@article {pmid41579925,
year = {2026},
author = {Li, T and Wu, J and Kuai, Z and Cui, M and Du, T and Wu, L},
title = {Mechanistic insights into ozone-induced reduction in antibiotic resistance gene abundance in PM2.5.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {127725},
doi = {10.1016/j.envpol.2026.127725},
pmid = {41579925},
issn = {1873-6424},
abstract = {Antibiotic resistance genes (ARGs) in PM2.5 have received great attention due to their potential risks to human health and ecological balance. The distribution and abundance of ARGs are known to be influenced by various environmental factors. However, the effect of ozone-a major atmospheric pollutant-on the abundance of ARGs in PM2.5 remains poorly understood. In this study, we show that as ozone pollution levels increase, the abundance of eight typical ARGs in PM2.5 collected from four monitoring sites across three representative cities in China's Jianghuai region generally decreases. Notably, tetW, sul1, and blaTEM genes exhibit the most substantial reduction in abundance, demonstrating the highest sensitivity to ozone. Ozone affects the abundance of these three ARGs through both vertical and horizontal gene transfer, but with differing mechanisms. For vertical gene transfer, ozone reduces the abundance of these sensitive ARGs by inhibiting potential bacterial hosts. The identity of these potential hosts varies depending on the type of ARG and the sampling location. For horizontal gene transfer, ozone diminishes the abundance of tetW and blaTEM genes by reducing the abundance of mobile genetic elements. In contrast, the guanine-rich and ozone-responsive sul1 gene is primarily decreased through ozone-driven efficient degradation of extracellular sul1. These findings advance our understanding on the interactions between atmospheric pollutants and antibiotic resistance, providing a theoretical foundation for accurately assessing their human exposure risks.},
}

@article {pmid41578848,
year = {2026},
author = {Kim, W and Jost, M and Nickrent, D and Zhou, R and Acar, P and Langschied, F and Ebersberger, I and Wicke, S and Wanke, S},
title = {Progress and Prospects of Parasitic Plant Biodiversity Genomics.},
journal = {Plant & cell physiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/pcp/pcag009},
pmid = {41578848},
issn = {1471-9053},
abstract = {Parasitic plants have evolved independently at least a dozen times across angiosperms, yielding some of the most extreme examples of genomic reconfiguration in plants. Comparative analyses of plastid, mitochondrial, and nuclear genomes reveal striking convergence across lineages such as progressive plastid genome reduction with retention of a minimal core gene set, alongside lineage-specific divergences, including unusual mitochondrial genome architectures, rampant horizontal gene transfer, and repeated loss or expansion of nuclear gene families linked to photosynthesis, haustorium development, and host interaction. Expanded sampling largely confirms stepwise plastid genome condensation but also uncovers rare losses of presumed essential genes, novel tRNA retention patterns, and extremes in genome size and base composition. Mitochondrial genomes size largely vary (<60 kb ~ 4 Mb), shaped by repeat proliferation, recombination, and massive acquisition of foreign DNA. Nuclear genomes integrate these organellar changes with structural and regulatory innovations via e.g., polyploidy and repeat-driven evolution, as well as large-scale gene losses. These insights are increasingly translatable to agriculture through predictive weed management and resistance breeding pipelines that combine pre-attachment control, post-attachment defense, and molecular surveillance to slow virulence evolution. The same genomic toolkits including high-quality assemblies, organelle haplotyping, and quantitative diagnostics, can support conservation of non-weedy parasites by refining species boundaries, identifying evolutionarily significant units, and informing IUCN Red List assessments and recovery plans. By bridging fundamental and applied research, parasitic plant genomics is poised to move beyond descriptive cataloguing toward design-based strategies that safeguard crop production while conserving some of the most specialized and ecologically vulnerable plants on Earth.},
}

@article {pmid41578173,
year = {2026},
author = {Rahimian, M and Aghazadeh-Soltan-Ahmadi, M and Panahi, B},
title = {Genomic landscape of biosynthetic gene clusters in Iranian extremophiles reveals prolific metabolite potential, prophage associations, and integrated defensive-metabolic islands.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-025-04690-1},
pmid = {41578173},
issn = {1471-2180},
abstract = {The extreme and underexplored ecosystems of Iran represent a significant reservoir of microbial diversity with profound biosynthetic potential. To systematically investigate this resource, we employed a comprehensive genome mining approach on 16 bacterial isolates from hypersaline, desert, and petroleum-contaminated soils. Our analysis revealed an extraordinary density and complexity of biosynthetic gene clusters (BGCs), identifying 229 BGCs in total. A substantial majority (56.8%) showed no significant similarity to known clusters, underscoring the extensive novelty encoded within these extremophiles. Notably, we discovered highly intricate "trio" and "quartet" hybrid BGCs, which encode the machinery for three or four distinct classes of secondary metabolites, pushing the boundaries of known biosynthetic complexity. Parallel analysis identified six novel, high-quality prophages, largely uncharacterized in public databases. These prophages were found to carry a putative bacteriocin cluster (UviB) indicating a direct role in enhancing host fitness. Furthermore, we uncovered a dynamic co-evolutionary arms race, with bacterial genomes fortified by diverse defense systems, including abundant CRISPR-Cas arrays, and prophages encoding a repertoire of counter-defense anti-CRISPR proteins. Genomic architecture analysis revealed widespread co-localization of BGCs, prophages, and defense systems into functional genomic islands, suggesting a synergistic linkage between secondary metabolism and phage resistance. This study illuminates the remarkable biosynthetic and defensive landscape of Iranian extremophiles, highlighting them as a premier resource for discovering novel natural products and understanding virus-host evolutionary dynamics.},
}

@article {pmid41577508,
year = {2026},
author = {Worning, P and Ibarra-Chávez, R},
title = {Gene sharing has stabilised the genetic code.},
journal = {Trends in genetics : TIG},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tig.2025.12.006},
pmid = {41577508},
issn = {0168-9525},
abstract = {The genetic code is nearly universal across life. Yet, The National Center for Biotechnology Information (NCBI) genetic code table recognises 27 distinct variants, most of which are confined to eukaryotic nuclei and organelles. Comparative genomics and synthetic recoding studies reveal that the code is far more flexible than once believed, but why has the standard code remained so remarkably conserved among prokaryotes? Here, we propose that horizontal gene transfer (HGT) acts as a stabilising evolutionary force by enforcing translational compatibility among gene-sharing organisms. In prokaryotes, extensive HGT among prokaryotes creates strong selection for code uniformity, whereas genetic isolation in eukaryotes, driven by sexual reproduction, compartmentalisation, and reduced DNA exchange, has permitted divergence. This dynamic parallels human languages: communities that communicate frequently maintain a shared language, while isolated groups develop distinct ones. Although mobile genetic elements can locally perturb decoding through recoding and translational hijacking, these effects rarely propagate across microbial communities. We argue that the near universality of the genetic code is not a frozen historical accident but an emergent property of dense microbial connectivity shaped by HGT.},
}

