, whereas the rhizobium-T3SS, T2SSs, and alt cluster do not contribute to symptom development on red onion scales. Notably, the alt cluster confers in vitro thiosulfinate tolerance, supporting bacterial survival against onion-derived antimicrobial compounds. Additionally, homologous recombination in P. alliivorans occurs infrequently (at approximately one-tenth the rate of point mutations) and involves divergent DNA segments. The alt cluster is acquired through horizontal gene transfer, as evidenced by its lower GC content and the presence of adjacent transposases. In summary, our research provides valuable insights into the genetic diversity, evolutionary dynamics, and virulence mechanisms of P. alliivorans strains from Georgia, USA.IMPORTANCEPseudomonas alliivorans is an emerging plant pathogen that threatens onion and other plants of economic importance. This study identifies key traits that help this bacterium cause disease, such as a specific secretion system critical for infecting onions, and a gene cluster that aids bacterial survival in onion tissues. Beyond highlighting weed as a potential inoculum source and supporting better weed management, the findings of this research open avenues for more targeted disease menegement. By unraveling the genetics of this pathogen, we can develop improved ways to detect, prevent, and reduce its impact, protecting crop health and yields.},
}

@article {pmid41285067,
year = {2025},
author = {Chen, W and Li, L and Dai, X and Feng, L and Yu, X},
title = {Health risk and benefit assessment methods for antibiotic resistance bacteria/genes in the environment: A critical review.},
journal = {Journal of environmental management},
volume = {396},
number = {},
pages = {128071},
doi = {10.1016/j.jenvman.2025.128071},
pmid = {41285067},
issn = {1095-8630},
abstract = {Antibiotics are widely used across various sectors, leading to significant environmental residues. These residues exert continuous selective pressure, which facilitates the proliferation and dissemination of antibiotic resistance genes (ARGs) and antibiotic resistant bacteria (ARB) in the environment. The spread of ARGs and ARB undermines the clinical efficacy of antibiotics and poses substantial risks to public health. Recognized as emerging environmental contaminants, ARGs and ARB have garnered increasing global concern. While existing research has extensively investigated their sources, species, environmental distribution, fate, and removal mechanisms, studies evaluating their health risks and benefits remain limited, hindering the development of a comprehensive knowledge system. This review discussed the crucial considerations for establishing a comprehensive health risk and benefit assessment system for ARGs and ARB. It also systematically examined the existing relative grading and quantitative health assessment frameworks, as well as benefit assessment frameworks based on the economic burden of antibiotic resistance. Additionally, the limitations of these frameworks in practical applications were discussed, along with future challenges and opportunities for improving the assessment systems. These insights aim to inform the management of environmental antibiotic resistance and provide scientific references for policymaking related to environmental health and public health security.},
}

@article {pmid41282978,
year = {2025},
author = {Han, X and Liu, H and Bai, X and Li, D and Wang, T and Zhong, H and Yao, Y and Sun, J},
title = {Insights into antibiotic resistomes from metagenome-assembled genomes and gene catalogs of soil microbiota across environments.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e20348},
pmid = {41282978},
issn = {2167-8359},
mesh = {*Soil Microbiology ; *Metagenome ; China ; *Microbiota/genetics ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/drug effects ; Metagenomics ; },
abstract = {Antibiotic resistance poses a significant global health threat, and soil is recognized as a critical reservoir for antibiotic resistance genes (ARGs). To investigate soil microorganisms in the areas where both humans and common domestic animals (such as pigs and chickens) are present and active. In this study, we employed metagenomic sequencing to investigate the soil resistome across four Chinese provinces-Yunnan, Guizhou, Sichuan, and Jiangsu. From 111 soil samples, we generated metagenome-assembled genomes (MAGs) and gene catalogs to analyze microbial community composition, ARG distribution, and mobile genetic elements (MGEs). Our results revealed notable regional differences in microbial communities and ARG profiles. Pseudomonadota and Actinomycetota were the dominant phyla across samples, and ARG abundance was significantly higher in Sichuan, Yunnan, and Jiangsu compared to Guizhou. We also identified microbial taxa likely serving as ARG vectors, suggesting potential for horizontal gene transfer. Functional annotation indicated that metabolic functions, particularly carbohydrate and amino acid metabolism, were predominant, which may be associated with the composition of organic matter in the soil environment. Multidrug resistance genes are widespread in soil microbial communities and may spread through food chains or soil-water-plant systems, posing potential ecological and public health risks. MGEs showed significant regional variation and play a key role in the horizontal spread of ARGs. Together, these findings provide new insights into the soil antibiotic resistome and offer a foundation for developing targeted strategies to manage environmental antibiotic resistance.},
}

*Soil Microbiology
*Metagenome
China
*Microbiota/genetics
*Drug Resistance, Microbial/genetics
Anti-Bacterial Agents/pharmacology
*Bacteria/genetics/drug effects
Metagenomics

@article {pmid41280044,
year = {2025},
author = {Teipen, AE and Holt, JD and Lynch, DL and Peng, Y and Dalia, TN and Gumbart, JC and Nadell, CD and Dalia, AB},
title = {Structural modeling reveals the mechanism of motor ATPase coordination during type IV pilus retraction.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.10.30.685630},
pmid = {41280044},
issn = {2692-8205},
abstract = {UNLABELLED: Diverse bacterial species utilize surface appendages called type IV pili (T4P) to interact with their environment. These structures are dynamically extended and retracted from the cell surface, which is critical for diverse functions. Some T4P systems rely on two distinct motor ATPases, PilT and PilU, whose combined activities are required to power forceful T4P retraction. However, the mechanism by which these motors coordinate to facilitate T4P retraction has remained unclear. Here, we utilize the competence T4P in V. cholerae as a model system to elucidate the molecular basis for PilT-PilU coordination during T4P retraction. Specifically, we modeled the interactions between PilT and PilU using AlphaFold 3 and molecular dynamics (MD) simulations. We then empirically tested these models using a combination of cytological and high-resolution genetic approaches. Our results reveal that interactions between PilT and the PilU C-terminus are critical for these motors to coordinate to drive T4P retraction. Finally, we show that PilT-PilU interactions are broadly conserved in T4P systems from diverse bacterial species, and we experimentally validate that they are required for T4P retraction in Acinetobacter baylyi . Together, this work expands our fundamental understanding of T4P dynamics, and more broadly it provides mechanistic insight into how these ATPases coordinate to assemble some of the strongest biological motors in nature.

SIGNIFICANCE: Diverse bacterial species use filamentous surface appendages called type IV pili (T4P) to move along surfaces, take up DNA for horizontal gene transfer, and stick to biotic and abiotic surfaces. The forceful retraction of these filaments is often required for these behaviors. In many T4P systems, the combined activity of two distinct motor ATPase proteins is required for forceful retraction; however, a detailed understanding of how these motor proteins interact to promote forceful retraction is currently lacking. Here, we use an integrated approach to uncover the molecular mechanism for motor ATPase coordination. Furthermore, we show that this mechanism is broadly conserved in diverse T4P systems.},
}

@article {pmid41279647,
year = {2025},
author = {Douglas, GM and Tromas, N and Gaudin, M and Lypaczewski, P and Bobay, LM and Shapiro, BJ and Chaffron, S},
title = {Co-occurrence is associated with horizontal gene transfer across marine bacteria independent of phylogeny.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.03.25.645238},
pmid = {41279647},
issn = {2692-8205},
abstract = {Understanding the drivers and consequences of horizontal gene transfer (HGT) is a key goal of microbial evolution research. Although co-occurring taxa have long been appreciated to undergo HGT more often, this association is confounded with other factors, most notably their phylogenetic relatedness. To disentangle these factors, we analyzed 15,339 marine prokaryotic genomes (mainly bacteria) and their distribution in the global ocean. We identified HGT events across these genomes and enrichments for functions previously shown to be prone to HGT. By mapping metagenomic reads from 1,862 ocean samples to these genomes, we also identified co-occurrence patterns and environmental associations. Although we observed an expected negative association between HGT rates and phylogenetic distance, we only detected an association between co-occurrence and phylogenetic distance for closely related taxa. This observation refines the previously reported trend to closely related taxa, rather than a consistent pattern across all taxonomic levels, at least here within marine environments. In addition, we identified a significant association between co-occurrence and HGT, which remains even after controlling for phylogenetic distance and measured environmental variables. In a subset of samples with extended environmental data, we identified higher HGT levels associated with particle-attached bacteria and associations of varying directions with specific environmental variables, such as chlorophyll a and photosynthetically available radiation. Overall, our findings demonstrate the significant influence of ecological associations in shaping marine bacterial evolution through HGT.},
}

@article {pmid41279561,
year = {2025},
author = {Spaulding, JA and Fierst, JL},
title = {The eukaryotic horizontal gene transfer dataset a compendium.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.11.05.686818},
pmid = {41279561},
issn = {2692-8205},
abstract = {With more eukaryotic genomes available for study researchers have been able to identify a growing number of horizontal gene transfer (HGT) candidates. We compiled 9,511 protein coding genes that were identified as horizontally transferred in the published literature. This dataset contains gene transfers from bacteria, fungi, archaea and protists to metazoans. We assigned a level of certainty to each gene based on the methods used in the scientific paper reporting HGT. A supplemental file contains all the coding sequences and protein sequences for the HGT genes. This dataset can be used to identify trends in genome and protein evolution and provide a foundation for creating a centralized HGT database for eukaryotes.},
}

@article {pmid41279009,
year = {2025},
author = {Morgese, EA and Ferrell, BD and Toth, SC and Polson, SW and Wommack, KE and Fuhrmann, JJ},
title = {Comparative Analysis Reveals Host Species-Dependent Diversity Among 16 Virulent Bacteriophages Isolated Against Soybean Bradyrhizobium spp.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.10.06.680108},
pmid = {41279009},
issn = {2692-8205},
abstract = {Phages play a role in shaping ecosystems by controlling host abundance via cell lysis, driving host evolution via horizontal gene transfer, and promoting nutrient cycling. The genus Bradyrhizobium includes bacteria able to symbiotically nodulate the roots of soybean (Glycine max), providing the plant with a direct source of biologically fixed nitrogen. Optimizing this symbiosis can minimize the use of nitrogen fertilizers and make soybean production more sustainable. Phages targeting Bradyrhizobium may modify their hosts' genotype, alter phenotypic traits such as symbiotic effectiveness, and mediate competition among strains for nodulation sites. Sixteen phages were isolated against B. elkanii strains USDA94 and USDA31, and B. diazoefficiens strain USDA110. Comparative analyses revealed host species-dependent diversity in morphology, host range, and genome composition, leading to the identification of three previously undescribed phage species. Remarkably, all B. elkanii phages shared a siphophage morphology and formed a single species with >97% nucleotide identity, even when isolated from farms separated by up to ∼70 km, suggesting genomic stability across geographic scales. In contrast, phages isolated against B. diazoefficiens displayed podophage-like morphology, greater genetic diversity, and divided into two distinct species. Although no phages were recovered against B. japonicum strains or native Delaware Bradyrhizobium isolates tested, some Delaware isolates showed susceptibility during the host range assay. The phage genomes demonstrated features predicting phenotypes. Terminase genes predicted headful packaging among the phages which is critical for generalized transduction. The B. elkanii phages all carried tmRNA genes capable of recruiting stalled ribosomes and both phage groups carried DNA polymerase A indicating greater control of phage genome replication. State-of-the-art structural annotation revealed a tail fiber gene within a phage genome having the highest proportion (80.77%) of unknown genes. Together this work expands the limited knowledge available on soybean Bradyrhizobium phage ecology and genomics.},
}

@article {pmid41277979,
year = {2025},
author = {Ribeiro, RAC and Guidotti-Takeuchi, M and Dumont, CF and Buiatte, ABG and de Araújo Brum, B and Martins, TJ and Ramos, LMS and Guerra, W and Polveiro, RC and de Melo, RT and Rossi, DA},
title = {Transfer of blaTEM gene between Salmonella and Escherichia coli under processing conditions of animal products: influence of a copper(II) complex.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1676649},
pmid = {41277979},
issn = {1664-302X},
abstract = {The high prevalence of infections caused by contaminated food, coupled with growing antimicrobial resistance, especially through horizontal gene transfer, is a challenge for public health worldwide. It is possible that this situation is intensified in the presence of by-products from animal product processing industries. In view of this, we investigated the horizontal transfer of the blaTEM gene from S. Heidelberg to E. coli J53 AzR, in the absence and presence of whey (WH) and chicken juice (CJ) in: (i) liquid medium for 3 h under agitation; (ii) solid medium overnight; (iii) liquid medium overnight and the influence of the copper(II) complex Lu54 in mitigating this transfer. The first protocol showed the highest relative conjugation frequency (RCF) of 2.23% in the absence of supplements and increased by three and four orders of magnitude in the presence of CJ and WH and was selected for treatment with Lu54. In solid/overnight, there were RCFs of less than 1%, while the liquid/overnight medium showed RCFs higher than the first protocol only in WH. The presence of WH acidified the medium, which resulted in higher RCF. Lu 54 reduced RCF from 2.2 to 0.3%, 8.2 to 1.7% and 6.2 to 0.9%, respectively, for the tests without by-products and with WH and CJ. In addition, the genomes were sequenced to map the blaTEM gene and β-lactamase families in transconjugants. The results showed that three plasmids containing blaTEM were detected in the controls and the same gene was not identified in the treatments, suggesting plasmid loss induced by the copper(II) complex (Lu54). The results prove that WH and CJ increase the frequency of conjugation in liquid media, and the Lu54 complex is a promising alternative to mitigate conjugation and, consequently, the spread of antimicrobial resistance, especially in milk and meat processing industries.},
}

@article {pmid41277839,
year = {2025},
author = {Qian, M and Zhu, D and Yao, K-y and Liu, S-y and Li, M-k and Ye, M and Zhu, Y-g},
title = {Coexistence of virome-encoded health-associated genes and pathogenic genes in global habitats.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0150125},
doi = {10.1128/aem.01501-25},
pmid = {41277839},
issn = {1098-5336},
abstract = {UNLABELLED: Viral remnants constitute approximately 8% of the human genome, reflecting extensive historical gene exchange between viruses and their hosts. Some viral genomes harbor genes acquired through horizontal gene transfer that are associated with potential benefits to human health, alongside genes associated with pathogenicity. However, their global distribution, functional characteristics, and coexistence patterns remain poorly understood. Here, using the Integrated Microbial Genomes and Virome (IMG/VR v4) database, we identified 4,556 viruses carrying gene segments associated with human health across eight habitat types spanning 13 regions and 76 countries worldwide. Among viruses with identifiable hosts, those distributed in humans (478) accounted for the highest proportion. The viral genes associated with human health included BCO1 (beta-carotene oxygenase 1), bioB (biotin synthase), COQ2 (4-hydroxybenzoate polyprenyltransferase), GPX1 (glutathione peroxidase 1), GSTs (glutathione transferases), GSTT1 (glutathione S-transferase theta 1), GULO (L-gulonolactone oxidase), and menA (1,4-dihydroxy-2-naphthoate polyprenyltransferase). These genes not only associate with human health but also function as auxiliary metabolic genes in viral genomes. Notably, four pathogenic genes were found in viral sequences carrying health-associated genes, with potential for transcription and expression, indicating functional interactions. Experimental transduction of the viral bioB gene into Escherichia coli altered the expression of host pathogenic genes GCH1 (GTP cyclohydrolase IA) and UGDH (UDP-glucose 6-dehydrogenase), supporting potential cross-regulatory interactions. Overall, this study incorporates health-associated genes into viral genomics, highlighting their coexistence with pathogenic genes, and provides new insights into virus-host coevolution and potential biotechnological applications.