@article {pmid41576587,
year = {2026},
author = {Bouchet, VMP and Muller, L and Brown, A and Deldicq, N and Deiss, A and Tailliez, L and Bertile, F},
title = {Exposure to aged polypropylene nurdle leachates disrupts photosymbiosis in a kleptoplastic unicellular eukaryote.},
journal = {The Science of the total environment},
volume = {1015},
number = {},
pages = {181394},
doi = {10.1016/j.scitotenv.2026.181394},
pmid = {41576587},
issn = {1879-1026},
abstract = {Kleptoplasty, i.e. the sequestration of functional algal chloroplasts by a host organism, represents a natural case of photosymbiosis from which the host derives crucial energetic benefits. We explored here how this host-symbiont relationship is affected by polypropylene nurdle leachates in a kleptoplastidic foraminifera. When exposed to virgin nurdles, a mild proteome regulation was observed in the host, whereas photosynthetic proteins were more abundant in kleptoplasts, supplying energy to the host. These results show that, de novo protein synthesis in stolen chloroplasts and delivery of host proteins and algal proteins encoded by the host following horizontal gene transfer are necessary to maintain efficient photosymbiosis in a virgin nurdle leachate polluted environment. Conversely, aged nurdles strongly reduced the content of photosynthesis-related proteins in kleptoplasts, disrupting the host-symbiont association. Remodeling of the proteome nevertheless suggested the possibly for an increased energy production in foraminifera, through a switch from mixotrophy to heterotrophy. Benthic foraminifera are therefore truly efficient unicellular eukaryotes, with diverse and sophisticated metabolic adaptive strategies that we are just beginning to discover.},
}

@article {pmid41576514,
year = {2026},
author = {Hao, Y and Li, Y and Liu, F and Long, J and Yang, H},
title = {Metagenomic insights into the influence of goose farming on the gut microbiome and antibiotic resistome of workers.},
journal = {Poultry science},
volume = {105},
number = {4},
pages = {106487},
doi = {10.1016/j.psj.2026.106487},
pmid = {41576514},
issn = {1525-3171},
abstract = {Antimicrobial resistance (AMR) seriously threatens the health of humans and animals. Antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) were enriched in the goose farms. However, the influence of goose farming exposure on the gut microbiota and ARGs of workers was unclear. In this study, metagenomic analysis was used to characterize gut microbiome structures, annotate bacterial taxa, and quantify the abundances of ARGs and MGEs in geese and human samples. Results showed that goose feces harbored more abundant ARGs and ARB than human feces. Significantly higher abundances of special ARGs (such as vanY, lsaE, AAC3-IId and ampC) were identified in workers compared to villagers. Compositions of gut bacteria were significantly different between workers and villagers, and some certain gut pathogens were abundant in the feces of workers, including Bacillus anthracis, Clostridium perfringens, and Escherichia coli O45:K1:H7. A total of 51 ARGs were pinpointed in the metagenome-assembled genomes (MAGs). Based on ARG-MGE associations and co-occurrence signals in MAGs, the potential for horizontal gene transfer (HGT) was inferred. With this transfer capacity and ubiquitous gut colonization, E. coli carrying 38 ARGs is proposed as a putative AMR indicator for the goose farm. This study demonstrates that goose farming had non-ignorable influences on the gut microbiome and antibiotic resistome of workers. More efforts should be made to control the ARGs and ARB in the goose farm.},
}

@article {pmid41576417,
year = {2026},
author = {Enríquez-Belenguer, A and Flores Ventura, E and Valls-Verdoy, A and Collado, MC},
title = {Evolution of the gut microbiome in infancy: recent advances.},
journal = {Current opinion in clinical nutrition and metabolic care},
volume = {},
number = {},
pages = {},
pmid = {41576417},
issn = {1473-6519},
abstract = {PURPOSE OF REVIEW: The early-life gut microbiome is a dynamic ecosystem that alongside other niches, such as the oral and skin microbiomes, undergoes rapid assembly and genetic evolution from birth through to adulthood. Although it was originally considered to be a passive colonisation process, recent findings suggest that early microbial development is a co-evolving, host-modulated process influenced by multiple factors, including maternal microbiota, mode of delivery, human milk, feeding practices, environmental exposure, and genetics, highlighting the timeliness of this review.

RECENT FINDINGS: In recent years, high-resolution sequencing and longitudinal multiomics have enabled the detailed observation of the early stages of microbial adaptation, assembly, strain transmission, diversification, and horizontal gene transfer in the early stages of life. New data also reveal maternal-foetal microbial signalling via metabolites and extracellular vesicles, as well as the evolutionary role of human milk oligosaccharides, and the involvement of phages, plasmids, and mobile genetic elements in infant gut microbial evolution.

SUMMARY: This review provides a summary of advances during gestation, birth, breastfeeding and infancy. However, further research is required into microbial evolution, and predicting its clinical significance, as well as  the role of artificial intelligence tools. Understanding early microbial adaptation processes could transform nutrition, precision medicine, and paediatric care.},
}

@article {pmid41576165,
year = {2026},
author = {Kuang, X and Gorzynski, J and Touchon, M and Shkoporov, A and Rocha, EPC and Fitzgerald, JR and Chen, J and Rostøl, JT and Penadés, JR},
title = {Bacteriophages mobilize bacterial defense systems via lateral transduction.},
journal = {Science advances},
volume = {12},
number = {4},
pages = {eadx5749},
doi = {10.1126/sciadv.adx5749},
pmid = {41576165},
issn = {2375-2548},
mesh = {*Bacteriophages/genetics/physiology ; *Gene Transfer, Horizontal ; *Bacteria/genetics/virology ; *Transduction, Genetic ; Genomic Islands ; },
abstract = {To counter challenges from bacteriophages (phages), bacteria use defense mechanisms that can reside on mobile genetic elements or within chromosomes. These immune systems are easily gained and lost, allowing adaptation to threats. However, the mechanism of mobilization of chromosomally encoded defense genes remains poorly understood. Here, we show that phage- and phage-inducible chromosomal island (PICI)-mediated lateral transduction (LT), a highly efficient horizontal gene transfer mechanism, facilitates the transfer of these defense genes between bacteria. Using several bacterial models, we demonstrate that defense systems are often positioned near phage or PICI attachment sites, allowing them to exploit LT for their mobility. In addition, LT diversifies defense genes carried by prophages and PICIs, driving immune system evolution and turnover. These processes provide phage resistance to new bacterial hosts and profoundly affect population genomics. Our findings reveal LT as a crucial mechanism shaping bacterial evolution and influencing the trajectory of pathogenic clones in nature.},
}

*Bacteriophages/genetics/physiology
*Gene Transfer, Horizontal
*Bacteria/genetics/virology
*Transduction, Genetic
Genomic Islands