IMPORTANCE: Viruses are the most abundant biological entities on Earth and key drivers of microbial evolution through horizontal gene transfer. While often studied for their pathogenic effects, viruses can also carry genes that influence host metabolism and health. Genes associated with human health have been identified in viral genomes, yet their global distribution, functions, and coexistence with pathogenic genes remain largely unexplored. This study integrates datasets of health-associated genes into viral genomic analyses, revealing for the first time the coexistence of viral health-associated genes with those linked to pathogenicity. This dual genetic potential is observed across diverse habitats, highlighting viruses as multifaceted reservoirs of both beneficial and harmful genes. The study findings advance understanding of viral functional diversity and open new avenues for exploring viral roles in microbial ecology, biotechnology, and human health.},
}

@article {pmid41277474,
year = {2025},
author = {Kim, S and Kang, JY and Lee, JS},
title = {Comparative Genomics and Virulence Mechanisms to Identify Genes Related to Mucin O-Glycan Degradation and Pathogenicity in a Potentially Multidrug-Resistant Clostridium tertium Strain.},
journal = {MicrobiologyOpen},
volume = {14},
number = {6},
pages = {e70169},
doi = {10.1002/mbo3.70169},
pmid = {41277474},
issn = {2045-8827},
support = {//This study was supported by the government of the Republic of Korea (MSIT) and the National Research Foundation of Korea (NRF-2021R1A2C1005811; NRF-2023K2A9A1A01098813, FY2023 to Seonghun Kim and NRF-2016M3A9F3947962 to Jung-Sook Lee) and partially by KRIBB Research Initiative Program grant./ ; },
mesh = {Humans ; *Mucins/metabolism ; *Virulence Factors/genetics ; Genome, Bacterial ; Genomics ; Feces/microbiology ; Virulence/genetics ; *Polysaccharides/metabolism ; Phylogeny ; *Clostridium/genetics/pathogenicity/isolation & purification/metabolism/drug effects/classification ; *Drug Resistance, Multiple, Bacterial/genetics ; },
abstract = {Clostridium tertium is a pathogenic bacterium that directly colonizes the gastrointestinal mucosa, causing inflammation and neutropenia. The virulence factors and pathogenic mechanisms of C. tertium are not well known. In this study, C. tertium HGMC01 was isolated by enrichment culture of human feces, and its whole chromosome genome was sequenced without extra plasmids. C. tertium HGMC01 had a larger genome and a higher gene count compared with five other C. tertium strains. A pangenome analysis of six strains showed that C. tertium HGMC01 had the highest number of unique genes and the lowest number of accessory genes clustered phylogenetically with C. tertium src5, a strain of animal origin. C. tertium HGMC01 genome showed a variety of secreted glycoside hydrolases and carbohydrate-binding modules for mucin O-glycan degradation and sialic acid catabolism including sialidase and sialic acid transporter. These genes strongly suggested that the strain could interact the human gut cells through recognition or adhesion to mucin glycans. Moreover, various mobile genetic elements in its genome also indicated the genetic diversity and plasticity of the strain to gain virulence factors and antibiotic/multidrug-resistant genes potentially acquired by horizontal gene transfer for the evolution of the pathogenicity. Additionally, experiments with human embryonic kidney cells revealed that components of C. tertium HGMC01 cell wall may play roles as virulence factors by modulating cytokine signaling pathways dependent on Toll-like receptors. Overall, this comparative genomic analysis provides information about how C. tertium strains cause disease through mucin glycan degradation, colonization, multidrug resistance, and modulation of immune responses.},
}

Humans
*Mucins/metabolism
*Virulence Factors/genetics
Genome, Bacterial
Genomics
Feces/microbiology
Virulence/genetics
*Polysaccharides/metabolism
Phylogeny
*Clostridium/genetics/pathogenicity/isolation & purification/metabolism/drug effects/classification
*Drug Resistance, Multiple, Bacterial/genetics

@article {pmid41276040,
year = {2025},
author = {Gong, S and Miswan, N and Shah, NHA and Anis, SNS and Abdullah, AA and Lau, NS},
title = {Genomic characterisation and gene editing of Marinibacterium sp. CCB-SX1 as a new marine chassis for polyhydroxyalkanoate production.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {149133},
doi = {10.1016/j.ijbiomac.2025.149133},
pmid = {41276040},
issn = {1879-0003},
abstract = {The development of robust microbial platform with customised genetic traits is crucial for advancing polyhydroxyalkanoate (PHA) production as a biodegradable plastic alternative. This study genomically characterised a new marine isolate, Marinibacterium sp. CCB-SX1, for its potential as a PHA-producing chassis. The complete genome comprises a 6.14 Mb chromosome and nine plasmids. Phylogenomic analysis placed CCB-SX1 within Marinibacterium, with genomic metrics (average nucleotide identity and digital DNA-DNA hybridisation) suggesting it represents a new species. Comparative genomics of the family Paracoccaceae revealed an open pangenome with a small core and a large accessory genome, abundant in functions for energy production and conversion, replication, recombination and repair, and transcription. Mobile genetic elements were dominated by integration/excision and transfer-associated genes, reflecting extensive horizontal gene transfer and genomic plasticity. PHA-related genes (phaC, phaB, phaP, phaR, phaZ) were conserved in the soft-core genome, mostly organised as phaR-phaP-phaC-phaZ. Genome annotation of CCB-SX1 revealed a complete pathway for 3-hydroxybutyrate synthesis and methylmalonyl-CoA enzymes enabling 3-hydroxyvalerate formation. CCB-SX1 synthesised PHA from multiple carbon sources, with acetate yielding the highest PHA content (27.3 wt%) and producing the copolymer poly(3-hydroxybutyrate-co-3-hydroxyvalerate) with 1.2 mol% 3 HV, while other carbon sources formed poly(3-hydroxybutyrate). A CRISPR-Cas9-nickase system was established to generate single and double knockouts of intracellular depolymerases (phaZ1, phaZ2). Disruption of phaZ1 significantly increased PHA accumulation, while phaZ2 deletion had negligible effect. These findings establish Marinibacterium sp. CCB-SX1 as a genetically tractable marine chassis with potential for metabolic engineering and biopolymer production.},
}

@article {pmid41274873,
year = {2025},
author = {Peng, H and Andreu-Sanchez, S and Ruiz-Moreno, AJ and Fernández-Pato, A and Wu, J and Gacesa, R and Zhernakova, A and Wang, D and Fu, J},
title = {Longitudinal gut microbiota tracking reveals the dynamics of horizontal gene transfer.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-66612-z},
pmid = {41274873},
issn = {2041-1723},
abstract = {Horizontal gene transfer (HGT) is a major driver of bacterial evolution, but its role in shaping the human gut microbiome over time remains poorly understood. Here, we present a longitudinal metagenomic analysis of 676 fecal samples from 338 individuals in the Lifelines-DEEP study collected ~4 years apart, using a newly developed workflow to detect recent HGT events from metagenome-assembled genomes. We identified 5,644 high-confidence HGT events occurring within the past ~10,000 years across 116 gut bacterial species. We find that species pairs with an HGT relationship were significantly more likely to maintain stable co-abundance relationships over the 4-year period, suggesting that gene exchange contributes to community stability. Notably, HGT and strain replacement act together to disseminate mobile genes in the population. Furthermore, our observation that an individual's mobile gene pool remains highly personalized and stable over time indicates that host lifestyles drive specific gene transfer. For example, proton pump inhibitor usage is linked to increased transfer of multidrug transporter genes. Our findings demonstrate, at the individual gut microbiome level, that HGT is both an integral and stabilizing force in the human gut ecosystem and an important mechanism for disseminating adaptive functions, underscoring HGT potential for tracking host lifestyle.},
}

@article {pmid41273849,
year = {2025},
author = {White, RT and Thornley, CN and Bloomfield, M and Dyet, K and Elvy, J and Perez, H and Hardaker, A and Harrington, M and Jackson, S and Kelly, M and Mangalasseril, L and Nesdale, A and Ren, X and Szeto, J and Underwood, C and Winter, D and Woodhouse, R and Yang, Z},
title = {Integration of blaOXA-48 into a Col156 plasmid drove a carbapenem-resistant Escherichia coli ST131 outbreak in New Zealand: Global genomic evidence for the gene's multilayered dissemination.},
journal = {Drug resistance updates : reviews and commentaries in antimicrobial and anticancer chemotherapy},
volume = {84},
number = {},
pages = {101327},
doi = {10.1016/j.drup.2025.101327},
pmid = {41273849},
issn = {1532-2084},
abstract = {AIMS: To investigate the genetic diversity in OXA-48-producing Escherichia coli ST131 in a New Zealand community outbreak, and to characterize the mobile genetic elements carrying blaOXA-48, with emphasis on the gene's global dissemination.

METHODS: Forty outbreak isolates underwent short-read sequencing; 36 also underwent long-read sequencing. Bayesian phylogenetics reconstructed the emergence and spread of the outbreak. A pangenome graph of 543 Col156 plasmids and 806 global blaOXA-48-positive contigs were analyzed to assess structural diversity, mobility, and global distribution.

RESULTS: The outbreak clone likely emerged circa 2017, following a single introduction into New Zealand after acquiring blaOXA-48 on a 7872 bp Col156 plasmid. It shares ancestry (circa 2009) with Southeast Asian E. coli ST131 genomes. Long-read sequencing and pangenome graph analyses identified a single IS1-mediated transposition of blaOXA-48 into a Col156 plasmid backbone, observed across species and continents. Globally, blaOXA-48 is present in diverse plasmid contexts and insertion sequence arrangements and is widely distributed among Enterobacterales.

CONCLUSIONS: This is the first high-resolution genomic reconstruction of a community-associated blaOXA-48 outbreak, identifying a compact Col156 plasmid as a key vector driving carbapenem resistance. Our findings demonstrate the value of complete genome assemblies and pangenome graph analyses in resolving the structural and evolutionary dynamics of antimicrobial resistance.},
}

@article {pmid41272433,
year = {2025},
author = {Zeng, Q and Zhao, Y and Zhuang, L and Jiang, W and Wang, L and Zhang, J and Wang, L and Guo, H and Li, Y and Wang, Z and Li, Y and Wang, Q},
title = {Comparative genomics of Bacillus velezensis and Bacillus subtilis reveals distinction and evolution of lipopeptide antimicrobial gene clusters.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {1071},
pmid = {41272433},
issn = {1471-2164},
mesh = {*Bacillus/genetics/classification/metabolism ; *Bacillus subtilis/genetics/classification ; *Multigene Family ; Phylogeny ; *Lipopeptides/genetics/pharmacology ; *Genomics/methods ; *Evolution, Molecular ; Genome, Bacterial ; },
abstract = {Species belonging to the genus Bacillus are recognized as important biocontrol agents, especially the Bacillus subtilis and Bacillus velezensis exhibit the excellent antifungal activity, being found in a variety of habitats and demonstrating significant metabolic versatility. However, knowledge regarding the genetic diversity of different Bacillus species is limited. In this study, we employed comparative genomics to elucidate the genetic diversity and evolutionary relationships between B. velezensis and B. subtilis. Our results indicated that the antibacterial activity and colonization features, including biofilm formation and swarming, of B. velezensis strains were significantly greater than those of B. subtilis strains. We conducted a comprehensive genomic analysis of various Bacillus group strains and found that the genome size of B. velezensis was larger than that of B. subtilis, while the GC content of B. subtilis was higher than that of B. velezensis. The Average Nucleotide Identidy (ANI) value and phylogenetic analysis revealed ambiguous classifications among some Bacillus strains. Furthermore, the 20 Bacillus strains examined yielded a pangenome size of 7068 genes, with strain-specific genes ranging from 24 to 305. The core and specific genome of B. velezensis strains, annotated for secondary metabolite biosynthesis, transport and catabolism, were significantly more abundant than those of B. subtilis. The most pronounced difference between B. velezensis and B. subtilis strains was observed in the gene cluster encoding the iturin family of lipopeptides. Evolutionary analysis suggested that the iturin gene cluster of Bacillus may have been transferred from Paenibacillus spp. via horizontal gene transfer (HGT) events during the evolution. Additionally, functional analysis demonstrated that the iturin gene cluster effectively inhibits Fusarium pathogens. Collectively, these findings provide a foundation for a deep understanding of the evolution of different Bacillus strains and establish a theoretical basis for the application of Bacillus strains in agricultural production.},
}

*Bacillus/genetics/classification/metabolism
*Bacillus subtilis/genetics/classification
*Multigene Family
Phylogeny
*Lipopeptides/genetics/pharmacology
*Genomics/methods
*Evolution, Molecular
Genome, Bacterial

@article {pmid41271665,
year = {2025},
author = {Dai, B and Sperl, AW and Polack, L and Mejia, I and Dame, H and Huynh, T and Deveney, C and Lavoie, N and Lee, C and Doench, JG and Daugherty, MD and Heldwein, EE},
title = {ER protein CLCC1 promotes nuclear envelope fusion in herpesviral and host processes.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10256},
pmid = {41271665},
issn = {2041-1723},
support = {R01AI147625//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; R35GM133633//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; T32GM133351//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; Faculty Scholar grant 55108533//Howard Hughes Medical Institute (HHMI)/ ; },
mesh = {*Nuclear Envelope/metabolism/virology ; Humans ; Animals ; *Herpesvirus 1, Human/genetics/physiology/metabolism ; *Membrane Fusion ; *Endoplasmic Reticulum/metabolism ; *Herpesviridae/genetics ; Capsid/metabolism ; Host-Pathogen Interactions ; *Membrane Proteins/metabolism/genetics ; Active Transport, Cell Nucleus ; },
abstract = {Herpesvirales are an ancient viral order that causes lifelong infections in species from mollusks to humans. They export their capsids from the nucleus to the cytoplasm by a noncanonical nuclear egress route that involves capsid budding at the inner nuclear membrane followed by fusion of this temporary envelope with the outer nuclear membrane. Here, using a whole-genome CRISPR screen, we identify ER protein CLCC1 as important for the fusion stage of nuclear egress in herpes simplex virus 1. We also find that the genomes of Herpesvirales that infect mollusks and fish encode CLCC1 genes acquired from host genomes by horizontal gene transfer. In uninfected cells, loss of CLCC1 causes a nuclear blebbing defect, suggesting a role in host nuclear export. We hypothesize that CLCC1 facilitates an ancient cellular membrane fusion mechanism that Herpesvirales have hijacked or co-opted for capsid export and propose a mechanistic model.},
}

*Nuclear Envelope/metabolism/virology
Humans
Animals
*Herpesvirus 1, Human/genetics/physiology/metabolism
*Membrane Fusion
*Endoplasmic Reticulum/metabolism
*Herpesviridae/genetics
Capsid/metabolism
Host-Pathogen Interactions
*Membrane Proteins/metabolism/genetics
Active Transport, Cell Nucleus

@article {pmid41267490,
year = {2025},
author = {Sharma, P and Dagariya, S and Sharma, S and Singh, M},
title = {Uncovering the nexus of human health hazards of nanoplastics, gut-dysbiosis and antibiotic-resistance.},
journal = {Journal of environmental science and health. Part C, Toxicology and carcinogenesis},
volume = {},
number = {},
pages = {1-60},
doi = {10.1080/26896583.2025.2578871},
pmid = {41267490},
issn = {2689-6591},
abstract = {Nanoplastics (1-1000 nm) (NPs) represent a novel and insidious class of emerging contaminants with the potential to profoundly disrupt gut microbial ecology and accelerate the spread of antibiotic resistance two critical and converging threats to global health. While prior studies have examined the toxicokinetics of NPs and their general microbial interactions, this review provides the first comprehensive synthesis specifically focused on the nexus between NPs, gut dysbiosis, and the propagation of antibiotic resistance genes (ARGs). This review highlights how NPs alter gut microbiota composition, suppressing beneficial microbes while fostering opportunistic pathogens and how such imbalances may contribute to human health issues. Importantly, emerging evidence also suggests that NPs may serve as unrecognized vectors for horizontal gene transfer (HGT), enabling the rapid dissemination of ARGs via conjugation, transformation, transduction, and extracellular vesicles within the gastrointestinal tract. In addition, this review also identifies urgent methodological gaps in detecting NPs in biological matrices and the environment, as well as assessing their mechanistic impacts, calling for innovation in analytical approaches. By presenting an interdisciplinary perspective that bridges nanotoxicology, microbiome science, and antimicrobial resistance, this article sheds light on an underexplored yet urgent frontier in environmental health, offering novel insights to guide future research, risk assessment, and policy development.},
}

@article {pmid41262458,
year = {2025},
author = {Gao, Z and Gao, Y and Wang, S and Li, X and Cao, W and Deng, W and Yao, L and Wei, X and Zhang, Z and Wang, S and Zhang, Y and Li, M and Xie, Y},
title = {Application progress and biosafety challenges of gene editing and synthetic biotechnology in diagnosis, treatment and prevention of infectious diseases.},
journal = {Biosafety and health},
volume = {7},
number = {5},
pages = {312-322},
pmid = {41262458},
issn = {2590-0536},
abstract = {Global infectious disease prevention faces escalating challenges due to the continual emergence of novel pathogens and rapid viral mutations. Synthetic biology has revolutionized this field by enabling precise diagnostics, innovative vaccine platforms, and targeted therapeutics, yet it simultaneously raises concerns regarding dual-use potential, biosafety, and ethical governance. This systematic review (2015-2025, PubMed, Web of Science, Scopus) focuses on CRISPR-based diagnostics, synthetic vaccines, and engineered probiotics. CRISPR/Cas systems such as DETECTR (Cas12a) and SHERLOCK (Cas13a) demonstrate high sensitivity and rapid pathogen detection (e.g., SARS-CoV-2, Ebola), but their misuse could enhance pathogen virulence or enable bioweapon development. mRNA and viral vector vaccines offer flexible and rapid responses to emerging infections but encounter limitations in molecular stability, delivery system toxicity, and ecological safety. Engineered probiotics, designed as "living therapeutics," can detect pathogens and modulate immune responses, yet pose potential risks of horizontal gene transfer and host-specific variability. Overall, while synthetic biology provides transformative tools for infectious disease control, it necessitates robust global regulatory frameworks, standardized biosafety practices, and ethical oversight to ensure responsible and sustainable application.},
}

@article {pmid41259923,
year = {2025},
author = {Wang, YC and He, LY and Wu, DL and Gao, FZ and Liu, YS and Ying, GG},
title = {Long-term manure applications promote persistent antibiotic resistance in soil.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140476},
doi = {10.1016/j.jhazmat.2025.140476},
pmid = {41259923},
issn = {1873-3336},
abstract = {Manure application has the potential to influence soil microbial composition and the antibiotic resistome; however, its long-term effects remain largely unknown. This study investigated the prolonged impacts of manure applications (pig and chicken manure/compost) on soil antibiotic resistance over a two-year period. Compared with the control (51.9-85.1 ng/g), manure-amended soils contained markedly higher antibiotic concentrations (356-26100 ng/g), remaining 4-300 times higher after 730 days, especially in pig compost treatments. The abundances of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) in amended soils (4.48 × 10[8]-2.74 × 10 [12] copies/g) consistently exceeded those in controls (1.24 × 10[7]-6.10 × 10[7] copies/g). Notably, 62.5 % of ARGs were located on plasmid-associated contigs, and high-risk genes such as floR and aph(3')-III persisted throughout incubation. Elevated MGE levels after 730 days indicated sustained horizontal gene transfer (HGT) potential under antibiotic selection pressure. Overall, these results reveal the long-lasting enrichment of ARGs and highlight the need for improved manure management and long-term.},
}

@article {pmid41259914,
year = {2025},
author = {Yang, W and Wang, X},
title = {Transmission mechanisms and risk tracing of antibiotic resistance genes in rivers driven by wastewater inputs.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140523},
doi = {10.1016/j.jhazmat.2025.140523},
pmid = {41259914},
issn = {1873-3336},
abstract = {Aquatic environments are critical for ARG dissemination, yet contributions from different wastewater sources, dominant HGT mechanisms, and residual risks in natural waters remain unclear. Based on 863 metagenomic samples across China, we systematically analyzed wastewater inputs, HGT mechanisms, and risks of riverine ARGs. Wastewater treatment plants were the primary source, contributing about 50 % of riverine ARGs. Conjugation dominated ARG transfer, primarily via F-type type IV secretion systems. High-transmission plasmids were widespread. Although phage-mediated transduction represented only 3 % of HGT, it facilitated cross-environmental spread of clinically significant blaGES-18. Metagenome-assembled genomes revealed 78 % of resistant bacteria belonged to Pseudomonadota; 42 % co-harbored virulence factors. Phylogenetic analysis showed high inter-generic mobility of sul1/sul2, explaining their environmental persistence. Overall risk in rivers decreased by 44 % - 93 % compared to wastewaters. However, Acinetobacter carrying blaOXA and Cellvibrio sp002483145 carrying blaKHM-1 were phylogenetically close to Acinetobacter baumannii and Pseudomonas aeruginosa, indicating potential pathways toward key pathogens. Our study identifies wastewater as the main source of riverine ARGs, reveals conjugation as the primary transmission mechanism with transduction playing a secondary role, and demonstrates that high-risk ARGs can still spread to pathogenic bacteria in rivers. These findings are crucial for developing effective strategies to mitigate ARG risks.},
}