@article {pmid41575223,
year = {2026},
author = {Han, N and Peng, X and Zhang, T and Qiang, Y and Li, X and Zhang, W},
title = {Hidden reservoir of highly adaptable multi-host plasmids that propagate antibiotic genes in healthy human populations.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag004},
pmid = {41575223},
issn = {1751-7370},
abstract = {Plasmids are key vectors for disseminating antibiotic resistance genes, yet their diversity and dynamics in the healthy human gut microbiome remain largely unexplored. Using fecal metagenomes from two cohorts (n = 498 samples), we constructed a comprehensive atlas of the healthy human gut plasmidome. We observed a polarization: while 97.4% of 19 151 plasmid clusters exhibited low prevalence (<5%), we identified 17 plasmid clusters detected in >30% of individuals. Among these, plasmid pGut1 emerged as a paradigm of a stealth vector. Prevalent globally (>50% in independent cohorts), pGut1 possesses a minimal 4-kb conserved backbone ensuring stability and a hypervariable region acting as a "plug-and-play" module. We documented 40 distinct cargo inserts, including multiple antibiotic resistance genes like cfr(C), erm(B), and aphA, across individuals, within individuals over time, and even within single fecal samples, validated by single-cell and Nanopore sequencing. Screening 2.3 million bacterial genomes revealed pGut1 in 93 strains across 49 genera and 2 phyla, including pathogenic Clostridioides difficile and three distinct Salmonella enterica strains. This suggests potential repeated cross-species transmission events, equipping pathogens with new antibiotic resistance genes. Our study exposes a hidden reservoir of highly adaptable, multi-host plasmids like pGut1 silently propagating antibiotic resistance genes in healthy populations. These plasmids, pre-adapted for cross-boundary dissemination, may pose a threat for fueling multidrug-resistant pathogens.},
}

@article {pmid41572473,
year = {2026},
author = {Kawano-Sugaya, T and Izumiyama, S and Nozaki, T},
title = {Draft genome of Entamoeba marina provides insights into the attenuation of pathogenicity and adaptation to the marine environment.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evag020},
pmid = {41572473},
issn = {1759-6653},
abstract = {Entamoeba is the amoebozoan parasite commonly found in the intestines of animals. E. marina is the first exception isolated from marine sediments, possibly adapting from animal intestines to the sea. However, the evolutionary process of E. marina remains uncertain due to the lack of a genome sequence. Here, we present the de novo genome and transcriptome of E. marina using Oxford Nanopore MinION and Illumina HiSeq/MiSeq. The genome of E. marina is approximately 37.5 Mbp in length and consisted of 202 contigs, which is the second longest next to E. invadens. E. marina showed significant reduction in the major virulence-associated gene families, including cysteine proteases, lysosomal enzyme transporters, and surface galactose/N-acetylglucosamine-specific lectins, suggesting diversification, more specifically reduction of pathogenicity-related genes. Genome and RNA-seq analyses also indicated genes either conserved throughout eukaryotes or laterally transferred from prokaryotes, and potentially responsible for salt tolerance. Our study provides insights into the mechanism underlying the lifestyle changes in the evolution of parasitic eukaryotes.},
}

@article {pmid41570777,
year = {2026},
author = {Wang, Z and Lu, J and Wang, X and An, W and Zhao, Y and Han, B and Tao, H and Liu, J and Guo, J and Wang, J},
title = {Long-term pet ownership promotes resistome similarity between cats and their owners.},
journal = {Environment international},
volume = {208},
number = {},
pages = {110074},
doi = {10.1016/j.envint.2026.110074},
pmid = {41570777},
issn = {1873-6750},
abstract = {Pet ownership offers physical and mental health benefits, but the risks of antibiotic resistance genes (ARGs) transmission between pets and humans remain underexplored. In this study, we used metagenomics analysis of fecal samples to compare resistome profiles among four groups: owned cats and their owners, and caged cats and non-cat owners. Our findings show significant similarities in gut microbial composition, ARGs, and mobile genetic elements (MGEs) between owned cats and their owners, identifying 73 shared core ARGs and 80 shared MGEs. In contrast, caged cats and non-cat owners shared only 30 ARGs and 73 MGEs. Long-term contact was positively correlated with a higher number of shared ARGs (from 20 + to 60 +) and MGEs (from 10 + to 40 +), as well as increased resistome risk (2.47- to 4.92-fold) between pet cats and owners. The gut microbiota played a key role in shaping the ARGs and MGEs profiles, with Escherichia coli and Klebsiella pneumoniae identified as primary carriers, each genome harboring 20 to 62 ARGs and 6 to 29 MGEs. ARGs transfer events were more frequent between pet cats and their owners than in other groups. These findings underscore a potential risk of shared antimicrobial resistance between companion animals and humans within the studied population in China.},
}

@article {pmid41570776,
year = {2026},
author = {Xu, J and Liu, X and Zhang, S and Li, J and Yang, Q},
title = {Sodium hypochlorite residual in the environment facilitated the spread of antibiotic resistance genes: through microplastics as a medium.},
journal = {Environment international},
volume = {208},
number = {},
pages = {110048},
doi = {10.1016/j.envint.2026.110048},
pmid = {41570776},
issn = {1873-6750},
abstract = {Most pollutants in the environment exist in complex forms, and exploring the impact of a single pollutant lacks wide applicability. The co-exposure of microplastics (MPs) and NaClO in wastewater treatment plants (WWTPs) is a widespread occurrence. At present, relevant reports on the impact of individual NaClO or MPs on antibiotic resistance genes (ARGs) have been established. Herein, this study investigated the fate of antibiotic-resistant bacteria (ARB) and ARGs after exposure to MPs with or without NaClO stress. In this study, the total ARG abundance increased by 11.83% under MPs stress, and further increases by 17.89% under NaClO stress with MPs co-exposure. The mechanism was that the presence of NaClO promoted the selective enrichment of potential ARB and ARGs on the MPs-biofilm. The surface morphology of the MPs was changed and the attached biofilm became thicker, which provided a suitable environment for the proliferation of ARB and the spread of ARGs. Vertical gene transfer (VGT) and horizontal gene transfer (HGT) of ARGs were facilitated by MPs under NaClO stress. Specifically, the VGT of ARGs was facilitated via enhanced bacterial cell proliferation (by 132.66%), and relevant functional genes are also increased. HGT of ARGs is promoted by the increasing relative abundance of mobile genetic elements (MGEs). ARG-carrying plasmids are also demonstrated that MPs promoted HGT of ARGs in the presence of NaClO. The increase in oxidative stress, cell membrane permeability, and Type IV secretion system (T4SS) collaboration facilitated the HGT of ARGs. In summary, co-exposure to NaClO and MPs promote VGT and HGT of ARGs through the variation in MPs structure and the enhancement of MPs-biofilms. Furthermore, the presence of MPs restrained the disinfection effect of NaClO, with an inhibition rate higher than 50%.},
}