@article {pmid41259652,
year = {2025},
author = {Khan, MF},
title = {Microbial Remediation of Agrochemical-Contaminated Soils: Enzymatic Mechanisms, Quorum Sensing, and Emerging Opportunities.},
journal = {Integrated environmental assessment and management},
volume = {},
number = {},
pages = {},
doi = {10.1093/inteam/vjaf167},
pmid = {41259652},
issn = {1551-3793},
abstract = {The intensive and repeated use of agrochemicals, including synthetic pesticides, herbicides, and fertilisers, has led to persistent contamination of agricultural soils, endangering soil health, ecosystem services, biodiversity, and sustainable food production. Soil microbiomes, with their remarkable metabolic versatility, represent a promising resource for in situ remediation of these pollutants. This review provides an integrated overview of the enzymatic and regulatory mechanisms underpinning microbial remediation, placing greater emphasis on enzymatic degradation as the central process driving pollutant breakdown. The biodegradation of soil pollutants is orchestrated by a network of microbial enzymes, including organophosphorus hydrolases, dehalogenases, oxidoreductases, dioxygenases, plastic-degrading and alkane-catabolising enzymes, that catalyse oxidation, hydrolysis, and dehalogenation reactions, transforming toxic compounds into less harmful intermediates that feed into metabolic pathways. Understanding the relationship between these enzymes, their encoding genes, and microbial hosts is crucial for designing robust bioremediation strategies. Complementing these biochemical processes, quorum sensing (QS) is discussed as a regulatory system that modulates microbial cooperation, biofilm formation, and catabolic gene expression during degradation. Emerging strategies, including microbial consortia design and synthetic biology-based engineering, are evaluated with a focus on the integration of QS-mediated interactions. Critical challenges, including soil heterogeneity, abiotic inhibition of QS signals, enzyme instability, biosafety concerns related to engineered strains, and horizontal gene transfer, are discussed. Future perspectives highlight enzyme engineering, QS-based biosensors, artificial intelligence-driven modelling, and synthetic QS circuits as tools to optimise bioremediation outcomes. Collectively, these insights outline pathways for advancing ecologically sound and sustainable approaches to the remediation of agrochemical-contaminated soils.},
}

@article {pmid41259345,
year = {2025},
author = {Rafic, T and Alarawi, M and Alkhnbashi, OS and Al-Thukair, A and Okeyode, AH and G, K and Nzila, A},
title = {Whole genome sequencing, characterization and analysis of coronene degrading bacterial strain Halomonas elongata.},
journal = {PloS one},
volume = {20},
number = {11},
pages = {e0334420},
pmid = {41259345},
issn = {1932-6203},
mesh = {*Halomonas/genetics/metabolism ; *Whole Genome Sequencing ; *Genome, Bacterial ; Biodegradation, Environmental ; *Polycyclic Aromatic Hydrocarbons/metabolism ; Phylogeny ; Gene Transfer, Horizontal ; Salinity ; },
abstract = {Polycyclic aromatic hydrocarbons (PAHs) are persistent environmental pollutants with significant ecological and health risks. Among them, coronene, a high molecular weight PAH, is particularly resistant to biodegradation due to its complex structure. This study characterizes a halophilic bacterial strain, initially identified as Halomonas caseinilytica and later reclassified as Halomonas elongata, capable of utilizing coronene as its sole carbon source under high salinity (10% NaCl). Whole genome sequencing using Oxford Nanopore technology (ONT) revealed 4,308 predicted genes, including those linked to hydrocarbon metabolism, stress adaptation, and secondary metabolite biosynthesis. Pathway analysis identified genes associated with xenobiotic degradation, although no canonical coronene specific degradative enzymes were identified, implying that the bacteria may be utilising an alternative or novel pathway. Comparative annotation uncovered operons and enzymes relevant to aromatic compound breakdown. Notably, the presence of ectoine biosynthesis genes suggests a robust osmoadaptation system. Features such as mobile genetic elements and horizontal gene transfer events were also investigated. These findings expand current knowledge on PAH-degrading halophiles and highlight the potential of H. elongata in bioremediation of saline and hypersaline environments contaminated with complex hydrocarbons. The study also emphasises the potential of long read sequencing technologies in environmental genomics and bioremediation.},
}

*Halomonas/genetics/metabolism
*Whole Genome Sequencing
*Genome, Bacterial
Biodegradation, Environmental
*Polycyclic Aromatic Hydrocarbons/metabolism
Phylogeny
Gene Transfer, Horizontal
Salinity

@article {pmid41259146,
year = {2025},
author = {Dewailly, M and Fauconnet, Y and Ducrot, C and Soulet, AL and Campo, N and Guerois, R and Radicella, JP and Polard, P and Andreani, J and Johnston, CHG},
title = {A tripartite protein complex promotes DNA transport during natural transformation in Firmicutes.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {47},
pages = {e2511180122},
doi = {10.1073/pnas.2511180122},
pmid = {41259146},
issn = {1091-6490},
support = {ANR-22-CE44-0044//Agence Nationale de la Recherche (ANR)/ ; ANR-22-CE44-0044//Agence Nationale de la Recherche (ANR)/ ; ANR-22-CE44-0044//Agence Nationale de la Recherche (ANR)/ ; ANR-22-CE44-0044//Agence Nationale de la Recherche (ANR)/ ; },
mesh = {*Streptococcus pneumoniae/genetics/metabolism ; *Bacterial Proteins/metabolism/genetics/chemistry ; DNA, Single-Stranded/metabolism/genetics ; *Transformation, Bacterial ; Gene Transfer, Horizontal ; *DNA, Bacterial/metabolism/genetics ; Helicobacter pylori/genetics/metabolism ; Models, Molecular ; DNA-Binding Proteins/metabolism/genetics ; Multiprotein Complexes/metabolism ; },
abstract = {Natural genetic transformation is a conserved mechanism of bacterial horizontal gene transfer, which is directed entirely by the recipient cell and facilitates the acquisition of new genetic traits such as antibiotic resistance. Transformation proceeds via the capture of exogenous DNA, its internalization in single strand form (ssDNA) and its integration into the recipient chromosome by homologous recombination. While the proteins involved in these steps have mainly been identified, the specific mechanisms at play remain poorly characterized. This study takes advantage of recent advances in structural modeling to explore the uptake of ssDNA during transformation. Using the monoderm human pathogen Streptococcus pneumoniae, we model a tripartite protein complex composed of the transmembrane channel ComEC, and two cytoplasmic ssDNA-binding proteins ComFA and ComFC. Using targeted mutation and transformation assays, we propose that pneumococcal ComEC features a narrow channel for ssDNA passage, and we show this channel is conserved in the diderm Helicobacter pylori. We identify key residues involved in protein-protein and protein-ssDNA interactions in the pneumococcal tripartite complex model and we show them to be crucial for transformation efficiency. Structural modeling reveals that this tripartite protein complex and its interaction with ssDNA are conserved in Firmicutes. Overall, this study validates a tripartite complex required for the internalization of ssDNA during transformation in Firmicutes, providing insights into the molecular mechanisms involved in this horizontal gene transfer mechanism central to bacterial adaptation. It also demonstrates the power of recent structural modeling techniques such as AlphaFold3 as hypothesis generators and guides for designing experiments.},
}

*Streptococcus pneumoniae/genetics/metabolism
*Bacterial Proteins/metabolism/genetics/chemistry
DNA, Single-Stranded/metabolism/genetics
*Transformation, Bacterial
Gene Transfer, Horizontal
*DNA, Bacterial/metabolism/genetics
Helicobacter pylori/genetics/metabolism
Models, Molecular
DNA-Binding Proteins/metabolism/genetics
Multiprotein Complexes/metabolism

@article {pmid41258718,
year = {2025},
author = {Markkanen, M and Pezzutto, D and Virta, M and Karkman, A},
title = {Sulfonamide resistance gene sul4 is hosted by common wastewater sludge bacteria and found in various newly described contexts and hosts.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0085725},
doi = {10.1128/spectrum.00857-25},
pmid = {41258718},
issn = {2165-0497},
abstract = {UNLABELLED: The introduction of the first broad-spectrum antibiotics, sulfonamide drugs, fundamentally revolutionized medicine in the 1930s. Shortly after, and ever since, sulfonamide resistance genes (sul genes) have been widely detected. Still, the most recent variant of these genes, sul4, was first described only in 2017, and its host range and transmission mechanisms are still largely unknown. Here, we applied PacBio long-read metagenomic sequencing and bacterial methylation signals to investigate the genetic contexts and bacterial carriage of the sul4 gene in wastewater. Furthermore, we extended our description of sul4 carriers to previously published data sets. Our results indicate that sul4 is prominently found in sludge and hosted by various bacteria, such as the species from the phyla Myxococcota and Chloroflexota and genera Trichlorobacter and Desulfobacillus, which are commonly found in activated sludge. Additionally, according to our results, sul4 has already spread into multiple strains of opportunistic human pathogens, such as Aeromonas and Moraxella, in addition to the previously described Salmonella. The sequence region flanking sul4 included a truncated folK gene and an ISCR28 element and exhibited a high degree of conservation across the investigated sequences. Furthermore, the module was associated with various integron integrase genes. Also, other mobility-related elements that could further increase the likelihood of sul4 mobilization were detected. Altogether, our results describing the sul4 hosts of bacteria from distant lineages indicate the efficient mobility of sul4 by genetic elements that traverse both clinical and environmental bacteria. Finally, we suggest that wastewater may provide favorable conditions for such horizontal gene transfer events.

IMPORTANCE: Antibiotic resistance is an ancient phenomenon and a common trait of many environmental bacteria. However, human activities in the post-antibiotic era, coupled with the bacteria's ability to exchange genetic material across different lineages, have drastically increased the spread of resistance traits among bacteria from various niches. The primary concern is the resistance genes encoded by infections causing pathogens, already causing over 1 million deaths annually and indirectly contributing to nearly 4 million more. Therefore, understanding the bacteria that harbor ARGs and the genetic mechanisms driving their mobilization is crucial for understanding the dynamics and emerging trends of resistance. Here, we focus on revealing these crucial aspects of the newly discovered sulfonamide resistance gene, sul4. Given the limitations of the metagenomic approach in linking the functional genes to their host genomes, the significance of our research lies in our workflow, which allows this linkage through the identification of shared methylation profiles.},
}

@article {pmid41257541,
year = {2025},
author = {Peketi, ASK and Nagaraja, V and Bulagonda, EP},
title = {Genomic islands and plasmid borne antimicrobial resistance genes drive the evolution of high-risk, ST-131 uropathogenic E. coli NS30.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {1065},
pmid = {41257541},
issn = {1471-2164},
support = {2020e5867; OMI/27/2020-ECD-I and AMR/Adhoc/281/2022-ECD-II//Indian Council of Medical Research/ ; },
mesh = {*Genomic Islands ; *Uropathogenic Escherichia coli/genetics/drug effects/pathogenicity/classification ; *Plasmids/genetics ; *Evolution, Molecular ; Humans ; Genome, Bacterial ; Drug Resistance, Multiple, Bacterial/genetics ; Phylogeny ; Escherichia coli Infections/microbiology ; Urinary Tract Infections/microbiology ; Genomics ; *Drug Resistance, Bacterial/genetics ; Virulence Factors/genetics ; },
abstract = {BACKGROUND: Urinary tract infections (UTIs) caused by Uropathogenic Escherichia coli (UPEC) belonging to global strains such as ST-131 pose a significant health challenge. To understand the evolutionary landscape and molecular mechanisms defining ST-131 UPEC, the complete genome of E. coli NS30 was generated and analyzed.

RESULTS: The complete genome assembly of E. coli NS30, belonging to high-risk ST-131, C2 subclade, revealed a chromosome and two plasmids. A large conjugative plasmid, pNS30-1, harboured a multi-drug resistance (MDR) cassette within a Tn402-like class 1 integron, which was functionally demonstrated to be transferable. Comparative genomic analysis identified four distinct genomic islands (GIs) that are absent in its closest ST-131 neighbour. Two of these, including a novel pathogenicity island (PAI), were acquired from other E. coli lineages, harbouring Virulence factors (VFs) and efflux pump genes. The remaining two GIs are phage-like elements contributing to genome plasticity.

CONCLUSIONS: E. coli NS30 is distinct from the other ST-131 UPEC genomes by the acquisition of novel GIs. The presence of GIs, virulence factors and AMR genes in a conjugative MDR plasmid has driven its evolution into a formidable uropathogen with a high potential to spread resistance and virulence traits.},
}

*Genomic Islands
*Uropathogenic Escherichia coli/genetics/drug effects/pathogenicity/classification
*Plasmids/genetics
*Evolution, Molecular
Humans
Genome, Bacterial
Drug Resistance, Multiple, Bacterial/genetics
Phylogeny
Escherichia coli Infections/microbiology
Urinary Tract Infections/microbiology
Genomics
*Drug Resistance, Bacterial/genetics
Virulence Factors/genetics

@article {pmid41257464,
year = {2025},
author = {Liu, H and Yao, J and Tian, C and Min, P and Zhou, L and Wu, W and Chen, M and Moran, RA and Yu, Y and Li, X},
title = {New resistance threat in difficult-to-treat resistance Pseudomonas aeruginosa co-producing AFM and KPC carbapenemases: plasmid dynamic transfer and global phylogeography perspective.},
journal = {Emerging microbes & infections},
volume = {14},
number = {1},
pages = {2585632},
pmid = {41257464},
issn = {2222-1751},
mesh = {*beta-Lactamases/genetics/metabolism ; *Pseudomonas aeruginosa/genetics/drug effects/enzymology/isolation & purification/classification ; *Plasmids/genetics ; Humans ; *Bacterial Proteins/genetics/metabolism ; China/epidemiology ; *Pseudomonas Infections/microbiology/epidemiology/drug therapy ; Gene Transfer, Horizontal ; Anti-Bacterial Agents/pharmacology ; Phylogeography ; Carbapenems/pharmacology ; Microbial Sensitivity Tests ; Drug Resistance, Multiple, Bacterial/genetics ; },
abstract = {Metallo-β-lactamase (MBL) production is one of the primary carbapenem resistance mechanisms in carbapenem-resistant Pseudomonas aeruginosa (CRPA). The emergence of the novel MBL gene blaAFM poses a significant threat to global public health. Concerningly, we have identified clinical CRPA strains co-producing AFM and the widely-disseminated carbapenemase KPC-2. Here, we describe AFM-producing, KPC-2-producing, and AFM/KPC-2 co-producing clinical CRPA isolates that were collected from three patients in two different hospital buildings in China. Comparative genomics suggested horizontal transfer of a blaAFM-2-harboring plasmid may have contributed to the spread of the AFM carbapenemase between different hospital areas, and to the emergence of dual carbapenemase-producing CRPA. Further epidemiological source tracing revealed the likely involvement of cross-patient nursing care and cross-area patient transfer in carbapenemase transmission. Experimental data confirmed the transfer ability of clinical blaAFM-2-bearing plasmids into P. aeruginosa PAO1. As the global epidemiology of blaAFM has not been systematically evaluated, we further examined 30,800 publicly available P. aeruginosa genome sequences. Including those generated in this study, blaAFM genes were detected in 36 isolates in total, which were derived from China (35/36) or Australia (1/36). AFM-containing genomes were sourced from six Chinese provinces, with 63.9% (23/36) isolated in Zhejiang between 2020 and 2024. The most prominent AFM-associated P. aeruginosa clone was ST463 (17/36 genomes). Our study highlights the concerning challenge presented by blaAFM-harboring CRPA in clinical settings. Horizontal transfer of blaAFM-bearing plasmids can contribute to difficult-to-treat resistance (DTR) phenotypes. Surveillance should be strengthened to prevent the further spread of these plasmids, particularly into and within ICUs.},
}

*beta-Lactamases/genetics/metabolism
*Pseudomonas aeruginosa/genetics/drug effects/enzymology/isolation & purification/classification
*Plasmids/genetics
Humans
*Bacterial Proteins/genetics/metabolism
China/epidemiology
*Pseudomonas Infections/microbiology/epidemiology/drug therapy
Gene Transfer, Horizontal
Anti-Bacterial Agents/pharmacology
Phylogeography
Carbapenems/pharmacology
Microbial Sensitivity Tests
Drug Resistance, Multiple, Bacterial/genetics

@article {pmid41256488,
year = {2025},
author = {Downing, BE and Gupta, D and Shalvarjian, KE and Nayak, DD},
title = {Genus-specific remodeling of carbon and energy metabolism facilitates acetoclastic methanogenesis in Methanosarcina spp. and Methanothrix spp.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {41256488},
issn = {2692-8205},
support = {F32 GM150233/GM/NIGMS NIH HHS/United States ; },
abstract = {Methanogenic archaea (methanogens) are microorganisms that obligately produce methane as a byproduct of their energy metabolism. While most methanogens grow on CO2+H2, isolates of the Genus Methanosarcina and Methanothrix can use acetate as the sole substrate for methanogenesis. Methanogenic growth on acetate, i.e., acetoclastic methanogenesis, is hypothesized to require two distinct genetic modules: one for the activation of acetate to acetyl-CoA and the other for producing a chemiosmotic gradient using electrons derived from ferredoxin. In Methanosarcina spp., the activation of acetate to acetyl-CoA is mediated by acetate kinase (Ack) and phosphotransacetylase (Pta) whereas Methanothrix spp. encode AMP-forming acetyl-CoA synthetases (Acs). The Rhodobacter nitrogen fixation complex (Rnf) or Energy converting hydrogenase (Ech) are critical for energy conservation in Methanosarcina spp. during growth on acetate, and a F420:phenazine oxidoreductase-like complex (Fpo') likely plays an analogous role in Methanothrix spp. Here, we tested the proposed modularity of these pathways to facilitate acetoclastic methanogenesis. First, we surveyed over a hundred genomes within the Class Methanosarcinia to show that the genomic potential for acetoclastic methanogenesis using distinct combinations of modules is widespread. We then used the genetically tractable strain, Methanosarcina acetivorans, to build all modular combinations for acetoclastic methanogenesis. Our results indicate that Acs, while functional, cannot replace Ack+Pta to rescue acetate growth in M. acetivorans. Similarly, the Fpo' bioenergetic complex cannot replace Rnf. As such, our work suggests that, in addition to horizontal gene transfer of core catabolic modules, acetoclastic metabolism in methanogens requires changes in energetic modules too.},
}