@article {pmid41569151,
year = {2026},
author = {Zhang, W and Kong, J and Zeng, Y and Su, Y and Zhang, S and Li, Y and Hu, C and Chen, Q and Xiao, Y and Lu, M},
title = {Structural plasticity enables broad cAn binding and dual activation of CRISPR-associated ribonuclease Cdn1.},
journal = {Nucleic acids research},
volume = {54},
number = {3},
pages = {},
doi = {10.1093/nar/gkaf1524},
pmid = {41569151},
issn = {1362-4962},
support = {2023YFC3402300//National Key Research and Development Program of China/ ; 2021ZD0203400//STI2030-Major Projects/ ; 31970547//National Natural Science Foundation of China/ ; },
mesh = {*CRISPR-Cas Systems/genetics ; *Bacterial Proteins/chemistry/metabolism/genetics ; Protein Binding ; *CRISPR-Associated Proteins/metabolism/chemistry/genetics ; Models, Molecular ; Adenine Nucleotides/metabolism/chemistry ; Catalytic Domain ; *Ribonucleases/metabolism/chemistry/genetics ; Oligoribonucleotides ; },
abstract = {Prokaryotes have naturally evolved diverse RNA-guided defense systems against viral infections, with the type III CRISPR-Cas systems representing the most intricate. These systems feature accessory proteins activated by cyclic oligoadenylates (cOAs) produced upon target RNA recognition, synergizing with the CRISPR-Cas machinery to defend against exogenous invaders. Typically, each accessory protein is activated by only one specific cOA type. Here, we characterize Cdn1, a type III-B CRISPR accessory protein from Psychrobacter lutiphocae, which binds to cA3, cA4, and cA6, but activated by cA4 and cA6 with different efficacies to catalyze ssRNA cleavage. Combined structural and biochemical analyses reveal that cOA binding triggers dramatic conformational reorganization, including the formation of a dimerization interface of nuclease domains, the emergence of substrate binding cleft, and the reconstruction of a metal-dependent catalytic center essential for RNA cleavage. This dual activation mechanism illustrates evolutionary innovation within CRISPR-associated Rossman-fold nucleases. We propose that such structural plasticity evolved to maximize defensive resilience during microbial competition and horizontal gene transfer, while preserving broad-spectrum antiviral ability. These findings not only elucidate the activation mechanisms of Cdn1 within the type III systems but also underscore the functional complexity and adaptability of CRISPR-Cas ancillary proteins.},
}

*CRISPR-Cas Systems/genetics
*Bacterial Proteins/chemistry/metabolism/genetics
Protein Binding
*CRISPR-Associated Proteins/metabolism/chemistry/genetics
Models, Molecular
Adenine Nucleotides/metabolism/chemistry
Catalytic Domain
*Ribonucleases/metabolism/chemistry/genetics
Oligoribonucleotides

@article {pmid41568973,
year = {2026},
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 = {Journal of bacteriology},
volume = {},
number = {},
pages = {e0044825},
doi = {10.1128/jb.00448-25},
pmid = {41568973},
issn = {1098-5530},
abstract = {UNLABELLED: 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 genera 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 another 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) is critical for energy conservation in Methanosarcina spp. during growth on acetate, and a F420:methanophenazine 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 100 genomes within the class Methanosarcinia to show that the genomic potential for acetoclastic methanogenesis is widespread. We then used the genetically tractable strain, Methanosarcina acetivorans, to build all modular combinations that might support 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 to core energy metabolism too.

IMPORTANCE: A large fraction of biogenic methane is derived from acetate, yet acetoclastic methanogens, i.e., methanogens that grow on acetate, remain poorly characterized due to their slow growth. Two groups of methanogens, Methanosarcina spp. and Methanothrix spp., perform acetoclastic methanogenesis using distinct sets of genes for acetate activation and energy conservation. It is widely hypothesized that these genetic modules from Methanosarcina spp. and Methanothrix spp. are functionally analogous and would thus be interchangeable. To test this hypothesis, we engineered different combinations of modules for acetoclastic growth in Methanosarcina acetivorans. Our results challenge this hypothesized paradigm of modularity, and we posit that other changes to the carbon and electron transfer pathways are crucial for the emergence of acetoclastic methanogenesis.},
}

@article {pmid41568963,
year = {2026},
author = {Nieto Noblecia, J and Bellis, NF and Antichi, CA and Aminian, S and Forti, F and Falchi, FA and Sposato, D and Imperi, F and Cingolani, G and Briani, F},
title = {Pseudomonas aeruginosa DEV phage exploits the essential LptD outer membrane protein as receptor for adsorption.},
journal = {mBio},
volume = {},
number = {},
pages = {e0356125},
doi = {10.1128/mbio.03561-25},
pmid = {41568963},
issn = {2150-7511},
abstract = {UNLABELLED: Pseudomonas aeruginosa bacteriophage (phage) DEV is a podovirus of the Schitoviridae family, related to the prototypical Escherichia coli phage N4. N4 uses the novel glycan receptor (NGR) surface glycan, presumably bound by the gp66 appendages, and the NGR transporter NfrA, recognized by the phage gp65 tail sheath, as receptors for adsorption. In contrast, DEV relies on the O-antigen moiety of lipopolysaccharide (LPS) as the primary receptor recognized by the gp53 long tail fibers. However, DEV can infect deep-rough strains that lack the O-antigen moiety by using another, still unknown receptor. Here, we provide evidence that the essential LPS transporter LptD serves as the DEV secondary receptor and that DEV gp54 is its cognate receptor-binding protein. gp54 is encoded within the essential gp56-gp55-gp54 operon, which also includes gp56, the short tail fiber gene. Using cryogenic electron microscopy, AlphaFold modeling, and genetic analysis, we show that DEV gp56, gp55, and gp54 assemble into a receptor-binding fiber (RBF) positioned laterally to a previously uncharacterized tail plug protein, gp74. The DEV RBF is functionally equivalent to the N4 sheath protein gp65, which associates with the tail plug gp53. Thus, DEV and N4 both use a glycan and its surface-exposing transporter as receptors for adsorption. To our knowledge, this is the first example of a P. aeruginosa phage using an essential outer membrane protein as a receptor, with implications for phage therapy.

IMPORTANCE: Pseudomonas aeruginosa phage DEV uses the O-antigen of lipopolysaccharide as its primary receptor. In this study, we found that LptD, an essential and highly conserved outer membrane protein, serves as the secondary receptor for DEV. This interaction is mediated by a specialized receptor-binding fiber composed of the DEV proteins gp54, gp55, and gp56. We posit that the gp56-gp55-gp54 genes form a functional module, possibly disseminated via horizontal gene transfer among distantly related phages, involved in tail sealing and the regulated unplugging of the tail upon interaction with the bacterial receptor. Given the high conservation of receptor-binding proteins among phages in the DEV Litunavirus genus, we anticipate that other members of this genus may also use LptD as their receptor. Since Litunaviruses are actively explored for phage therapy, insights into the interaction between DEV and its receptors could help develop more effective and targeted phage-based treatments.},
}

@article {pmid41568054,
year = {2025},
author = {Meng, Q and Chang, L and Wang, S and Lu, G},
title = {Genomic characterization, antimicrobial resistance, and virulence profiling of Escherichia coli isolated from diarrheic calves in Gansu, China.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1729295},
pmid = {41568054},
issn = {1664-302X},
abstract = {INTRODUCTION: This study provides a comprehensive genomic investigation of Escherichia coli isolated from diarrheic calves in Gansu Province, China, a region with significant livestock production.

METHODS: We employed whole-genome sequencing on 15 isolates from 15 different farms to characterize their molecular subtypes, plasmid repertoires, virulence gene profiles, and antibiotic resistance mechanisms.

RESULTS: Our analysis revealed high genetic diversity with 10 sequence types and 9 serotypes, including a novel serogroup. Phenotypic testing demonstrated widespread multidrug resistance, yet canonical resistance genes were absent in many resistant strains. Phylogenetic analysis elucidated the roles of both clonal dissemination and horizontal gene transfer.

DISCUSSION: These findings highlight the extensive genomic complexity of bovine E. coli in this region. The discrepancy between observed resistance and its genotypic basis underscores the need for integrated molecular surveillance. The small sample size limits generalizability, warranting confirmation in larger studies. This work situates its importance within the global "One Health" framework.},
}

@article {pmid41413462,
year = {2025},
author = {Martins, BTF and Rodrigues, RDS and Nero, LA},
title = {Comparative pangenome analysis of Yersinia enterocolitica in a one health approach.},
journal = {BMC genomics},
volume = {27},
number = {1},
pages = {76},
pmid = {41413462},
issn = {1471-2164},
support = {finance code 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; },
abstract = {UNLABELLED: Yersinia enterocolitica is a Gram-negative pathogen frequently associated with swine and pork products. Despite its global importance, little is known about the genomic characteristics of Y. enterocolitica in Brazil. Furthermore, the antimicrobial resistance (AMR) in Y. enterocolitica has been associated to be driven by horizontal gene transfer, especially in environments with intensive antimicrobial use. This study aims to investigate the phylogenetic and population structure of Y. enterocolitica, and antimicrobial resistance and virulence gene distribution using genome sequences to compare isolates obtained in Brazil with other isolates deposited in online databases. In this study, a total of 998 high-quality genomes from Y. enterocolitica deposited in the National Center for Biotechnology Information (NCBI) were evaluated for pangenome using the Roary software with MAFFT for alignment. Pangenome analysis and phylogenetic inference were also performed on a subset of 837 genomes from isolates obtained from both pig and human. The analyses followed the procedures determined by ModelTest-NG. ABRicate with PlasmidFinder database, Virulence Factor Database (VFDB) and CARD database were used to investigate plasmid markers, virulence genes and resistance genes. Comparative analysis with international strains from public databases suggests that specific Y. enterocolitica strains circulate in Brazil. Swine and human isolates from Brazil were consistently grouped together, suggesting a strong zoonotic link. Additionally, the study underscores the correlation between antimicrobial use in pig farming and resistance gene prevalence. Our findings contribute to the understanding of Y. enterocolitica epidemiology in Brazil and emphasize the importance of genomic surveillance under the One Health approach to prevent foodborne diseases and combat antimicrobial resistance.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-025-12420-0.},
}

@article {pmid41402709,
year = {2025},
author = {Sui, J and Wang, X and Su, Y and Gao, M and Huang, H and Liu, H and Zhang, J and Tang, Y},
title = {ProMoHGT: a heterogeneous graph transformer with graph contrastive learning for robust microbial protein function prediction.},
journal = {BMC genomics},
volume = {27},
number = {1},
pages = {73},
pmid = {41402709},
issn = {1471-2164},
support = {2023JJB140329//Guangxi Medical University,the Department of Science and Technology of Guangxi Zhuang Autonomous Region/ ; GXMUYSF202416//Youth Science Foundation of Guangxi Medical University/ ; },
abstract = {UNLABELLED: Proteins serve as the central executors of life activities, performing diverse functions such as metabolic catalysis, genetic regulation, signal transduction, and cytoskeletal maintenance. However, microbial proteins face unique challenges: their rapid evolution leads to low sequence conservation, and structural diversity complicates functional inference. Experimental annotation lags far behind due to scalability limits—over 70% of microbial proteins in UniProt remain uncharacterized, compared to roughly 50% for model eukaryotes. Traditional homology-based tools (e.g., FASTA/BLAST) often fail on highly divergent microbial families, and existing machine-learning methods rarely account for microbial-specific signals such as horizontal gene transfer. To address this gap, this study presents the first publicly available dataset for microbial protein function annotation and introduces ProMoHGT, a novel model that extracts evolutionary and contextual sequence features using ESM-2, constructs three-dimensional spatial proximity graphs from AlphaFold2 predictions, and encodes residue-specific physicochemical properties. Its core heterogeneous Transformer architecture incorporates super-nodes and multi-head self-attention to integrate global topology with long-range dependencies, while graph contrastive learning adds regularization to enhance robustness and prevent overfitting. ProMoHGT outperforms state-of-the-art methods across all three Gene Ontology categories (MF, BP, CC) and in Enzyme Commission number prediction, with the smallest performance decay observed across varying homology scenarios, thereby validating its superior generalization capability. A case study on three representative microbial proteins (ArcA, CodY, and SPT16) further confirmed these advantages, where ProMoHGT most accurately recovered key experimentally validated functions such as DNA binding, transcription activation, chromatin remodeling, and metabolic regulation, achieving the highest F1 scores among all methods.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-025-12383-2.},
}

@article {pmid41566227,
year = {2026},
author = {Proctor, RH and Busman, M and Kim, HS and Menke, J and Villani, A and Lohmar, JM and Brown, DW and Turgeon, BG and Susca, A and Moretti, A and Bushley, KE},
title = {Distribution and shared evolutionary history of the Fumonisin and AAL toxin biosynthetic gene clusters.},
journal = {BMC genomics},
volume = {27},
number = {1},
pages = {71},
pmid = {41566227},
issn = {1471-2164},
}

@article {pmid41564764,
year = {2026},
author = {Liu, S and Zhao, J and Zhai, K and Zhang, Z and Wang, X and Xu, H and Mao, D},
title = {Alkyl chain extension of parabens influences their ability to disrupt antibiotic resistome in aquatic ecosystems.},
journal = {Journal of hazardous materials},
volume = {503},
number = {},
pages = {141152},
doi = {10.1016/j.jhazmat.2026.141152},
pmid = {41564764},
issn = {1873-3336},
abstract = {The widespread use of different parabens as preservatives has raised significant concerns regarding antibiotic resistance genes (ARGs) in aquatic ecosystems. Although the elongation of alkyl chains enhances the antimicrobial properties of parabens, it remains unclear whether this modification influences their ability to disrupt ARGs. Here, we selected four parabens to investigate how parabens with varying alkyl chain lengths affect ARGs through both experimental and theoretical methods. Our results revealed that the ARG composition was altered differently by parabens with varying alkyl chain lengths. Furthermore, different parabens triggered distinct antimicrobial resistance mechanisms. Specifically, methylparaben, ethylparaben, propylparaben, and butylparaben promoted mechanisms related to reduced membrane permeability, protection of cellular targets, efflux pumps, and drug inactivation, respectively. The extension of alkyl chain lengths altered several molecular characteristics (e.g., hydrophobicity and chemical potential) of the parabens, which were critical upregulating the specific resistance mechanisms by different parabens. Additionally, the lengths of alkyl chains influenced the capacity of parabens to facilitate the spread of ARGs to pathogens through SOS responses and horizontal gene transfer, thereby contributing to the health risks of parabens. Overall, this study highlights the structural dependency of parabens in disturbing ARGs and suggests a need for improved regulatory strategies of parabens.},
}