@article {pmid41254203,
year = {2025},
author = {Deng, W and Li, C and Huang, Y and Liu, C and Li, R and Li, T and Wu, D and He, Y and Li, D and Yang, S and Zou, L and Zhao, K},
title = {Lignocellulose degradation capabilities and distribution of antibiotic resistance genes and virulence factors in Clostridium from the gut of giant pandas.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {1602},
pmid = {41254203},
issn = {2399-3642},
mesh = {*Lignin/metabolism ; Animals ; *Clostridium/genetics/metabolism/pathogenicity/drug effects/isolation & purification ; *Ursidae/microbiology ; *Virulence Factors/genetics ; *Drug Resistance, Microbial/genetics ; *Gastrointestinal Microbiome ; Phylogeny ; *Drug Resistance, Bacterial/genetics ; },
abstract = {Clostridium is a vital gut anaerobe in giant pandas (GPs), aiding bamboo digestion and gut homeostasis. The present study optimizes anaerobic culturing to isolate Clostridium species from GPs, evaluating their ecological roles in bamboo digestion while assessing associated pathogenic and antibiotic resistance threats. The results show that the enriching samples in liquid media facilitated the isolation of Clostridium species. A total of 14 species are obtained, with C. perfringens, C. sardiniense, and C. baratii being most prevalent. 86.30% of strains exhibit lignocellulose-degrading activity, with all C. butyricum strains displaying activity for β-glucosidase, xylanase, and manganese peroxidase. Genomic analysis identifies carbohydrate-active enzymes and metabolic pathways involved in lignocellulose degradation, short-chain fatty acid production, and essential amino acid biosynthesis. C. butyricum possesses the most hemicellulose- and cellulose-degrading genes. We also identify 19 antibiotic resistance genes (ARGs), predominantly glycopeptide-resistant van genes, and 23 virulence factors (VFs) encoded by 408 virulence genes (VGs). Notably, C. perfringens harbors the most ARGs and VFs, some of which are flanked by mobile genetic elements, suggesting risks of horizontal gene transfer. Overall, this study describes the dual role of Clostridium in GPs, contributing to dietary adaptation while also posing potential hazards due to pathogenic traits and antimicrobial resistance.},
}

*Lignin/metabolism
Animals
*Clostridium/genetics/metabolism/pathogenicity/drug effects/isolation & purification
*Ursidae/microbiology
*Virulence Factors/genetics
*Drug Resistance, Microbial/genetics
*Gastrointestinal Microbiome
Phylogeny
*Drug Resistance, Bacterial/genetics

@article {pmid41254129,
year = {2025},
author = {Allam, TA and Abdel-Kader, F and Kadry, M},
title = {Isolation, toxin gene profiling, and phylogenetic analysis of Clostridium perfringens in Egyptian fruit bats: public health and epidemiological implications.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {40354},
pmid = {41254129},
issn = {2045-2322},
mesh = {Animals ; *Clostridium perfringens/genetics/isolation & purification/classification ; *Chiroptera/microbiology ; Phylogeny ; Egypt/epidemiology ; *Clostridium Infections/epidemiology/microbiology/veterinary ; *Bacterial Toxins/genetics ; Public Health ; Feces/microbiology ; },
abstract = {Clostridium perfringens (C. perfringens) is spore forming, toxin producing bacterium causing serious diseases in both animals and man and its presence in bats, especially the Egyptian fruit bat, are ecologically important yet increasingly interact with human environments due to habitat changes which raise the concerns about their role as reservoirs for zoonotic pathogens. This study, the first of its kind in Egypt, investigates the occurrence and characteristics of C. perfringens in bats to evaluate their potential role as reservoirs for this toxin-producing, environmentally persistent foodborne pathogen. Fifty fruit bats were captured using mist nets at foraging and roosting sites. The bats were identified morphologically, and for each bat, fecal swabs and internal organs were collected (n = 100). The samples were examined bacteriologically to investigate the C. perfringens detection then confirmed biochemically and via gram staining. DNA was extracted, and toxin genotyping was conducted using multiplex PCR for main toxin genes " cpa, cpb, etx, ia, netB, cpe" whereas uniplex PCR for cpb2. Sequencing and phylogenetic analysis of cpb2 gene from four isolates were analyzed to determine genetic relatedness. Out of 100 samples examined, C. perfringens was detected in 31% (31/100) of samples, with similar occurrence in internal organs (30%) and fecal swabs (32%). All isolates carried the cpa gene (100%), while cpb, cpe, and cpb2 were detected in 83.9%, 64.5%, and 64.5% of isolates, respectively; ia, etx, netB genes were not detected. Notably, 35.5% of isolates harbored both cpe and cpb2 genes. Toxinotyping showed type C as predominant (83.9%), followed by type F (12.9%) and type A (3.2%), highlighting the epidemiological significance of type C strains. Phylogenetic analysis of cpb2 sequences indicated high genetic similarity among bat isolates and close relationships with strains from domestic animals and environmental sources, suggesting possible shared habitats and horizontal gene transfer. These findings identify bats as potential reservoirs of toxigenic C. perfringens, reinforcing the importance of integrating wildlife into One Health surveillance strategies. This study reports the first detection of C. perfringens from Egyptian fruit bats. Phylogenetic analysis revealed close genetic links to strains from domestic animals and environmental sources and these findings highlight bats' potential role as reservoirs of virulent C. perfringens.},
}

Animals
*Clostridium perfringens/genetics/isolation & purification/classification
*Chiroptera/microbiology
Phylogeny
Egypt/epidemiology
*Clostridium Infections/epidemiology/microbiology/veterinary
*Bacterial Toxins/genetics
Public Health
Feces/microbiology

@article {pmid41252978,
year = {2025},
author = {Zhu, L and Chen, X and Zhao, Z and Huang, M and Zhu, Y and Li, H and Shao, Y and Wang, M and Xiong, S and Xing, B},
title = {Plasmid engineering reveals size-dependent effects of plastic particles on horizontal gene transfer via transformation in Escherichia coli: Critical roles of plasmid size and plastic particle-bacteria spatial configuration.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140507},
doi = {10.1016/j.jhazmat.2025.140507},
pmid = {41252978},
issn = {1873-3336},
abstract = {Plastic particles impact antibiotic resistance genes (ARGs) dissemination majorly via horizontal gene transfer (HGT) in environmental media, yet how different ARGs respond to plastic particles during HGT is rarely studied, and size-dependent effects of plastic particles on HGT remain debated. Here, we investigated polystyrene (PS) particles (20 nm, 80 nm, 2000 nm, 20000 nm) mediating HGT via transformation in Escherichia coli, using engineered pUC19-derived plasmids differing in size (3.75, 5.00, 7.50 kb) and replication capacity. Nanoplastics (NPs) enhanced transformation of 3.75 kb and 5.00 kb plasmids at 0.5 mg/L but inhibited transformation at 18, 36, and 72 mg/L, while consistently inhibiting that of 7.50 kb plasmids. Meanwhile, 2000-nm microplastics (MPs) monotonously promoted HGT efficiencies, yet 20000-nm MPs decreased them (0-72 mg/L). PS particle effects on HGT were independent of plasmid replication capacity. Enhancing mechanisms for HGT majorly involved increased membrane permeability via forming bacterial surface pores (NPs, 2000-nm MPs). The inhibiting mechanism stemmed from size-dependent physical barriers on cell membranes, as observed through scanning electron microscopy and laser scanning confocal microscopy. Three-dimensional models further simulated PS particle-induced spatial barriers on cell surfaces. Our findings improve understanding of environmental ARG dissemination driven by plastic pollution.},
}

@article {pmid41251562,
year = {2025},
author = {Hu, X and Sheng, Y and Xu, Y and Li, X and Qin, C and Shen, Q and Gao, Y},
title = {Type- and Treatment Duration-Dependent Efficacy of Metal-Organic Frameworks for Combating Antibiotic Resistance Genes in Real Wastewater.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c05126},
pmid = {41251562},
issn = {1520-5851},
abstract = {Antibiotic resistance genes (ARGs) in aquatic environments pose enormous health risks. Metal-organic frameworks (MOFs) show promise in mitigating antibiotic resistance by diminishing antibiotic selection pressures and killing specific antibiotic-resistant bacteria. However, their effectiveness in reducing ARGs in real wastewater containing intact microbial communities remains unclear. This study investigated the effects of two typical MOFs, NH2-MIL-53 (Al) and NH2-UiO-66 (Zr), on ARG abundance dynamics in collected manure-contaminated wastewater. Without MOFs, ARGs naturally declined after 15 days, with a slight initial rise. The influence of MOFs on ARG abundances depends on their types and treatment time. NH2-UiO-66 (Zr) reduced ARG abundances by 13.94-29.63% after 5 days treatment, whereas NH2-MIL-53 (Al) exhibited limited efficacy. Both MOFs impeded natural ARG attenuation after 15 days, reducing attenuation efficiency by 13.06-126.37%. MOFs modified potential bacterial host abundances of ARGs (e.g., DMER64, Pigmentiphaga, and Aminobacter), likely by alleviating hydrogen competition among bacteria and inducing degradative bacterial proliferation by spontaneous degradation products, which was further supported by microbial function analysis. Additionally, MOFs stimulated antibiotic biosynthesis, potentially increasing corresponding ARG abundances. NH2-MIL-53 (Al) also enhanced ARG horizontal transfer, aligning with abundance trends. This study highlights limited efficiencies of MOFs for ARG contamination control in real wastewater, providing insights for future material development.},
}

@article {pmid41246282,
year = {2025},
author = {Ville, CJN and Orwin, PM},
title = {Completed genomes from Variovorax provide insight into genome diversification through horizontal gene transfer.},
journal = {Current research in microbial sciences},
volume = {9},
number = {},
pages = {100497},
pmid = {41246282},
issn = {2666-5174},
abstract = {Approximately 10% of all bacterial genomes sequenced thus far contain a secondary replicon. This property of bacterial populations vastly increases genomic diversity within phylogenetically narrow groups. Members of the genus Variovorax have extensive heterogeneity in genome architecture, including sequenced isolates containing plasmids, megaplasmids, and chromids. Many of the Variovorax genomes in the NCBI database were generated using short-read data exclusively and were assembled to the permanent draft stage. We acquired a set of these isolates and used the Oxford Nanopore MinION to generate additional data to allow for hybrid assembly of these genomes. Here we present the finished assemblies of 15 Variovorax isolates from diverse ecosystems that were previously only available as permanent drafts. When added to the previously published Variovorax assemblies for EPS, CSUSB, and VAI-C and those published by other groups, we found significant diversity in genome architecture. We found that there are plasmids, megaplasmids, and chromids that are distinguishable using Guanine-Cytosine (G+C content) content as a signal. We identified a plasmid integration event in NFACC27 and suggest potential evolutionary relationships in the secondary replicons based on ParB homology as well as ANI. The evidence suggests that Variovorax, like its sister taxon Burkholderia, is highly capable of acquiring and maintaining stable secondary replicons. The plasticity of these architectures and the mechanisms for maintenance remain a topic for future research.},
}

@article {pmid41243649,
year = {2025},
author = {Zhou, L and Reuter, T and Schumann, K and Mayer, M and Hanauska, DM and Barra, L},
title = {Homoterpene Biosynthesis in Fungi.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {},
number = {},
pages = {e17837},
doi = {10.1002/anie.202517837},
pmid = {41243649},
issn = {1521-3773},
support = {//Deutsche Forschungsgemeinschaft/ ; },
abstract = {Homoterpenes carrying an additional methyl group in their carbon backbones are an emerging class of natural products that challenge the biogenic isoprene rule, stating that terpenes are composed of integer multiples of C5 units. We and others have recently shown that biosynthetic pathways to homoterpenes are widespread in bacteria, leading either to specialized scaffolds such as the "Greek philosophers homoterpenes" in Pseudomonadota or to simple methyl analogs of central eudesmanes and germacranes ("humanists homoterpenes") in Actinomycetota. Here we report the discovery of the first homoterpene biosynthetic pathway in the fungal kingdom using targeted genomic data mining in combination with in vitro pathway reconstitution. Functional analyses of a fungal methyltransferase (NdiMT) and terpene cyclase (NdiTC) pair from the plant-pathogenic fungus Neonectria ditissima, the causative agent of apple canker, led to the discovery of a novel homosesquiterpene featuring an intriguing heptamethylbicyclo[3.3.1]nonane scaffold. Phylogenetic analyses indicate that the fungus acquired the key methyltransferase via horizontal gene transfer from bacteria, whereas the terpene cyclase appears to have evolved from a fungal ancestor. The discovery raises fundamental questions about the evolutionary rationale and functional consequences of terpene methylation in nature.},
}

@article {pmid41242524,
year = {2025},
author = {Debatisse, K and Brunie, M and Darracq, B and Bandini, E and Littner, E and Rocha, EPC and Mazel, D and Loot, C},
title = {Bacterial natural transformation drives cassette shuffling and simplifies recombination in chromosomal integrons.},
journal = {Nucleic acids research},
volume = {53},
number = {21},
pages = {},
pmid = {41242524},
issn = {1362-4962},
support = {CNRS-UMR 3525//Institut Pasteur, the Centre National de la Recherche Scientifique/ ; EQU202103012569//Fondation pour la Recherche Médicale/ ; EQU201903007835//Fondation pour la Recherche Médicale/ ; FDT202404018553//Fondation pour la Recherche Médicale/ ; ANR-21-CE12-0002-01//Agence Nationale de la Recherche/ ; ANR-24-CE12-7883-01//Agence Nationale de la Recherche/ ; ANR-20-CE35-014//Agence Nationale de la Recherche/ ; ANR-10-LABX-62-IBEID//French Government's Investissement d'Avenir program Laboratoire d'Excellence 'Integrative Biology of Emerging Infectious Diseases'/ ; //French Government/ ; PIA/ANR-16-CONV-0005 INCEPTION//Investissement d'Avenir program/ ; //Direction Générale de l'Armement/ ; },
mesh = {*Integrons/genetics ; *Recombination, Genetic ; *Vibrio cholerae/genetics ; Integrases/metabolism/genetics ; Attachment Sites, Microbiological/genetics ; *Transformation, Bacterial ; *Chromosomes, Bacterial/genetics ; Gene Transfer, Horizontal ; },
abstract = {Integrons act as biobanks of gene cassettes conferring functions crucial for bacterial defense, including protection against phages and antibiotics. They enable bacterial on-demand adaptation through capture and shuffling of the cassettes under stress conditions. Our results underscore the significant role of horizontal gene transfer in integron cassette recombination. We discover that sedentary chromosomal integrons (SCIs), such as those found in Vibrio cholerae, efficiently excise and recruit cassettes from linear single-stranded DNA fragments acquired during natural transformation. We propose a simplified mechanism for the cassette excision process from this type of substrates, requiring only a single strand exchange at the attC recombination sites, ruling out any replicative mechanism. We also observe a higher specificity of the V. cholerae integrase for attC recombination sites from the V. cholerae repeat-type, a trait differentiating SCI integrases from the mobile integron (MI) ones. This specificity, likely stemming from a long-term co-evolution between SCI integrases and attC sites, impedes the recruitment of cassettes from phylogenetically distant integrons. Collectively, our findings may explain the greater attC site homogeneity observed in SCIs compared to MIs and showcase the role of natural transformation in driving cassette shuffling and simplifying the cassette recombination mechanism, thereby expanding bacterial phenotypic diversity.},
}

*Integrons/genetics
*Recombination, Genetic
*Vibrio cholerae/genetics
Integrases/metabolism/genetics
Attachment Sites, Microbiological/genetics
*Transformation, Bacterial
*Chromosomes, Bacterial/genetics
Gene Transfer, Horizontal

@article {pmid41241240,
year = {2025},
author = {Wang, J and Song, T and Gao, Q and Zhou, Y and Yang, Y and Gao, X and Ma, R and Li, G and Jiang, T and Chang, J and Yuan, J},
title = {Overlooked closed reactor thermal steam discharge: steering ARGs fate and microbiome evolution in kitchen waste-livestock manure composting.},
journal = {Bioresource technology},
volume = {441},
number = {},
pages = {133651},
doi = {10.1016/j.biortech.2025.133651},
pmid = {41241240},
issn = {1873-2976},
abstract = {Steam condensation and reflux in closed conditions impairs composting efficiency, which can be effectively addressed by a negative pressure condensation system. However, microecological dynamics driving microbial succession and antibiotic resistance genes (ARGs) fate during steam discharge-induced rapid maturation remain unclear. This study investigates the effect of real-time steam emission on the removal of ARGs in a closed composting system. Results show that steam discharge significantly expedites the temperature elevation and boosts the high-temperature removal efficiency of ARGs. Compared with the initial level, the total abundance removal rate of target ARGs reached 98 %. However, it promotes the spread and enrichment of specific ARGs (tetX, aadA, strB, ermF, and sul2) during the maturity stage by stimulating bacterial community dynamics, thereby reducing the removal rate to 68 %. The main mechanisms affecting ARGs changes are as follows: steam discharge relieves the environmental stress on bacteria, shifts community assembly toward non-dominant stochastic processes (|βNTI| < 2), thereby enhancing biodiversity (Shannon index) and the stability of bacterial communities. Meanwhile, these highly active bacteria exhibit strong network connectivity, facilitating horizontal gene transfer (HGT) mediated by intl1 and intl2 during the maturation stage. This study shows steam emission improves ARGs removal but exacerbates specific ARGs spread via microbial redistribution.},
}