@article {pmid41563910,
year = {2026},
author = {Rondinelli, M and Kaur, S and Ledwell, OA and Wong, H and Sheth, PM and diCenzo, GC},
title = {Variations in carbapenem resistance associated with the VIM-1 metallo-β-lactamase across the Enterobacterales.},
journal = {Microbiology (Reading, England)},
volume = {172},
number = {1},
pages = {},
doi = {10.1099/mic.0.001646},
pmid = {41563910},
issn = {1465-2080},
mesh = {*beta-Lactamases/genetics/metabolism ; *Anti-Bacterial Agents/pharmacology ; *Carbapenems/pharmacology ; Microbial Sensitivity Tests ; Humans ; Plasmids/genetics ; Integrons/genetics ; Enterobacteriaceae Infections/microbiology ; Whole Genome Sequencing ; Gene Transfer, Horizontal ; Meropenem/pharmacology ; *Enterobacteriaceae/genetics/drug effects/enzymology/isolation & purification ; Ontario ; Ertapenem/pharmacology ; Enterobacter/genetics/drug effects/isolation & purification/enzymology ; },
abstract = {The VIM-1 metallo-β-lactamase enzyme, encoded within class 1 integrons, is found in Gram-negative clinical isolates worldwide and has been linked to outbreaks of bacterial pathogens in nosocomial settings. Six vim-1+ clinical isolates, from the genera Escherichia, Klebsiella and Enterobacter, were obtained from Kingston, Ontario, Canada. Whole-genome sequencing revealed that vim-1 was plasmid-borne in all strains and situated as the first gene in In916 or In110 integrons. Analysis of related plasmids suggested that these vim-1-containing plasmids are globally disseminated and have spread via horizontal gene transfer and autochthonous vertical spread within Ontario. Interestingly, the MICs of ertapenem and meropenem, two clinically relevant carbapenem antibiotics, against these six isolates varied more than tenfold, suggesting that the effects of VIM-1 are dependent on the genomic content of the host microbe. Introducing vim-1 into three common Enterobacterales laboratory strains was not sufficient to confer resistance to ertapenem and meropenem. Instead, adaptive laboratory evolution of the vim-1 [+] laboratory strains revealed that vim-1-mediated carbapenem resistance in these strains was dependent on epistatic interactions with ompC mutations, likely due to decreased outer membrane permeability to these antibiotics. Together, these results provide additional support for the role of gene epistasis in modulating the antimicrobial resistance phenotypes of acquired resistance genes, as well as previous results suggesting that the presence of a β-lactamase gene is insufficient to confer strong resistance to carbapenems without being paired with reduced outer membrane permeability.},
}

*beta-Lactamases/genetics/metabolism
*Anti-Bacterial Agents/pharmacology
*Carbapenems/pharmacology
Microbial Sensitivity Tests
Humans
Plasmids/genetics
Integrons/genetics
Enterobacteriaceae Infections/microbiology
Whole Genome Sequencing
Gene Transfer, Horizontal
Meropenem/pharmacology
*Enterobacteriaceae/genetics/drug effects/enzymology/isolation & purification
Ontario
Ertapenem/pharmacology
Enterobacter/genetics/drug effects/isolation & purification/enzymology

@article {pmid41563902,
year = {2026},
author = {Rodriguez, S and Rey-Varela, D and Martinez, C and Martinez, P and Travers, MA and Barja, JL and Dubert, J},
title = {Genomic plasticity and mobilome architecture of Vibrio europaeus reveal key mechanisms of evolutionary adaptation.},
journal = {Microbial genomics},
volume = {12},
number = {1},
pages = {},
doi = {10.1099/mgen.0.001600},
pmid = {41563902},
issn = {2057-5858},
mesh = {*Vibrio/genetics/pathogenicity/classification ; *Genome, Bacterial ; Animals ; *Evolution, Molecular ; Adaptation, Physiological/genetics ; Aquaculture ; Bacteriophages/genetics ; Genomics ; Interspersed Repetitive Sequences ; Plasmids/genetics ; Phylogeny ; },
abstract = {Vibrio europaeus has emerged as a significant pathogen in shellfish aquaculture, causing mass mortality outbreaks in key bivalve species and leading to severe economic losses for the industry. Studies on the structure and characteristics of the accessory genome in aquaculture pathogens remain scarce, despite its crucial role in evolutionary and ecological adaptation. The accessory genome provides indeed genetic variability that enables rapid responses to environmental challenges, host adaptation and selective pressures such as antibiotics or phage predation. Here, we present the first comprehensive comparative genomic analysis of the V. europaeus pangenome to investigate the structural organization and functional content of its accessory genome. The soft mobilome of V. europaeus comprises 73% of accessory genes and 44% of the total pangenome, including non-chromosomic (plasmids) and chromosomic genetic elements such as prophages, integrative and conjugative/mobilizable elements, phage satellites and other mobile genetic elements (MGEs) designated as unclassified chromosomic regions of genomic plasticity (unclassified chromosomic RGPs). Among accessory elements, unclassified chromosomic RGPs were the primary drivers of evolutionary dynamics in V. europaeus, acting as the main genetic reservoir of anti-phage defence systems and antimicrobial resistance genes. Notably, the identification of abundant insertion hotspots in chromosomic genetic elements facilitates the rapid acquisition of anti-phage defence systems, thereby enabling rapid turnover of these systems and enhancing host fitness. In addition, novel pVE1-like plasmids (>300 kb) - only found in this species and its closest relative Vibrio tubiashii - emerged as the largest and most ubiquitous MGEs in V. europaeus. These plasmids encode the highest number of virulence genes and secondary metabolite biosynthetic genes, as well as a remarkable diversity of anti-phage defence systems among closely related strains. Although the genome dataset analysed here is limited to strains isolated from moribund/dead animals in aquaculture environments, this study provides new insights into the role of accessory genetic elements in the evolution, adaptation and diversification of the shellfish pathogen V. europaeus. The findings reveal the complexity and plasticity of its pangenome and highlight the importance of RGPs and plasmids in bacterial fitness.},
}

*Vibrio/genetics/pathogenicity/classification
*Genome, Bacterial
Animals
*Evolution, Molecular
Adaptation, Physiological/genetics
Aquaculture
Bacteriophages/genetics
Genomics
Interspersed Repetitive Sequences
Plasmids/genetics
Phylogeny

@article {pmid41562598,
year = {2026},
author = {Jia, H and Lu, S and Jia, Y and Yu, Y and Wu, Y and Bao, D and Zhang, Y and Fang, J and Butaye, P and Furlan, JPR and Elhadidy, M and Quiñones Pérez, D and Yang, Q and Ruan, Z},
title = {Human intestinal colonization by Escherichia coli ST4014 co-harboring tet(X4) and blaNDM-1 gene: a potential reservoir for antimicrobial resistance dissemination.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0333625},
doi = {10.1128/spectrum.03336-25},
pmid = {41562598},
issn = {2165-0497},
abstract = {UNLABELLED: This study aims to elucidate the genomic characteristics of three Escherichia coli strains isolated from stool specimens of healthy individuals co-carrying tet(X4) and blaNDM-1 gene, which confer resistance to tigecycline and carbapenems, respectively. Whole-genome sequencing (WGS) and bioinformatic analysis were conducted to identify the genomic characteristics. Fourteen E. coli strains belonging to the same sequence type (ST) 4014, comprising eleven strains retrieved from public databases and three strains from this study, were integrated into a phylogenetic analysis. Conjugation experiments were conducted to evaluate the transferability of the resistance plasmids. Three E. coli strains exhibited resistance to both tetracyclines and carbapenems, consistent with the presence of tet(X4) and blaNDM-1 genes in their genomes. All strains belonged to the rare ST 4014 and were identified in healthy individuals within a 1-week period. WGS revealed that tet(X4) and blaNDM-1 genes were each located on separate plasmids, both exhibiting 100% sequence identity to others previously reported in various bacterial species. Conjugation experiments confirmed the transferability of both tet(X4) and blaNDM-1-carrying plasmids. Phylogenetic analysis based on cgSNPs revealed limited genetic diversity among the three strains (2-6 SNPs), but substantial differences compared to 11 publicly available ST4014 strains (116-172 SNPs). This study reports E. coli ST4014 strains from healthy individuals harboring conjugative plasmids carrying tet(X4) and blaNDM-1 genes, conferring resistance to tigecycline and carbapenems, respectively. These findings highlight the silent spread of multidrug-resistant strains in community populations and emphasize the need for enhanced surveillance of antimicrobial resistance beyond clinical settings.

IMPORTANCE: The emergence of Escherichia coli strains co-harboring tet(X4) and blaNDM-1 genes in healthy individuals represents a critical public health concern. These genes mediate resistance to tigecycline and carbapenems, two of the few remaining options for treating infections caused by multidrug-resistant gram-negative bacteria. The detection of clonally related ST4014 strains carrying conjugative plasmids encoding both resistance determinants highlights the potential for horizontal gene transfer and silent dissemination of dual-resistance plasmids in community settings. Such colonization among healthy individuals suggests that antimicrobial resistance may be spreading unnoticed beyond hospitals, driven by environmental or foodborne transmission routes. These findings emphasize the urgent need for integrated genomic surveillance and One Health-based interventions encompassing human, animal, and environmental reservoirs to prevent the expansion of high-risk resistance genes and safeguard the clinical efficacy of last-line antibiotics.},
}

@article {pmid41562034,
year = {2026},
author = {Sanchez-Cid, C and Vrchovecká, S and Dehon, E and Wacławek, S and Vogel, TM},
title = {Environmental Consequences of Anthropogenic Pollution: Non-antibiotic-Drug-Driven Antibiotic Resistance Selection in a Model Aquatic Ecosystem.},
journal = {Environment & health (Washington, D.C.)},
volume = {4},
number = {1},
pages = {132-143},
pmid = {41562034},
issn = {2833-8278},
abstract = {Non-antibiotic drugs (NADs) used in human therapy may induce antibiotic resistance selection and dissemination in vitro. However, the potential risks of antibiotic resistance emergence associated with environmental NAD pollution have not been addressed. Here, we conducted a multidisciplinary study on river water microcosms using growth kinetics, qPCR, metagenomics, 16S rRNA sequencing, and liquid chromatography-tandem mass spectrometry (LC-MS/MS) to determine whether NADs alter river bacterial ecology and select for antibiotic resistance genes (ARGs). Four NADs with different mechanisms of action were included at a high (mg/L) and low (μg/L) dose to establish dose-response relationships: chlorpromazine (antipsychotic), diclofenac (anti-inflammatory), diphenhydramine (antihistamine), and fluoxetine (antidepressant). Although the community response to NAD pollution was compound-specific and dose-dependent, all NADs and doses were stable in the environment, altered the composition and activity of bacterial communities, and selected for several ARGs, mostly β-lactamases and aminoglycoside resistance genes, some of which were associated with horizontal gene transfer genes. Pseudomonas (including some ARG-harboring subpopulations) was identified as a key player in the response to NAD pollution. Here, we demonstrate NAD-driven antibiotic resistance selection in complex aquatic communities, raising concerns about the collateral effects on human and environmental health due to the extensive anthropocentric use of NADs.},
}

@article {pmid41561392,
year = {2026},
author = {Choudhary, DK and Turgeman-Grott, I and Robinzon, S and Gophna, U},
title = {CRISPR-Cas targeting in Haloferax volcanii promotes within-species gene exchange by triggering homologous recombination.},
journal = {microLife},
volume = {7},
number = {},
pages = {uqaf047},
pmid = {41561392},
issn = {2633-6693},
abstract = {CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-Cas (CRISPR-associated genes) systems provide adaptive immunity in bacteria and archaea against mobile genetic elements, but the role they play in gene exchange and speciation remains unclear. Here, we investigated how CRISPR-Cas targeting affects mating and gene exchange in the halophilic archaeon Haloferax volcanii. Surprisingly, we found that CRISPR-Cas targeting significantly increased mating efficiency between members of the same species, in contrast to its previously documented role in reducing interspecies mating. This enhanced mating efficiency was dependent on the Cas3 nuclease/helicase and extended beyond the targeted genomic regions. Further analysis revealed that CRISPR-Cas targeting promoted biased recombination in favor of the targeting strain (the strain containing the CRISPR-Cas system) during mating, resulting in an increased proportion of recombinant progeny that are positive for CRISPR-Cas. To test whether an increase in recombination is sufficient to increase mating efficiency, we tested whether strains lacking the Mre11-Rad50 complex, which are known to have elevated recombination activity, also exhibited higher mating success. Indeed, these strains showed higher mating, as did cells that were exposed to DNA damage using methyl methanesulfonate. These findings suggest that CRISPR-Cas systems in archaea play roles beyond their canonical immune function. They may contribute to speciation by facilitating within-species gene exchange while limiting between-species genetic transfer, thereby maintaining species boundaries.},
}