@article {pmid41240826,
year = {2025},
author = {Wu, K and Wang, Q and Liu, S and Sun, Y and Tang, Y and Zhang, A and Lei, C and Wang, H and Yang, X},
title = {A One Health perspective: Genomic insights into temporal trends of antimicrobial resistance and zoonotic transmission risks in Escherichia coli from human and swine.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140475},
doi = {10.1016/j.jhazmat.2025.140475},
pmid = {41240826},
issn = {1873-3336},
abstract = {Antimicrobial resistance (AMR) poses a significant challenge within the One Health framework. By integrating genomic data from 824 E. coli isolates obtained from 22 swine farms in southwestern China with 8432 publicly available genomes from human and swine sources, this study provides comprehensive insights into the temporal trends and divergence of AMR in human and swine E. coli populations, the risk of AMR transmission from swine to human, and the evolutionary mechanisms underlying the human adaptation of ST2 strains. The results revealed an overall increase in AMR until approximately 2016, followed by a subsequent decline. However, resistance to tetracyclines, quinolones, and phenicols continues to exhibit an upward trend, highlighting the urgency of enhancing regulatory measures targeting these drugs. Horizontal gene transfer play pivotal roles in shaping distinct AMR profiles in human and swine strains. ST2 E. coli was identified as a major carrier of AMR in both human and swine, and also served as the primary reservoir of blaNDM-5 within the human-associated lineage. During evolution, ST2 E. coli underwent significant genetic changes, including the enrichment of blaNDM-5 and remodeling of virulence factors, facilitating its transition from a generalist lineage colonizing both human and swine to a human-adapted lineage.},
}

@article {pmid41237728,
year = {2025},
author = {Meng, Q and Wang, J and Li, K and Zhang, Y and Hu, Z and Wang, F and Pan, F and Fu, J and Dang, C},
title = {Low-dose chlorine disinfection poses a greater potential risk of antibiotic resistance genes and their pathogenic hosts.},
journal = {Water research},
volume = {289},
number = {Pt B},
pages = {124895},
doi = {10.1016/j.watres.2025.124895},
pmid = {41237728},
issn = {1879-2448},
abstract = {Identifying the responses of antibiotic resistance genes (ARGs) and their hosts to chlorine disinfection is necessary because it has been paradoxically reported to both amplify and suppress antibiotic resistance in water treatment processes. In this study, our integrated metagenomic and metatranscriptomic analysis of sequencing batch reactors under different chlorine disinfection conditions (0, 2, 6, and 10 mg/L) in activated sludge reveals that low-dose chlorine obviously increases ARG abundance, diversity, and transcriptional activity, particularly for multidrug, β-lactam, and tetracycline types, while higher doses reduce transcriptional diversity and activity. Acinetobacter johnsonii, a pathogen abundant and active under chlorine-addition conditions, poses a high risk of ARG transmission due to its multiple mobile genetic elements and potential involvement in horizontal gene transfer with non-pathogens. Notably, chlorine disinfection may simultaneously promote the co-transfer of chlorine resistance and antibiotic resistance genes, such as the qacE gene, with the involvement of plasmids and integrons. Overall, this study demonstrates that low-dose chlorine may promote greater ARG enrichment, mobility, and pathogenic potential in activated sludge. The findings highlight overlooked risks of low-concentration residual chlorine, urging reconsideration of disinfection strategies to protect public health.},
}

@article {pmid41237727,
year = {2025},
author = {Zhao, Z and Zhao, Y and Hua, M and Yao, X and Hu, B},
title = {Deep metagenomic insights into the formation characteristics of the resistome in Pristine Saline Lakes.},
journal = {Water research},
volume = {289},
number = {Pt B},
pages = {124937},
doi = {10.1016/j.watres.2025.124937},
pmid = {41237727},
issn = {1879-2448},
abstract = {Pristine and isolated ecosystems remain underexplored in resistome research, leaving a major gap in understanding how antibiotic resistance genes (ARGs) persist and spread outside human influence. To address this, we performed the first long-term, systematic, ultra-deep metagenomic survey of four high-altitude pristine saline lakes in the Altun Shan National Nature Reserve-an uninhabited region of the Qinghai-Tibet Plateau-generating 1.8 terabases of sequencing data. We identified a total of 756 ARG subtypes spanning 28 ARG types in all sampled lakes, with the clinically relevant polymyxin resistance gene, ugd, accounting for 30.5 % of the total ARG abundance. Moreover, ugd showed high mobility potential, with 183 horizontal gene transfer (HGT) events identified across 18 genera, and was widely associated with mobile genetic elements (MGEs). Similarity analyses revealed that the ARG profiles of pristine saline lakes were most comparable to those of marine environments, suggesting that salinity is a key ecological driver shaping the prevalence of polymyxin resistance genes. These findings indicate that pristine saline lakes can act as previously underexplored reservoirs and exchange hubs for clinically important resistance genes. Our results reveal the abundance and dissemination potential of ugd in isolated ecosystems and provide new insights into how natural environmental factors independently shape the resistome, with implications for One Health antimicrobial resistance surveillance.},
}

@article {pmid41237617,
year = {2025},
author = {Cornacchia, A and Di Cesare, A and Corno, G and Sbaffi, T and Centorotola, G and Chiaverini, A and Saletti, MA and Ricchiuti, L and Cammà, C and Piccone, P and Ranieri, SC and D'Alterio, N and Pomilio, F},
title = {Bathing seawater and sand as reservoirs of clinically relevant and antimicrobial resistant Klebsiella pneumoniae strains.},
journal = {The Science of the total environment},
volume = {1006},
number = {},
pages = {180930},
doi = {10.1016/j.scitotenv.2025.180930},
pmid = {41237617},
issn = {1879-1026},
abstract = {Klebsiella pneumoniae is included in the ESKAPE list of bacteria, which are currently considered the greatest threat to human health. It is widely distributed in the environment, including waters, soils, and plants. According to the One Health concept, it is essential to enhance our understanding of the distribution and genetic characteristics of this human pathogen in aquatic ecosystems, particularly in environments with frequent human contact, such as beaches and seawater used for recreational purposes. The aim of this study is to investigate whether bathing seawater and sand could serve as reservoirs for antimicrobial- resistant and clinically relevant K. pneumoniae strains. A total of 60 seawater and 54 sand samples were collected along the Abruzzo Region (Central Italy) shoreline during the bathing season. K. pneumoniae was detected at 13 seawater and 12 sand sites, mainly in areas heavily impacted by anthropogenic pollution and close to river mouths. Several strains belonged to sequence types (STs) of clinical interest, and one classified as ST348 was multidrug-resistant and harbored multiple antimicrobial resistance genes (ARGs). All the collected strains had ARGs in their genome, several of which were located on putative plasmids or phages, enhancing the potential for their horizontal gene transfer. This study confirms that bathing seawater and sand could contribute to the selection and spread of clinically relevant K. pneumoniae, with anthropogenic pollution influencing its presence. These environments should be recognized as important reservoirs and monitored for their potential to transmit this pathogen to humans.},
}

@article {pmid41234739,
year = {2025},
author = {Jin, L and Chen, S and Kang, R and Li, C and Yang, S and Yang, Q and Zhao, K and Zou, L},
title = {Variation and spread of resistomes in swine manure, manure slurries, and long-term manure-fertilized soils.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1683394},
pmid = {41234739},
issn = {1664-302X},
abstract = {BACKGROUND: Application of swine manure to soils exacerbates environmental antimicrobial resistance (AMR). However, a comprehensive evaluation of anaerobic digestion's (AD) mitigation potential against AMR and its influencing factors in swine manure-to-soil systems remains lacking.

METHODS: We employed mass spectrometry, metagenomics, and whole-genome sequencing (WGS) to investigate the fate of antibiotics, metals, and antibiotic resistance genes (ARGs) across manures, slurries, and soils from eight pig farms.

RESULTS: Anaerobic digestion reduced antibiotic and metal (except ciprofloxacin) content and risks in manure, but had limited effects on total ARG abundance, while increasing ARG network modularity. High-risk ARG abundance significantly increased from 404.7 in manure to 843.2 in slurries, with health-risk scores rising 1.88-fold during anaerobic digestion. Metagenomic analysis showed metal resistance gene (MRG) diversity and abundance decreased during anaerobic digestion, along with reduced ARG-MRG co-occurrence frequency, whereas mobile genetic element (MGE) diversity and ARG-MGE co-occurrence frequency increased. Escherichia coli was identified as the dominant ARG host. WGS of E. coli strains confirmed horizontal gene transfer (HGT) of nine ARGs (e.g., sul3 and blaTEM-1), and metagenomics suggested HGT of four ARGs (e.g., tet(M)) across different pathogens. Chromium concentrations, bacterial communities and MGEs were significantly associated with ARG profiles. Long-term slurry application resulted in elevated antibiotic, metal, and ARG concentrations in soils, with concomitant increases in high-risk ARGs and health risks.

CONCLUSION: This study demonstrates AD's limited effect on mitigating overall ARG abundance and highlights MGEs as critical drivers of ARG maintenance and dissemination from manure to soil process, guiding manure treatment optimization to reduce agricultural AMR risks.},
}

@article {pmid41232214,
year = {2025},
author = {Shoaib, M and Hameed, MF and Aqib, AI and Wang, W and Wang, Q and Wang, S and Pu, W},
title = {Emerging threat of antimicrobial resistance determinants and plasmid replicon types acquisition by Escherichia coli of poultry and other food-producing animal origin in China: local findings with global implications.},
journal = {Poultry science},
volume = {104},
number = {12},
pages = {106055},
doi = {10.1016/j.psj.2025.106055},
pmid = {41232214},
issn = {1525-3171},
abstract = {Escherichia coli (E. coli) is a commensal and pathogenic bacterium responsible for harmless to severe infections in humans and food-producing animals inlcuding poultry. E. coli can significantly impact ecology and is a bioindicator of antimicrobial resistance (AMR) contamination. The global emergence of AMR is depleting the antimicrobial reserves for human use and highlights the need for antimicrobial stewardship. Generally, AMR emerges through the unjustified use of antibiotics in humans, food-producing animals, and agricultural settings. Animal species carry E. coli in their intestinal tract as a commensal organism; genetic flexibility and adaptability allow this bacterium to acquire diverse AMR determinants through selective pressure and horizontal gene transfer (HGT). HGT can be important in spreading the AMR determinants through the food chain and environmental exposure. Human exposure to this bacterium can occur through various sources, including meat contamination during animal slaughtering, animal waste, contamination of raw or processed animal milk, and the consumption of contaminated water, allowing E. coli carrying antimicrobial resistance genes (ARGs) to be transferred to humans. Animal waste can also be a potential contaminant of environmental sites and also facilitates the rapid dissemination of AMR determinants due to anthropogenic activities. There is an urgent need to establish proper guidelines for controlling the spread of AMR through E. coli from poultry and other food-producing animals to humans and the environment following the One Health approach. To meet this approach, potential knowledge about the recent AMR determinants acquired by E. coli and their dissemination drivers is needed. Therefore, this review concisely elaborates the E. coli epidemiology, phenotypic AMR, genotypic determinants acquired, and their dissemination driver.},
}

@article {pmid41231926,
year = {2025},
author = {Mirkin, FG and Mugford, ST and Thole, V and Marzo, M and Hogenhout, SA},
title = {Effector innovation in genome-reduced phytoplasmas and other host-dependent mollicutes.},
journal = {PLoS genetics},
volume = {21},
number = {11},
pages = {e1011946},
pmid = {41231926},
issn = {1553-7404},
mesh = {*Phytoplasma/genetics/pathogenicity ; *Genome, Bacterial ; Gene Transfer, Horizontal/genetics ; *Bacterial Proteins/genetics/metabolism ; Plant Diseases/microbiology/genetics ; *Host-Pathogen Interactions/genetics ; Animals ; Evolution, Molecular ; },
abstract = {Obligate host-associated bacteria with reduced genomes, such as phytoplasmas, face strong evolutionary constraints, including metabolic dependence on hosts, limited opportunities for horizontal gene transfer (HGT), and frequent population bottlenecks. Despite these limitations, phytoplasmas, which are parasitic, insect-transmitted plant pathogens, maintain a diverse arsenal of secreted effectors that manipulate both plant and insect hosts to promote infection and transmission. These effectors can suppress immunity and reprogram plant development, inducing alterations such as witch's broom and leaf-like flowers, through ubiquitin-independent degradation of key transcription factors. However, how phytoplasmas diversify and maintain these effectors in the absence of frequent genetic exchange remains unclear. To address this, we analysed the effectoromes of 239 phytoplasma genomes and identified a diverse set of secreted proteins, which we designated as putative Phytoplasma Effectors (PhAMEs). We found that PhAMEs targeting evolutionarily conserved and structurally constrained surfaces of host proteins are widespread across phytoplasmas. These effectors adopt compact, efficient folds. They often function as molecular scaffolds with dual interaction surfaces capable of linking host proteins or integrating signalling pathways. Such scaffolding PhAMEs have evolved multiple times independently, providing clear evidence of convergent evolution. Despite severe genomic constrains imposed by genome reduction and limited HGT, gene duplications, interface variations, domain fusions, and repeat expansions have helped the shaping effector fold and diversity. While the overall effector repertoire of phytoplasmas appeared largely unique, some PhAME domains share similarities with proteins from other mollicutes and pathogens. Collectively, our findings shed light on how genome-reduced bacteria innovate molecular functions and offer insights into phytoplasma biology, effector evolution, and host-pathogen dynamics. They also lay the groundwork for protein engineering approaches aimed at discovering or designing novel biomolecules with biotechnological potential.},
}

*Phytoplasma/genetics/pathogenicity
*Genome, Bacterial
Gene Transfer, Horizontal/genetics
*Bacterial Proteins/genetics/metabolism
Plant Diseases/microbiology/genetics
*Host-Pathogen Interactions/genetics
Animals
Evolution, Molecular

@article {pmid41231016,
year = {2025},
author = {Wang, YL and Aghdam, SA and Brown, AMV and Deonarine, A},
title = {Global Survey of Mercury Methylation and Demethylation Microbial Communities in Wastewater and Activated Sludge.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c11448},
pmid = {41231016},
issn = {1520-5851},
abstract = {Wastewater treatment plants (WWTPs) are an understudied source of mercury methylating and demethylating microbes to downstream aquatic and terrestrial environments, where methylmercury production and subsequent bioaccumulation in the food web occur. To identify methylators and demethylators and evaluate their occurrence in WWTPs, metagenomic and metatranscriptomic analyses of raw sewage, activated sludge, and effluent samples from WWTPs across the globe were conducted. Results indicated that hgcA- and merB-carriers were widespread in WWTPs, with higher abundance in raw sewage and sludge compared to treated effluent. Bdellovibrionota were identified as merB-carriers, linking them to demethylation for the first time. Novel conserved motifs of hgcB and fused hgcAB were also identified. 30% of hgcA genes were colocalized with arsenic-resistance operons on the same contig, while all merB-carriers contained arsenic resistance genes (ars), though merB and arsR were not colocated. Antibiotic resistance genes were also present in the genomes of multiple hgcA- amd merB-carriers, including one sample where hgcA and the antiseptic/antibiotic resistant gene (qacG) were colocated on the same contig, suggesting possible coselection in environments containing antibiotics. Mobile genetic element-mediated horizontal gene transfer was identified as a mechanism facilitating the genetic transfer of hgcA. Overall, these findings highlight WWTPs as reservoirs of genes involved in mercury methylation and demethylation, with potential implications for mercury cycling in downstream environments.},
}

@article {pmid41226516,
year = {2025},
author = {Sum, DKC and Chong, YY and Tan, JL},
title = {Comparative Analyses Suggest Genome Stability and Plasticity in Stenotrophomonas maltophilia.},
journal = {International journal of molecular sciences},
volume = {26},
number = {21},
pages = {},
pmid = {41226516},
issn = {1422-0067},
mesh = {*Stenotrophomonas maltophilia/genetics/pathogenicity ; *Genome, Bacterial ; *Genomic Instability ; Gene Transfer, Horizontal ; Interspersed Repetitive Sequences ; Evolution, Molecular ; Virulence/genetics ; Phylogeny ; Linkage Disequilibrium ; },
abstract = {Stenotrophomonas maltophilia (S. maltophilia) is a multidrug-resistant opportunistic pathogen. There are an increasing number of case reports on S. maltophilia infections in recent years, and the species is becoming a public health concern. Many studies have focused on profiling and pangenome of the species, particularly on their antibiotic resistance and virulence genes. However, there is a lack of studies on mobile genetic elements (MGEs), a subset of pangenome that significantly contributes to the diversity, stability, and plasticity of a population. In this study, 20 genomes of S. maltophilia were downloaded from the NCBI Genome database. The genomes were subjected to profiling of MGEs, their impact on the population structures, and the evaluation of evolutionary trends of the core genomes. The cataloguing of MGEs indicated active horizontal gene transfer events in the S. maltophilia's population. Multiple virulence and drug resistance genes were predicted within and outside of the MGEs. We observed multiple chromosomal rearrangements in the genomes, most likely caused by MGEs, affecting up to approximately 50% of a single genome sequence. A high number of linkage disequilibrium sites were also predicted in the core genomes. This study provides insights into stability in the core and plasticity in the accessory regions in the S. maltophilia population.},
}

*Stenotrophomonas maltophilia/genetics/pathogenicity
*Genome, Bacterial
*Genomic Instability
Gene Transfer, Horizontal
Interspersed Repetitive Sequences
Evolution, Molecular
Virulence/genetics
Phylogeny
Linkage Disequilibrium

@article {pmid41224769,
year = {2025},
author = {Ahn, E and Kim, J and Jiang, J and Kim, J and Muszyński, A and Kasperkiewicz, K and Shin, H and Cao, Y and Soh, Y and Park, Y and Heiss, C and Fernando, LDP and Azadi, P and Wang, Y and Jeon, B and Ryu, S},
title = {Colistin resistance plasmids dually enhance bacterial virulence and antibiotic resistance via surface polysaccharide biosynthesis.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {9966},
pmid = {41224769},
issn = {2041-1723},
support = {R24 GM137782/GM/NIGMS NIH HHS/United States ; R24GM137782//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; NRF-2023R1A2C1006359//National Research Foundation of Korea (NRF)/ ; DE-SC0015662//U.S. Department of Energy (DOE)/ ; },
mesh = {*Colistin/pharmacology ; *Plasmids/genetics/metabolism ; Virulence/genetics ; *Escherichia coli/genetics/pathogenicity/drug effects/metabolism ; Animals ; Escherichia coli Proteins/genetics/metabolism ; Mice ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Gene Expression Regulation, Bacterial ; Operon/genetics ; *Polysaccharides, Bacterial/biosynthesis ; Escherichia coli Infections/microbiology ; },
abstract = {Plasmids carrying the mobilized colistin-resistance gene mcr-1 are prevalent among multidrug-resistant Gram-negative pathogens, yet their broad impact on bacterial physiology and virulence remains unclear. Here, we demonstrate that acquisition of an mcr-1 plasmid concurrently increases antimicrobial resistance and pathogenicity in Escherichia coli. On the same plasmid, the XRE-family transcriptional regulator EcaR cooperates with MCR-1 to activate the wec operon, driving biosynthesis of two surface polysaccharides: enterobacterial common antigen (ECA) and a high-molecular-weight O-chain. Expression of these surface polysaccharides increases bile resistance and virulence in a murine model and further elevates colistin resistance. MCR-1 enhances transcription of upstream genes in the wec operon, whereas EcaR directly activates an internal promoter (PwecE) to induce downstream gene expression. Thus, both components are required for surface polysaccharide expression, and deletion of either abolishes the phenotype. Genomic analysis of publicly available mcr plasmids reveals widespread co-occurrence of mcr-1 and ecaR on IncI2 and IncX4 plasmids, indicating their functional complementarity. These findings uncover a mechanism by which resistance plasmids remodel the bacterial surface, linking horizontal gene transfer to coordinated regulation of antimicrobial resistance and virulence.},
}

*Colistin/pharmacology
*Plasmids/genetics/metabolism
Virulence/genetics
*Escherichia coli/genetics/pathogenicity/drug effects/metabolism
Animals
Escherichia coli Proteins/genetics/metabolism
Mice
*Drug Resistance, Bacterial/genetics
Anti-Bacterial Agents/pharmacology
Gene Expression Regulation, Bacterial
Operon/genetics
*Polysaccharides, Bacterial/biosynthesis
Escherichia coli Infections/microbiology

@article {pmid41222722,
year = {2025},
author = {Kulshreshtha, A and Jana, S and Rana, R and Khan, A},
title = {Clostridium botulinum serotype B: microbial genetics, toxin biosynthesis, current applications, and future prospects.},
journal = {Archives of microbiology},
volume = {208},
number = {1},
pages = {9},
pmid = {41222722},
issn = {1432-072X},
}

@article {pmid41221393,
year = {2025},
author = {Ijaz, UZ and Qiu, Y and Zhou, X and Yin, H and Li, B},
title = {Editorial: Horizontal transfer of antibiotic resistance genes in the environment: dynamic, contributing factors, and control.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1692478},
doi = {10.3389/fmicb.2025.1692478},
pmid = {41221393},
issn = {1664-302X},
}

@article {pmid41220211,
year = {2025},
author = {Muller, H and Andam, CP},
title = {Diversification of the staphylococcal cassette chromosome through distinct mechanisms of horizontal transfer.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evaf214},
pmid = {41220211},
issn = {1759-6653},
abstract = {The staphylococcal cassette chromosome mec (SCCmec) is a mobile genetic element that carries the mecA gene conferring resistance to beta-lactam antibiotics. While SCCmec is widely disseminated in Staphyloccocus aureus, its diversity and evolutionary history across different taxonomic scales have not been investigated in detail. To elucidate the mechanisms governing the diversification of SCCmec, we carried out the largest systematic analysis of SCCmec to date. We focused on the Staphylococcaceae family, which is the primary cellular host of SCCmec. We scanned 2,556 complete genomes, representing 75 species and eight genera within Staphylococcaceae. For this, we developed SCCeeker, a tailored pipeline to detect SCCmec across a large-scale genomic dataset. We uncovered 1,419 candidate SCCmec regions in 3 of 5 Mammaliicoccus species and 32 of 54 Staphylococcus species. SCCmec-carrying species are not more cladistically related than those without the SCCmec. The present study reveals that the evolution of SCCmec locus is driven by multiple mechanisms of horizontal transfer: transposition of insertion sequences IS1272 and IS6/IS431, transfer of entire cassette or fragments of it, cassettes carried by putative plasmids, formation of chimeric cassettes, and recombination of homologous sequences. The multimodal shuffling of SCCmec elements creates a genetically diverse cassette pool, and sheds light on the independent evolution of mobile elements and the origins of SCCmec.},
}

@article {pmid41217690,
year = {2025},
author = {Nguyen, HN and Kim, OTP and Tran, TT},
title = {Metagenomic analysis of microbial communities and associated resistance genes, virulence genes, and mobile genetic elements in natural honey from Mu Cang Chai, Vietnam.},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {11},
pages = {445},
pmid = {41217690},
issn = {1573-0972},
support = {B2023-SPH17; VINIF.2021.TS.127//The Ministry of Education and Training, Vietnam; PhD Scholarship Programme of Vingroup Innovation Foundation (VINIF)/ ; B2023-SPH17; VINIF.2021.TS.127//The Ministry of Education and Training, Vietnam; PhD Scholarship Programme of Vingroup Innovation Foundation (VINIF)/ ; },
mesh = {*Honey/microbiology ; Vietnam ; *Bacteria/genetics/classification/isolation & purification/pathogenicity/drug effects ; *Virulence Factors/genetics ; *Metagenomics/methods ; *Interspersed Repetitive Sequences/genetics ; *Drug Resistance, Bacterial/genetics ; Bees/microbiology ; Animals ; Anti-Bacterial Agents/pharmacology ; *Microbiota/genetics ; Genes, Bacterial ; Virulence/genetics ; },
abstract = {Natural honey is preferred over honey from farmed bees in Vietnam, often commanding higher prices; therefore, it needs proper guidance. Environmental DNA from natural honey can be used to monitor its safety and authenticate its quality, as it contains DNA traces from various organisms. In this study, shotgun metagenomic sequencing was employed to identify risk factors in three natural honey samples from Mu Cang Chai, one of the central honey-producing regions in Northwest Vietnam. Our data revealed that more than 95% of the identified DNA belonged to bacteria in all three samples. Some opportunistic pathogenic bacteria, such as Klebsiella pneumoniae, Burkholderia contaminans, and Ralstonia picketti, were found dominant in the examined samples. Moreover, the bacteria in these honey samples carried numerous antibiotic resistance genes (ARGs), as well as virulence genes (VGs). The resistome profiles revealed the detection of 491 ARG sequences across three honey samples, belonging to 43 gene families that encode various resistance proteins. The most frequently encountered drug classes associated with these ARGs were cephalosporins, fluoroquinolones, and tetracyclines. On the other hand, the virulome profiles showed a rich composition of VGs: a total of 94 unique VGs linked to 25 virulence factors. They included nutritional factors, secretion systems, biofilm formation, exotoxins, and immunomodulation; the nutritional factors were the most prevalent function of these VGs. Mobilome profiles showed that only a small fraction of ARGs (0.6%) and VGs (15%) were located on mobile genetic elements (MGEs) such as plasmids and proviruses, suggesting most were chromosomally encoded; however, the presence of MGEs carrying these determinants (ARGs and VGs) still indicates a latent potential for horizontal gene transfer. Although these results are based on a case study of only three samples of natural honey collected in Mu Cang Chai, they highlight the need for a broader examination and the importance of monitoring the risk of pathogenicity in unprocessed foods, such as natural honey.},
}

*Honey/microbiology
Vietnam
*Bacteria/genetics/classification/isolation & purification/pathogenicity/drug effects
*Virulence Factors/genetics
*Metagenomics/methods
*Interspersed Repetitive Sequences/genetics
*Drug Resistance, Bacterial/genetics
Bees/microbiology
Animals
Anti-Bacterial Agents/pharmacology
*Microbiota/genetics
Genes, Bacterial
Virulence/genetics

@article {pmid41217184,
year = {2025},
author = {Creagh, JW and Rolfsmeier, M and Evans, KJ and Bizarria, R and Reetz, DC and Badigian, TJ and Fredericks, LR and Hasenoehrl, AM and Brown, AP and Graves, BM and Alexander, CK and Rodrigues, A and Stoffregen, EP and Patel, JS and Ytreberg, FM and Rowley, PA},
title = {The Saccharomyces killer toxin K62 is a protein of the aerolysin family.},
journal = {mBio},
volume = {},
number = {},
pages = {e0142525},
doi = {10.1128/mbio.01425-25},
pmid = {41217184},
issn = {2150-7511},
abstract = {UNLABELLED: K62 is an antifungal killer toxin produced by Saccharomyces paradoxus, encoded by a double-stranded RNA satellite. The toxin exhibits a unique antifungal activity but lacks sequence homology to other killer toxins, and its antifungal mechanism of action remains unknown. To understand the function of K62, its tertiary structure was predicted using AlphaFold, followed by molecular dynamics simulations to create high-confidence molecular models. These analyses revealed that K62 monomers closely resemble the five-beta-strand domain found in pore-forming aerolysin toxins. Models of K62 oligomers yielded a circular complex and beta-barrel with structural and biochemical similarities to aerolysin-family pre-pores and pores. Consistent with the formation of aerolysin-like pores, recombinant K62 assembled into membrane-associated high molecular weight oligomers (>250 kDa) that were heat- and detergent-resistant. K62 has more than 1,000 uncharacterized sequence homologs, which were mostly found in fungi of the Ascomycota, as well as in the Chytridiomycota, Basidiomycota, plants, and bacteria, with evidence of extensive horizontal gene transfer. Homologs were also identified in pathogenic fungal species, including human and plant pathogens from the Candida and Fusarium genera, but unlike aerolysins, K62 appeared to be non-toxic to higher eukaryotes. K62 is the first aerolysin family protein discovered in yeasts, revealing a likely role in fungal niche competition and establishing an entirely new, expansive family of aerolysin-like proteins.

IMPORTANCE: Pore-forming toxins are potent biological weapons used across nature, from virulence factors to immune defense proteins. This study identifies K62, a little-known antifungal toxin produced by a wild yeast, as a structural and functional relative of the aerolysin family, which is well-known for forming damaging pores in cell membranes. Using structure prediction, molecular simulations, and biochemical analysis, we show that K62 assembles into large, stable pore-like complexes. Remarkably, K62 is just one member of a large and previously unrecognized family of similar toxin-like proteins found in fungi, plants, and bacteria, including pathogens that affect humans and crops. These findings uncover an unexpected evolutionary link across kingdoms, suggesting that pore-forming toxins may play a widespread role in fungal pathogenesis and microbial warfare. This work lays the foundation for understanding a new group of antifungal molecules and their potential impacts on health, agriculture, and microbial ecology.},
}

@article {pmid41216876,
year = {2025},
author = {Zhao, M and He, M and Lin, X and Wu, K and Yang, F and Chen, X and Li, H and Wang, H and Tang, Y},
title = {Identification of Outer Membrane Vesicles as a New Vehicle Mediating Antibiotic Resistance Gene Transfer in Campylobacter.},
journal = {Journal of extracellular vesicles},
volume = {14},
number = {11},
pages = {e70195},
pmid = {41216876},
issn = {2001-3078},
support = {(32273061,U21A20257)//the National Natural Science Foundation of China/ ; (2023NSFSC0174,2021ZDZX0010)//the Sichuan Science and Technology Programs/ ; (2022YFC2303900,2023YFD1801001)//the National Key Research and Development Program of China/ ; },
mesh = {*Gene Transfer, Horizontal ; *Extracellular Vesicles/metabolism/genetics ; *Campylobacter jejuni/genetics/drug effects ; Plasmids/genetics ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; *Campylobacter coli/genetics/drug effects ; *Campylobacter/genetics ; *Bacterial Outer Membrane/metabolism ; },
abstract = {The emergence and worldwide dissemination of antibiotic resistance genes (ARGs) compromise antibiotic therapy and are a major public health crisis. Horizontal gene transfer (HGT) plays a major role in the spread of ARGs among bacterial pathogens. Outer membrane vesicles (OMVs), which are membrane-bound particles and naturally released by Gram-negative bacteria, have been reported to carry a variety of cargos such as DNA, proteins and lipids. However, it remains unknown whether OMVs mediate transfer of ARGs in Campylobacter, an important foodborne pathogen whose resistance to antibiotics poses a serious threat to public health. To close this knowledge gap, we determined the role of OMVs in ARG transfer. Using a non-conjugative plasmid (pRY112), we demonstrated that OMVs successfully transferred the plasmid from Campylobacter coli to Campylobacter jejuni. Additionally, OMVs transferred chromosomally encoded florfenicol resistance from a clinical C. coli isolate (SH89) to C. jejuni. The OMV-mediated transfer is independent of natural transformation as both DNase I treatment (for digestion of external-free DNA) and use of a strain deficient of natural transformation as the recipient strain did not affect OMV-mediated ARG transfer. Transmission electron microscopy revealed direct fusion between OMVs and recipient bacterial membranes, suggesting membrane fusion as the mechanism for OMV-mediated DNA transfer. Furthermore, we showed that OMVs derived from strains expressing a functionally-enhanced CmeB (FE-CmeB) transiently protect florfenicol-susceptible C. jejuni against selection by the antibiotic. Together, these findings indicate that OMVs mediate the transfer of both plasmid- and chromosome-encoded ARGs in Campylobacter and define OMVs as a novel pathway for Campylobacter to acquire antibiotic resistance via HGT.},
}

*Gene Transfer, Horizontal
*Extracellular Vesicles/metabolism/genetics
*Campylobacter jejuni/genetics/drug effects
Plasmids/genetics
Anti-Bacterial Agents/pharmacology
*Drug Resistance, Bacterial/genetics
*Campylobacter coli/genetics/drug effects
*Campylobacter/genetics
*Bacterial Outer Membrane/metabolism

@article {pmid41216030,
year = {2025},
author = {Naki, D and Gophna, U},
title = {Evolutionary insights into provirus-encoded CRISPR-Cas systems in halophilic archaea.},
journal = {microLife},
volume = {6},
number = {},
pages = {uqaf033},
pmid = {41216030},
issn = {2633-6693},
abstract = {Prokaryotic microorganisms coexist with mobile genetic elements (MGEs), which can be both genetic threats and evolutionary catalysts. In Haloferax lucentense, a halophilic archaeon, we have recently identified an unusual genomic arrangement: a complete type I-B CRISPR-Cas system encoded on a megaplasmid and an incomplete type I-B system within an integrated provirus in the main chromosome. The provirus-encoded system lacks the adaptation genes (cas1, cas2, and cas4), suggesting its potential reliance on the megaplasmid-encoded CRISPR-Cas module for the acquisition of new spacers. This arrangement suggests a potential instance of "adaptive outsourcing," where a provirus might leverage a co-resident MGE for a key function. Through comparative genomics, we show that similar proviral CRISPR-Cas systems are found in distantly related haloarchaea (e.g. Natrinema and Halobacterium), indicating probable virus-mediated horizontal transfer and suggesting they may function as mobile defense modules. Phylogenetic analysis highlights distinct evolutionary origins of the two systems: the plasmid system clusters with other Haloferax CRISPR-Cas systems, while the proviral system clusters with those from other genera, consistent with horizontal acquisition. Interestingly, spacer analysis reveals that the proviral systems predominantly target viral sequences, while the plasmid system appears to target both plasmids and viral sequences, a distribution mirroring broader trends observed in other plasmid- and chromosome-encoded CRISPR systems. This observed targeting preference suggests a potential for complementarity that could support a model of cooperative immunity, where each system may protect its genetic "owner" from competition and, indirectly, the host.},
}

@article {pmid41214905,
year = {2025},
author = {Tagirdzhanova, G and Raistrick, J and Talbot, NJ},
title = {Chromosome-level genome assembly of the photobiont microalga Trebouxia sp. 'A48' from the lichen Xanthoria parietina.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70728},
pmid = {41214905},
issn = {1469-8137},
support = {//The Gatsby Charitable Foundation/ ; //The Halpin Family/ ; BBS/E/J/000PR9798/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
abstract = {Lichens are symbiotic assemblies consisting of multiple organisms, chiefly a fungus and a photosynthetic microorganism, or photobiont. Among diverse photobionts, the most prevalent is the chlorophyte alga Trebouxia. We produced a chromosome-level assembly of Trebouxia sp. 'A48', a photobiont of Xanthoria parietina. The genome was assembled into 20 contigs, of which 16 had telomeric repeats at both ends and likely represent complete chromosomes. We compared this genome with those of other Trebouxia species and analyzed it to investigate adaptations to the lichen lifestyle. We then used the genome to profile gene expression in axenic culture and in lichen thalli. The predicted secretome is enriched in hydrolases and redox enzymes and contains carbohydrate-binding proteins potentially involved in cell-to-cell recognition and adhesion. We identified genes potentially involved in carbon concentrating and confirmed two instances of ancient horizontal gene transfer from fungi. The genome and the strain of Trebouxia sp. 'A48' provide a resource for the community to research algal evolution and lichen symbiosis.},
}

@article {pmid41212155,
year = {2025},
author = {Soto-Serrano, A and Sadovskaya, I and Vinogradov, E and Li, W and Yu, JH and White, K and van Sinderen, D and Krych, L and Deptula, P and Mahony, J},
title = {"Expanding the Lactococcal Cell Wall Polysaccharide Paradigm: Novel Structures and Metabolic Pathways in the Emerging Dairy Species Pseudolactococcus laudensis and Pseudolactococcus raffinolactis".},
journal = {MicrobiologyOpen},
volume = {14},
number = {6},
pages = {e70133},
pmid = {41212155},
issn = {2045-8827},
support = {//This research was supported by the Milk Levy Fund and co-financed by Arla Foods as part of the project "Cassandra: Quality Modelling Using Detailed Genomics." J.M. is the recipient of a Frontiers of the Future project grant from Science Foundation Ireland (grant number 20/FFP-P/8664)./ ; },
mesh = {*Cell Wall/chemistry/metabolism/genetics ; *Lactococcus/genetics/metabolism/classification/chemistry ; *Polysaccharides, Bacterial/chemistry/genetics/metabolism ; *Metabolic Networks and Pathways/genetics ; Genome, Bacterial ; Genotype ; Genetic Variation ; Phylogeny ; },
abstract = {Cell surface-associated polysaccharides, including cell wall polysaccharides (CWPSs), capsular polysaccharides (CPSs), and exopolysaccharides (EPSs), play vital roles in bacterial interactions with their environment, influencing critical aspects of dairy fermentations, such as phage-host dynamics. Pseudolactococcus laudensis and Pseudolactococcus raffinolactis (formerly Lactococcus laudensis and Lactococcus raffinolactis) are emerging dairy-associated species whose CWPSs remain uncharacterized. This study analyzed the complete genomes of 21 P. laudensis and seven P. raffinolactis strains to investigate the genetic diversity underlying CWPS and EPS production. Eight novel cwps genotypes (E-L) were identified, significantly expanding the known diversity within the dairy-associated (pseudo)lactococci. Notably, E and G genotypes diverge from the classical rhamnan-PSP organization, suggesting a CWPS biosynthesis pathway distinct from the dual-chain assembly found in previously studied Lactococcus. Additionally, eps loci were identified in 25 of the 28 strains, uncovering 11 distinct genotypes (I-XI) with evidence of horizontal gene transfer. Their integration into chromosomal genomic islands highlights their mobility and potential role in evolutionary adaptation. Chemical analysis revealed unprecedented CWPS structures. P. laudensis DSM 28961 (type E) presented a 6-deoxy-α-l-talan polysaccharide and a β-(1,4)-galactan, marking the first instance of d-talose replacing rhamnose and the first homopolysaccharide in (pseudo)lactococcal CWPS, respectively. These were structurally independent, confirming a novel CWPS organization and biosynthetic pathway. Conversely, P. raffinolactis DSM 20443 (type I) exhibited a typical rhamnan-PSP structure, composed of a variably glycosylated rhamnan and a glucose-lactose hexapolysaccharide, respectively. This study provides the first resolved CWPS structures for the Pseudolactococcus genus, expanding the understanding of polysaccharide biosynthesis in Lactic Acid Bacteria.},
}

*Cell Wall/chemistry/metabolism/genetics
*Lactococcus/genetics/metabolism/classification/chemistry
*Polysaccharides, Bacterial/chemistry/genetics/metabolism
*Metabolic Networks and Pathways/genetics
Genome, Bacterial
Genotype
Genetic Variation
Phylogeny

@article {pmid41212030,
year = {2025},
author = {Vereau Gorbitz, D and Schwarz, CP and McMullen, JG and Cerón-Romero, M and Doyle, RT and Lau, JA and Whitaker, RJ and Vanderpool, CK and Heath, KD},
title = {Plasmid transmission dynamics and evolution of partner quality in a natural population of Rhizobium leguminosarum.},
journal = {mBio},
volume = {},
number = {},
pages = {e0249725},
doi = {10.1128/mbio.02497-25},
pmid = {41212030},
issn = {2150-7511},
abstract = {Many bacterial traits important to host-microbe symbiosis are determined by genes carried on extrachromosomal replicons, such as plasmids, chromids, and integrative and conjugative elements. Multiple such replicons often coexist within a single cell and, due to horizontal mobility, have patterns of variation and evolutionary histories that are distinct from each other and from the bacterial chromosome. In nitrogen-fixing Rhizobium, genes carried on multiple plasmids make up a third of the genome, are necessary for the formation of symbiosis, and underlie bacterial traits, including host plant benefits. Thus, the genomics and transmission of plasmids in Rhizobium underlie the ecology and evolution of this important model symbiont. Here, we leverage a natural population of clover-associated Rhizobium in which partner quality has declined in response to long-term nitrogen fertilization. We use 62 novel, reference-quality genomes to characterize 256 replicons in the plasmidome and study their genomics and transmission patterns. We find that, of the four most frequent plasmid types, two (types II and III) have more stable size, larger core genomes, and track the chromosomal phylogeny (display more vertical transmission), while others (type I and type IV, or symbiosis plasmid, pSym) vary substantially in size and shared gene content and have phylogenies consistent with frequent horizontal transmission. We also find differentiation in pSym subtypes driven by long-term nitrogen fertilization. Our results highlight the variation in plasmid transmission dynamics within a single symbiont and implicate plasmid horizontal transmission in the rapid evolution of partner quality.IMPORTANCEUnderstanding how bacterial genes move through natural populations is critical for understanding how bacterial traits evolve. Nitrogen-fixing bacteria Rhizobium leguminosarum live in symbiosis with plants and are a model for studying plasmid transmission and how mobile genetic elements impact the evolution of bacteria and plants. Here, we characterize the genomes of a natural bacterial population, then use novel approaches to show that mechanisms of gene transmission vary across multiple plasmid types that coexist within R. leguminosarum cells. We find that changes in the frequency of specific pSym types are associated with the decline of symbiotic partner quality in strains isolated from environments undergoing long-term fertilization. These results underscore the importance of plasmid transmission and evolution in shaping ecosystem processes like nitrogen cycling via bacterial-plant symbiosis. Our study provides a framework for probing plasmid dynamics within natural bacterial populations and how plasmid transmission affects genetic diversity and ecological interactions in bacteria.},
}

@article {pmid41211966,
year = {2025},
author = {Moustaghfir, M and Destanque, T and François, P and Châtre, P and Louzier, V and Hammed, A and Hauray, K and Madec, J-Y and Haenni, M and Prouillac, C and Lupo, A},
title = {Changes in fecal microbiota after therapeutic exposure to amoxicillin-clavulanic acid in veal calves receiving multiple antibiotics.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0131625},
doi = {10.1128/spectrum.01316-25},
pmid = {41211966},
issn = {2165-0497},
abstract = {Amoxicillin-clavulanic acid (AMC) is an important antibiotic in human and veterinary medicine. However, it can select antibiotic-resistant bacteria in the gut microbiota and alter its composition. In calves, AMC can be used to treat complicated infections. The impact of AMC on the calves' gut is unknown; thus, we analyzed the effect of a five-day AMC treatment in veal calves suffering from omphalitis. AMC-treated calves (n = 15) and a control untreated group (n = 15) were enrolled from two farms. Stools were collected before AMC administration (D0), one day (D6), one month (D35), and two months (D55) after AMC withdrawal. The effect of AMC treatment on gut microbiota composition and resistance gene selection was analyzed by full-length 16S rRNA operon sequencing and qPCR, respectively. Selection of Extended-Spectrum Cephalosporin-Resistant (ESC-R) Escherichia coli in calf's fecal samples and dissemination in the farms' environment were analyzed by cultivation and genome sequencing of isolates. After AMC treatment, alpha-diversity decreased in AMC-treated calves along with a decrease of the relative abundance of bacterial families beneficial for host health (Lachnospiraceae) and an increase of Pseudomonadota, grouping opportunistic pathogens. ESC-R E. coli carriage dynamics were different between calves sampled from each farm and seemed independent from AMC treatment. Besides, calves received other antibiotics that could have an impact on resistance selection. Certain clones of ESC-R E. coli demonstrated a widespread dissemination in the farm, both in calves hosted in distant zones and in their environment. To decrease the antibiotic resistance burden, it is essential to use antibiotics judiciously, alongside improving hygienic practices in farms.IMPORTANCEAntibiotic therapies can select resistant bacteria in the gut of treated hosts and deplete bacteria that are beneficial to the host health. Antibiotic-resistant bacteria selected in the gut of food-producing animals, like veal calves, are excreted and can then disseminate among animals, to the environment (through manure or water contamination) and to farmers who may further disseminate these organisms to other people in contact. Antibiotic resistance genes can disseminate among clones present in the gut of both animal and human hosts by horizontal gene transfer. Studying the impact of antibiotic therapies on the gut microbiota has One Health relevance. Thus, we aimed to (i) analyze the impact of AMC treatment on the selection of resistant bacteria in the calf gut and its composition and (ii) analyze the dissemination resistance in farms in order to advise on potential strategies to counteract further spread of these microorganisms.},
}

@article {pmid41207830,
year = {2025},
author = {Kiga, K and Ibarra-Chávez, R},
title = {The hitchhiker's guide to cross-species DNA delivery.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2025.10.014},
pmid = {41207830},
issn = {1878-4380},
abstract = {Microbial hitchhikers are rewriting the rules of horizontal gene transfer. He, Patkowski, et al. reveal how phage satellites assemble chimeric infective particles that deliver DNA across species boundaries through 'tail piracy'. This discovery reframes microbial innovation and provides a blueprint for next-generation biotechnologies, achieving what phage engineering has long pursued.},
}

@article {pmid41206754,
year = {2025},
author = {Lu, Z and Mclnnes, RS and Allen, F and Gadar, K and van Schaik, W},
title = {Resistance to last-resort antibiotics in enterococci.},
journal = {FEMS microbiology reviews},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsre/fuaf057},
pmid = {41206754},
issn = {1574-6976},
abstract = {The genus Enterococcus comprises a diverse group of species, many of which are commensal members of the gut microbiota of humans and animals. The two most prominent species associated with humans, Enterococcus faecalis and Enterococcus faecium, have also emerged as prominent opportunistic pathogens causing a range of infections in hospitalised patients, including urinary tract infections, bloodstream infections and endocarditis. The rise of antibiotic resistance in enterococci undermines the efficacy of the treatment of infections, thus posing a significant public health risk. Enterococci readily acquire resistance to antibiotics through chromosomal mutations and the horizontal gene transfer of antibiotic resistance genes. This review offers a comprehensive examination of the mechanisms of antibiotic resistance among enterococci, with an emphasis on resistance to last-line antibiotics, including to glycopeptide antibiotics like vancomycin and teicoplanin, oxazolidinones (primarily linezolid), and daptomycin. Furthermore, we evaluate relevant candidates in the current development pipeline for antibiotics and discuss alternative strategies (phage therapy and immunotherapeutics) for the treatment and prevention of infections with multidrug-resistant enterococci. As enterococci rapidly adapt to novel conditions, including by developing resistance to new drugs and therapies, sustained research efforts are required to ensure the continuous development of treatment options for these important opportunistic pathogens.},
}

@article {pmid41205659,
year = {2025},
author = {Suruchi, and Tiwari, M and Pal, D and Gupta, AK and Jain, SK},
title = {Breaking barriers in antimicrobial therapy: resistance mechanisms and novel antimicrobial strategies.},
journal = {Microbial pathogenesis},
volume = {210},
number = {},
pages = {108163},
doi = {10.1016/j.micpath.2025.108163},
pmid = {41205659},
issn = {1096-1208},
abstract = {INTRODUCTION: Modern healthcare systems face significant challenges from antimicrobial resistance (AMR), which threatens our ability to effectively manage infectious diseases. The widespread prevalence of AMR and its constantly evolving patterns define its epidemiological landscape, with multidrug-resistant organisms emerging at an alarming rate.

METHODS: A thorough examination of the literature was conducted using multiple databases, including Google Scholar, PubMed, Science Direct, and Springer Link. The search included keywords such as "antimicrobial resistance," "causes and mechanisms of antimicrobial resistance," "strategies to overcome antimicrobial resistance," "coordinated global action to address antimicrobial resistance," and "novel approaches to combat antimicrobial resistance."

RESULTS: This review investigates the causes and mechanisms of AMR, including restricted drug uptake, modifications and inactivation of drug targets, drug efflux, enzymatic changes, and alterations in metabolic pathways, biofilm formation, and horizontal gene transfer. These mechanisms drive the emergence and spread of resistant strains. Mitigation strategies emphasize the importance of continuous monitoring and rational antimicrobial use. In addition, novel therapeutic innovations such as antimicrobial peptides, nanotechnology-based systems, and metal-based compounds exhibiting multi-target mechanisms including ROS generation, enzyme inhibition, and membrane disruption, present promising opportunities to counter AMR.

CONCLUSIONS: This review summarizes drug development approaches designed to address antimicrobial resistant organisms, supporting stewardship efforts and guiding future research toward innovative strategies.},
}

@article {pmid41205588,
year = {2025},
author = {Kumar, KRR},
title = {Plant genome editing goes viral: balancing innovation and biosafety.},
journal = {Trends in biotechnology},
volume = {43},
number = {11},
pages = {2684-2685},
doi = {10.1016/j.tibtech.2025.09.006},
pmid = {41205588},
issn = {1879-3096},
mesh = {*Gene Editing/methods ; *Genome, Plant/genetics ; *Plants, Genetically Modified/genetics ; Genetic Vectors/genetics ; CRISPR-Cas Systems ; Containment of Biohazards ; },
abstract = {Weiss and colleagues demonstrated a breakthrough in transgene-free heritable genome editing using viral vectors. While promising for controlled laboratory applications, the open-field use envisaged by Sajjad and colleagues raises ecological and biosafety concerns. Rigorous risk assessment is essential to harness innovation responsibly while safeguarding biodiversity and public trust.},
}

*Gene Editing/methods
*Genome, Plant/genetics
*Plants, Genetically Modified/genetics
Genetic Vectors/genetics
CRISPR-Cas Systems
Containment of Biohazards

@article {pmid41205514,
year = {2025},
author = {Fu, Q and Wen, Q and Chen, Z and Tang, L},
title = {Ozone cooling phase treatment inhibit the rebounding of ARGs by hosts elimination during swine manure composting.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140389},
doi = {10.1016/j.jhazmat.2025.140389},
pmid = {41205514},
issn = {1873-3336},
abstract = {Antibiotic resistance genes (ARGs) residual in composting products pose a global threat to public health. The ARGs rebounding during cooling and mature phase of composting has been recognized as a critical barrier to controlling antibiotic resistance in composting systems. However, strategies to specifically inhibit the ARGs rebounding in the later stage of composting remain poorly understood. In this study, we optimized ozone treatment during the cooling phase of swine composting and identified 0.6 g/kg fresh weight (FW) as the optimal dosage. The absolute and relative abundance of ARGs were reduced by 50.34 % and 60.33 %, respectively, compared with control (p < 0.001). The suppression of ARGs hosts, including Pseudomonas, Lactobacillus, Clostridium, and Actinomycetales_unclassified, contributed substantially to ARGs reduction, particularly for intercellular ARGs (sul1、sul2、sul3、gyrA、ermF). Concurrently, microbial horizontal gene transfer (HGT) potential was mitigated through targeted inhibition of microorganisms harboring Type IV secretion system (particularly Pseudomonas). Furthermore, the demonstrated economic viability, operational safety, and ease of system retrofitting and technological upgrading support the theoretical feasibility of implementing ozonation in aerobic composting as an effective strategy for ARG mitigation.},
}

@article {pmid41205414,
year = {2025},
author = {Lee, M and Shin, JI and Hassan, A and Chung, YJ and Jung, SH and Park, KT},
title = {Prevalence, antimicrobial resistance, and genetic characterization of Listeria monocytogenes in the Korean pork production chain.},
journal = {International journal of food microbiology},
volume = {446},
number = {},
pages = {111515},
doi = {10.1016/j.ijfoodmicro.2025.111515},
pmid = {41205414},
issn = {1879-3460},
abstract = {Listeria monocytogenes, a major foodborne pathogen, causes invasive listeriosis with a high mortality rate. Its distribution and genomic diversity in livestock products in Korea remain poorly understood. This study investigated the prevalence and genomic characteristics of L. monocytogenes across Korean pork production and distribution chains. Samples from pigs, carcasses, meat, and the environment were collected from farms, slaughterhouses, and supermarkets nationwide. L. monocytogenes was recovered from 60 retail meat samples (19.0 %) but not from farms or slaughterhouses, suggesting that contamination occurs mainly during downstream processing and distribution. Whole-genome sequencing identified nine sequence types (STs) across two lineages, with Lineage II-ST9 being most prevalent. Within ST9, the core genome multilocus sequence typing-defined CT4379 subgroup was widespread across all provinces and harbored repUS43 plasmid replicon and tetM within a horizontal gene-transfer structure, also found in other Listeria STs and bacterial species. All ST9 isolates carried a premature stop codon (PMSC) in inlA. Two Lineage I-ST224 isolates were evolutionary linked to the outbreak strain FSCNU0110 in Korea in 2018, sharing an identical llsX PMSC in Listeria pathogenicity island (LIPI)-3. LIPI-4 was exclusively detected in ST87, a hypervirulent clone found in multiple provinces. Seven isolates from imported pork were ST3 and ST321, indicating potential international transmission via pork trade. All isolates possessed intrinsic antimicrobial resistance genes. The detection of persistent and hypervirulent clones in final pork products underscores the need for high-resolution genomic surveillance and strict hygiene interventions during meat processing and distribution for reducing the occurrence of listeriosis.},
}

@article {pmid41204637,
year = {2025},
author = {Li, J and Song, J and Wang, X and Li, W and Han, M and Li, M and Wang, S and Xu, J and Zhang, Q and Chen, J and Cui, S and Yang, B},
title = {Food-Associated Stressors and Their Synergistic Roles in Bacterial Antibiotic Resistance across the Food Supply Chain.},
journal = {Journal of agricultural and food chemistry},
volume = {73},
number = {46},
pages = {29310-29327},
doi = {10.1021/acs.jafc.5c10696},
pmid = {41204637},
issn = {1520-5118},
mesh = {*Bacteria/drug effects/genetics/metabolism ; *Drug Resistance, Bacterial ; *Anti-Bacterial Agents/pharmacology ; Food Chain ; Humans ; Food Supply ; },
abstract = {Global bacterial antibiotic resistance threatens health, food safety, and sustainability. The food supply chain is a critical "One Health" pathway, linking agriculture, environment, and processing. However, systematic reviews addressing the impact of coexisting stressors on antibiotic resistance emergence and transmission across this continuum are lacking. This review innovatively synthesizes environmental inputs (antibiotic residues, fertilizers, heavy metals, pesticides, microplastics, climate change, and grazing) and processing/transport stressors (temperature, nonthermal technologies, pH, osmosis, disinfectants, food additives, probiotics, and trade), focusing on their individual and synergistic effects. These stressors enhance resistance and horizontal gene transfer by activating bacterial stress responses (sigma factors, SOS), altering membranes, and triggering mutations/efflux pumps. Coexisting stressors can further intensify, accelerate, and amplify resistance emergence and transmission. We propose multilevel mitigation strategies across the food chain, including curbing selective pressures at the source, optimizing food processing techniques to avoid stress-induced resistance, guiding consumer behavior, and strengthening international regulatory governance.},
}

*Bacteria/drug effects/genetics/metabolism
*Drug Resistance, Bacterial
*Anti-Bacterial Agents/pharmacology
Food Chain
Humans
Food Supply

@article {pmid41202903,
year = {2025},
author = {Wu, Y and Yu, Y and He, X and Mao, W and Tong, Q and Bao, D and Jia, H and Kong, Y and Zhang, Y and Draz, MS and Furlan, JPR and Butaye, P and Elhadidy, M and Dong, S and Cao, Z and Xie, X and Wu, S and Ruan, Z},
title = {Genome-wide insight into the evolution and global transmission of tigecycline resistant tet(X4)-carrying Klebsiella species across reservoirs.},
journal = {International journal of antimicrobial agents},
volume = {},
number = {},
pages = {107665},
doi = {10.1016/j.ijantimicag.2025.107665},
pmid = {41202903},
issn = {1872-7913},
abstract = {The emergence of plasmid mediated tet(X4) gene compromises the clinical utility of tigecycline and underscores growing concerns regarding its environmental reservoirs and potential for interspecies transmission, particularly within Klebsiella species. To elucidate the dissemination patterns and evolutionary relationships of tet(X4)-harboring plasmids across clinical and environmental Klebsiella isolates, we conducted comprehensive phylogenetic analysis integrating both newly sequenced plasmids and publicly available datasets from the NCBI Plasmid database. Conjugation assays were performed to assess the horizontal transfer potential of tet(X4)-harboring plasmids. Furthermore, globally sourced genomic data of tet(X4)-carrying Klebsiella strains were subjected to infer their spatiotemporal distribution, transmission dynamics, and the time to the most recent common ancestor (tMRCA) using BEAST. The tet(X4) was located on conjugative plasmids ranging from 5.7 kb to 19.3 kb, predominantly embedded within a conserved abh-tet(X4)-ISCR2 structure flanked by mobile genetic elements such as IS26 and IS1, which likely facilitate horizontal gene transfer and plasmid integration. These plasmids commonly co-harbored multiple ARGs, including aadA1, floR, and tet(A). The tet(X4)-carrying Klebsiella isolates exhibited substantial genetic diversity, with ST534 and ST3393 identified as the most prevalent lineages. The tet(X4)-carrying K. pneumoniae strains exhibited clonal dissemination across clinical and environmental reservoirs, with the estimated tMRCA dating back to 1873. Moreover, the co-occurrence of tet(X4) with carbapenemase or colistin resistance genes highlights the significant public health threat posed by these high-risk strains. These findings highlight the urgent need for coordinated genomic surveillance under a One-Health framework to monitor and mitigate the global spread of multidrug-resistant tet(X4)-carrying Klebsiella isolates.},
}

@article {pmid41202544,
year = {2025},
author = {Zhang, H and Sun, H and Pan, X and Wu, D and Liang, H and Tang, J and Fang, H and Wu, X},
title = {Sediment archives urban-rural divergence in antibiotic resistance gene contamination within a freshwater lake.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140322},
doi = {10.1016/j.jhazmat.2025.140322},
pmid = {41202544},
issn = {1873-3336},
abstract = {Freshwater lakes are critical ecosystems for sustaining biodiversity and human well-being, yet increasing anthropogenic activities threaten their ecological safety through pollution such as antibiotic resistance genes (ARGs). Previous studies on ARG pollution in aquatic systems have largely overlooked the distinct impacts of urban versus rural landscapes, limiting targeted mitigation strategies. Here, we investigate the urban-rural heterogeneity of ARG pollution in Chaohu lake, a major urban-rural junction lake in China, using shotgun metagenomic sequencing and Bayesian source-tracking approaches. Our findings reveal significant spatiotemporal variations in ARG abundance, with urban-adjacent regions (western lake) exhibiting 1.22- to 1.25-fold higher ARG levels than rural-adjacent areas (eastern lake) in water and sediments, respectively. Notably, a significant distance-decay relationship of ARG profiles was observed in sediments, highlighting that sediments act as a stable environmental archive recording the urban-rural divergence. Agricultural activities were identified as the dominant source lake-wide, contributing over 60 % of the total ARG load, thereby surpassing urban sewage inputs. Meanwhile, the abundance of mobile genetic elements (MGEs), particularly transposases, was significantly higher in the western lake, indicating a greater potential for horizontal gene transfer. The presence of multidrug-resistant, ARG-carrying pathogens, such as Stenotrophomonas maltophilia and Pseudomonas putida, was significantly enriched in these areas, correlating with higher ecological and health risks as quantified by the antibiotic resistome risk index. These results underscore the urgent need for landscape-specific management strategies to curb ARG dissemination, prioritizing agricultural non-point source control in urban-rural transitional zones to safeguard freshwater ecosystems and human health.},
}

@article {pmid41201733,
year = {2025},
author = {Saleh, RM and Hassan, OM},
title = {The infectome framework: linking polymicrobial ecology and biofilm dynamics to precision diagnostic approaches.},
journal = {Infection},
volume = {},
number = {},
pages = {},
pmid = {41201733},
issn = {1439-0973},
abstract = {Chronic infections are a persistent global health problem and are frequently sustained by polymicrobial communities rather than by a single pathogen. This review brings together current evidence for the infectome concept, defined as the dynamic set of pathogenic or pathobiont taxa in the host, their shared functional capacities, and the interactions that connect them. We analyze how community-level processes promote persistence, cause diagnostic failure, and drive therapeutic resistance, with emphasis on multispecies biofilms, quorum sensing, horizontal gene transfer, metabolic cooperation, and immune modulation. We also highlight advances in multi-omics and computational integration that now permit high-resolution infectome profiling and reveal taxa and interspecies networks that are not captured by routine culture. Clinical examples such as periodontitis, bacterial vaginosis, chronic rhinosinusitis, device-associated infections, and recurrent urinary tract infections show the translational value of this shift. On the therapeutic side, we discuss infectome-informed options including antivirulence agents, biofilm-disrupting enzymes, bacteriophages and lysins, community-wide susceptibility-guided regimens, and microbiome-restoration strategies. Finally, we identify the main requirements for the field: standardized sampling and analytic workflows, reproducible infectome signatures linked to clinical outcomes, and trial designs able to capture ecological dynamics and meet regulatory expectations for community-targeted interventions. Adopting an infectome perspective can enable precision infectiology and reshape the management of chronic and recurrent infections.},
}

@article {pmid41197960,
year = {2025},
author = {Hu, R and Wu, J and Li, S and Yang, P and Wu, G and Niu, C and Zhan, S and Chen, Y},
title = {Coordinated horizontal transfer of multiple genes assembles a carotenoid biosynthesis pathway in aphids.},
journal = {Insect biochemistry and molecular biology},
volume = {186},
number = {},
pages = {104433},
doi = {10.1016/j.ibmb.2025.104433},
pmid = {41197960},
issn = {1879-0240},
abstract = {Horizontal gene transfer (HGT) plays a crucial role in genome evolution, especially when it enables the acquisition and assembly of multi-step biosynthetic pathways. Here, we investigate the evolutionary origins of carotenoid biosynthesis genes in aphids to determine whether multiple functionally related genes were acquired through HGT. We analyzed carotenoid biosynthesis genes in 23 aphid genomes based on homologs in plants, fungi, and bacteria. Phylogenetic analyses revealed that Geranylgeranyl pyrophosphate synthase (GPS), Phytoene synthase (PS), and Carotenoid desaturase (CD) were acquired via HGT from fungi by ancestral insect species, while Carotenoid cleavage oxygenase (CCO) appears to be a native insect gene. Most insect genomes contain two GPS copies, likely resulting from independent HGT events, whereas aphid genomes exhibit extensive duplication of PS and CD, a pattern uncommon in other insects. Expression analyses across aphid species with distinct pigmentation showed that these genes are broadly transcribed with substantial variability in expression levels. In Myzus persicae, comparative expression analysis between red and green clones, as well as a green-red clone with green and red color polymorphism, revealed that PS-4390 is a novel candidate for red pigmentation in M. persicae, in addition to CD-4400, a homolog of the tor gene in Acyrthosiphon pisum. These findings provide strong evidence that HGT can introduce multiple functionally related genes into recipient genomes, allowing them to be co-opted into a functional biosynthetic pathway.},
}

@article {pmid41197741,
year = {2025},
author = {Chen, Y and Chen, Y and Hu, C and Xing, X and Zhang, S and Zeng, K and Yin, Z and Meng, C and Situ, F and Li, J and Chen, C and Ma, K and Chen, J and Li, F},
title = {Simultaneous control of disinfection by-products, opportunistic pathogens, and antibiotic resistance genes in drinking water based on a novel advanced treatment process consisting of Fenton-like reaction and biological activated carbon.},
journal = {Bioresource technology},
volume = {441},
number = {},
pages = {133602},
doi = {10.1016/j.biortech.2025.133602},
pmid = {41197741},
issn = {1873-2976},
abstract = {Disinfection by-products (DBPs), opportunistic pathogens (OPs), and antibiotic resistance genes (ARGs) are typical drinking water quality risks today, and the synchronous control of these factors has always been an important challenge. Herein, a novel drinking water treatment process (Fe3C-NC/PMS-BAC) consisting of Fe3C-NC Fenton-like reaction and biological activated carbon (BAC) was established in this study. Fe3C-NC/PMS caused the decomposition of high molecular weight organic matter into low molecular weight organic matter, which was efficiently biodegraded in the subsequent BAC biofilter (PBAC). In addition, the suspended extracellular polymeric substances (EPS) in the effluent of PBAC contained only a small amount of polysaccharides, markedly weakening the biofilm stability and its protective effect against OPs. The changes in organic matter and EPS ultimately led to the reduction of DBPs precursors. More importantly, the Fe3C-NC/PMS treatment remarkably changed the microbial ecology in subsequent PBAC, including shaping the microbial community, regulating EPS characteristics, weakening quorum sensing, and even inhibiting microbial activities, contributing to the inhibition of horizontal gene transfer of ARGs. Therefore, the Fe3C-NC/PMS-BAC is a promising alternative to BAC treatment for future applications, providing new ideas for the collaborative removal of chemical and microbial water quality risks in drinking water.},
}

@article {pmid41197508,
year = {2025},
author = {Wen, M and Deng, C and Lei, J and Yang, X and Li, J and Al-Dhabi, NA and Wen, S and Tang, W and Feng, B and Zhang, P},
title = {Amoxicillin effects on pollutant removal, cyanophycin synthesis, and the proliferation of antibiotic resistance genes (ARGs) in the algal-bacterial biofilm.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140363},
doi = {10.1016/j.jhazmat.2025.140363},
pmid = {41197508},
issn = {1873-3336},
abstract = {The algal-bacterial wastewater treatment process is characterized by its efficiency in water quality purification and bioresource recovery. This study investigated the effects of amoxicillin (AMX) on pollutant removal, cyanophycin synthesis, and the proliferation of antibiotic resistance genes (ARGs) within the algal-bacterial biofilm. AMX significantly suppressed ammonia and phosphorus removal by inhibiting nitrogen and phosphorus assimilation in cyanobacteria. A total of 72 metagenomic assembled genomes carrying cyanophycin biosynthetic genes were identified, with Pantanalinema and Planktothrix being the primary cyanophycin-producing species. AMX concentrations of 0.5 and 1 mg/L suppressed both cyanobacterial growth and cyanophycin synthesis, with the inhibitory effect intensifying as AMX concentration increased. AMX also promoted the proliferation of sul1, OXA-101, VEB-3, and qacEdelta1, while decreased the abundance of OXA-36, erm(F), and tet types. Pseudomonadota and Bacteroidota were the primary hosts for ARGs proliferation and dissemination, with bacA and tetX1 actively spreading within the algal-bacterial biofilm. Cyanobacteria played a negligible role in the propagation of ARGs. This study offers new insights into the spread of ARGs and bioresource recovery in algal-bacterial systems, focusing on both gene and strain levels.},
}

@article {pmid41195361,
year = {2025},
author = {Qiao, X and Zhang, H and Xu, Y and Cao, T and Wang, R and Deng, X and Liang, W and Zheng, L},
title = {Study on resistance mechanisms and molecular epidemiology of carbapenem-resistant Pseudomonas aeruginosa to ceftazidime/avibactam in a certain region of China.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1643755},
pmid = {41195361},
issn = {2235-2988},
mesh = {*Ceftazidime/pharmacology ; *Pseudomonas aeruginosa/drug effects/genetics/isolation & purification ; China/epidemiology ; Humans ; Drug Combinations ; *Pseudomonas Infections/epidemiology/microbiology/drug therapy ; *Azabicyclo Compounds/pharmacology ; *Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics ; *Carbapenems/pharmacology ; Molecular Epidemiology ; Microbial Sensitivity Tests ; beta-Lactamases/genetics ; Male ; Female ; Biofilms/drug effects/growth & development ; *Drug Resistance, Multiple, Bacterial/genetics ; Middle Aged ; Multilocus Sequence Typing ; Aged ; Adult ; },
abstract = {UNLABELLED: Carbapenem-resistant Pseudomonas aeruginosa(CRPA) poses a serious threat in healthcare settings due to its multidrug resistance and high mortality. Although ceftazidime/avibactam (CZA) demonstrates potent activity against CRPA, resistance has emerged.

OBJECTIVE: This study investigates the epidemiology and molecular mechanisms of CZA resistance in CRPA isolates from Ningbo, China.

METHODS: A total of 279 non-duplicate clinical CRPA isolates (2022-2024) were classified as CZA-resistant (CZA-R, n = 68) or CZA-susceptible (CZA-S, n = 211). Carbapenemase genes were detected by PCR, clonality via MLST, biofilm formation by crystal violet assay, and efflux pump expression (mexA, mexC, mexE, mexY) via qRT-PCR. WGS was performed on selected isolates.

RESULTS: The CZA resistance rate was 24.37%. Risk factors included recent trauma, prior antibiotic exposure, central venous catheterization, and drainage tube placement (all p < 0.05). The CZA-R group showed higher recurrence (13.2% vs. 4.3%, p = 0.029) and lower clinical improvement (67.6% vs. 77.3%, p = 0.029). blaNDM prevalence was higher in CZA-R (7.4% vs. 0.5%, p = 0.003), and ST1076 was the predominant clone (29.3%), with higher representation in CZA-R (40.0%). Horizontal gene transfer mediated blaNDM spread. CZA-R isolates exhibited enhanced biofilm formation (p < 0.001) and mexA upregulation (2.04-fold, p = 0.007).

CONCLUSION: Our findings indicate a high prevalence of CZA resistance among CRPA isolates in Ningbo, driven by multiple mechanisms including blaNDM carriage, enhanced biofilm formation, and overexpression of efflux pumps. The dissemination of the high-risk clone ST1076 underscores the need for strengthened infection control measures to curb its spread. These findings provide important insights for optimizing infection control and treatment strategies against CRPA infections in this region.},
}

*Ceftazidime/pharmacology
*Pseudomonas aeruginosa/drug effects/genetics/isolation & purification
China/epidemiology
Humans
Drug Combinations
*Pseudomonas Infections/epidemiology/microbiology/drug therapy
*Azabicyclo Compounds/pharmacology
*Anti-Bacterial Agents/pharmacology
Bacterial Proteins/genetics
*Carbapenems/pharmacology
Molecular Epidemiology
Microbial Sensitivity Tests
beta-Lactamases/genetics
Male
Female
Biofilms/drug effects/growth & development
*Drug Resistance, Multiple, Bacterial/genetics
Middle Aged
Multilocus Sequence Typing
Aged
Adult

@article {pmid41194257,
year = {2025},
author = {Parsons, C and Fournier, GP},
title = {Horizontal transfer of matrix metalloproteinase genes links early animal and microbial evolution.},
journal = {Biology direct},
volume = {20},
number = {1},
pages = {107},
pmid = {41194257},
issn = {1745-6150},
support = {EAR-1615426//National Science Foundation/ ; },
mesh = {*Gene Transfer, Horizontal ; Animals ; *Bacteria/genetics/enzymology ; Phylogeny ; *Matrix Metalloproteinases/genetics ; *Evolution, Molecular ; Archaea/genetics/enzymology ; *Biological Evolution ; Metagenome ; },
abstract = {BACKGROUND: The early evolution of animals is characterized by the emergence of complex tissues, organs, and integument, made possible in part by the diversification of groups of structural proteins. The abundance of this new kind of organic material in the environment would have provided novel nutrient opportunities for microbes, as part of the beginnings of animal-microbial coevolution. Indeed, a diverse ensemble of extant microbial groups appear to possess the enzymatic ability to cleave collagen, the most abundant animal-specific protein, through the use of matrix metalloproteinases (MMPs). In animals, MMPs serve to reshape the extracellular matrix in the course of development, but their prevalence in the microbial world has been largely overlooked.

RESULTS: MMPs have extensive diversity in Bacteria, Eumetazoa, and Streptophyta. We show that in marine metagenomes, MMP abundance is highly correlated with chitinase abundance, implying that even microbial MMPs are associated with animal-derived substrates. Reconstructing the phylogeny of MMP proteins reveals a history of rapid diversification, as well as multiple interkingdom and interdomain horizontal gene transfers. Included among these is a transfer to the ancestral lineage of the archaeal family Methanosarcinaceae, constraining this group to postdate the evolution of collagen, and therefore animal diversification.

CONCLUSIONS: MMPs have an unusual genetic history, marked by multiple instances of gene transfer between bacteria and multicellular eukaryotes, a smoking gun for some of the earliest coevolution between prokaryotes and metazoans. By calculating an end-Permian divergence of Methanosarcina, we demonstrate that the phylogenies of substrate-specific enzymes can provide valuable older-bound age calibrations for improving molecular clock age estimates across the Tree of Life.},
}

*Gene Transfer, Horizontal
Animals
*Bacteria/genetics/enzymology
Phylogeny
*Matrix Metalloproteinases/genetics
*Evolution, Molecular
Archaea/genetics/enzymology
*Biological Evolution
Metagenome