@article {pmid41561308,
year = {2026},
author = {Mei, Z and He, C and Balcazar, JL and Fu, Y and Dou, Q and Liu, Y and Dercon, G and Jiang, X and Elsner, M and Wang, F},
title = {Antibiotic-degrading bacteria shape resistome dynamics and horizontal gene transfer potential in soils with contrasting properties.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycaf246},
pmid = {41561308},
issn = {2730-6151},
abstract = {Soils act as both reservoirs and filters of antimicrobial resistance genes (ARGs); however, the ecological and genetic traits of antibiotic-degrading bacteria (ADB) and their interactions with nondegrading bacteria (NADB) across soil types remain poorly understood. In particular, the role of ADB in ARG dynamics and their potential contribution to horizontal gene transfer (HGT) are still underexplored. Here, we applied [13]C-DNA stable isotope probing (DNA-SIP) combined with metagenomic sequencing to resolve active ADB from NADB in two contrasting soils: Ultisol and Mollisol. ADB harbored significantly more abundant and diverse chromosomal ARGs - especially multidrug and tetracycline resistance genes - often co-localized with mobile genetic elements (MGEs) and degradation genes, suggesting robust and regulated resistance strategies. In contrast, NADB relied more on plasmid-borne ARGs, reflecting flexible but potentially transient adaptation. Soil properties shaped both resistome composition and host taxa. Mollisol enriched enzymatic degraders such as Lysobacter and Nocardioides, while Ultisol favored stress-tolerant Burkholderia, which carried up to 34 ARGs and exhibited membrane-associated resistance. Notably, 89 ARGs or MGEs were found co-localized with degradation genes on assembled contigs, highlighting a strong potential for HGT. In addition, 24 high-potential ARG hosts were identified, including Ralstonia pickettii and Saccharomonospora viridis. These findings reveal that antibiotic degradation is embedded within complex, soil-specific resistome networks. This work enhances our understanding of ARG ecology and supports targeted mitigation strategies based on soil microbiome characteristics.},
}

@article {pmid41560929,
year = {2025},
author = {Ma, X and Yang, X and Wang, X and Tang, X and Li, X and Geng, D and Ma, Y and Pu, M and Shu, J},
title = {Genome-wide identification and expression analysis of the PEBP gene family in Ziziphus jujuba var. spinosa.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1700555},
pmid = {41560929},
issn = {1664-462X},
abstract = {Phosphatidylethanolamine-binding proteins (PEBPs) are known to regulate flowering time and morphogenesis in plants. However, their identification and functions in Ziziphus jujuba var. spinosa remain uncharacterized. In this study, seven ZjPEBP genes were identified and were unevenly distributed across six chromosomes. Phylogenetic analysis classified them into four subfamilies: FT-like, TFL1-like, MFT-like, and SMFT-like. The SMFT-like subfamily likely originated from horizontal gene transfer (HGT) of prokaryotic origin, exhibiting high sequence similarity to bacteria. In contrast, the remaining six members expanded through dispersed duplication events and possess conserved structures. Cis-acting element analysis suggests that ZjPEBP genes may be involved in growth, development, light responsiveness, hormone signaling, and stress adaptation. Reverse transcription quantitative PCR (RT-qPCR) revealed tissue-specific expression patterns among ZjPEBP genes. The key flowering regulators ZjFT and ZjTFL1 exhibited antagonistic expression dynamics during fruit-bearing shoot (FBS) development: ZjFT expression peaked when FBS reached 2-4 mm in length, coinciding with the initial stage of floral bud differentiation, whereas ZjTFL1 maintained low expression levels throughout all developmental stages. After flowering, a clear spatiotemporal expression gradient was observed, with ZjFT expression in basal leaves being significantly higher than in middle and apical leaves. This expression pattern aligned with the basipetal progression of floral organ differentiation. As the basal and middle sections entered the fruit-setting stage, ZjFT expression was markedly downregulated. Under abscisic acid (ABA) treatment, all ZjPEBP genes were significantly induced, suggesting their potential involvement in both flowering regulation and ABA signaling pathways. Notably, ZjSMFT exhibited the most pronounced response, with expression levels upregulated approximately 400-fold at 24 hours post-treatment. This study provides a systematic characterization of the ZjPEBP gene family in sour jujube, laying a solid foundation for further elucidating the molecular mechanisms of flowering regulation and its potential applications in molecular breeding.},
}

@article {pmid41560434,
year = {2026},
author = {Jang, YJ and Oh, SD and Hong, JK and Kim, NY and Lee, GM and Park, SY and Park, JC and Chang, A},
title = {Impact of herbicide-resistant genetically modified rapeseed on gut bacterial diversity of Eisenia fetida.},
journal = {GM crops & food},
volume = {17},
number = {1},
pages = {2617700},
doi = {10.1080/21645698.2026.2617700},
pmid = {41560434},
issn = {2164-5701},
mesh = {*Plants, Genetically Modified/genetics ; *Gastrointestinal Microbiome/genetics/drug effects ; Animals ; *Brassica rapa/genetics ; *Herbicides/pharmacology ; *Oligochaeta/microbiology/drug effects ; *Herbicide Resistance/genetics ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation & purification ; Biodiversity ; },
abstract = {The systematic evaluation of the safety and environmental impact associated with genetically modified (GM) crops is currently underway within the scientific community, with a particular focus on their effects on the gut microbiota, which plays a vital role in host health. In this study, we compared the effects of a non-GM rapeseed cultivar with those of an herbicide-resistant GM rapeseed cultivar containing the phosphinothricin acetyltransferase gene on the gut bacterial community of Eisenia fetida. The 16S rRNA amplicon sequencing and data analysis showed no significant differences in gut bacterial community composition or diversity between E. fetida fed GM rapeseed and those fed non-GM rapeseed. Principal component analysis indicated that, rather than plant type, external factors influenced the community structure. Polymerase chain reaction analysis revealed no evidence of horizontal gene transfer from GM rapeseed to microbes or earthworms. Overall, GM rapeseed had a negligible effect on gut microorganisms and did not significantly alter the gut bacterial community of E. fetida.},
}

*Plants, Genetically Modified/genetics
*Gastrointestinal Microbiome/genetics/drug effects
Animals
*Brassica rapa/genetics
*Herbicides/pharmacology
*Oligochaeta/microbiology/drug effects
*Herbicide Resistance/genetics
RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/classification/isolation & purification
Biodiversity

@article {pmid41559953,
year = {2026},
author = {Wu, J and Sun, D and Pan, Y and Liu, DF and Zhang, H and Zhou, JH and Gao, T and Wu, J and He, RL and Chen, YG and Li, WW},
title = {Overlooked Roles of Pharmaceutical Metabolic Products in Stimulating Microbial Metabolism and Antibiotic Resistance Gene Dissemination of Anaerobic Sludge.},
journal = {Environmental microbiology},
volume = {28},
number = {1},
pages = {e70247},
doi = {10.1111/1462-2920.70247},
pmid = {41559953},
issn = {1462-2920},
support = {51878638//National Natural Science Foundation of China/ ; 52192681//National Natural Science Foundation of China/ ; 22106160//National Natural Science Foundation of China/ ; U21A20160//National Natural Science Foundation of China/ ; 202423110050028//Key R&D Project of Anhui Province, China/ ; SYG2024111//Science and Technology Program of Suzhou/ ; WK2060000099//Fundamental Research Funds for the Central Universities/ ; //Fundamental and Interdisciplinary Disciplines Breakthrough Plan of the Ministry of Education/ ; JYB2025XDXM909//State Key Laboratory of Advanced Environmental Technology/ ; SKLAET2025-LH01//State Key Laboratory of Advanced Environmental Technology/ ; },
mesh = {*Sewage/microbiology ; Anaerobiosis ; *Drug Resistance, Microbial/genetics ; *Metformin/metabolism/pharmacology ; *Bacteria/genetics/metabolism/drug effects ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Biotransformation ; Wastewater/microbiology ; Water Pollutants, Chemical/metabolism ; },
abstract = {The roles of non-antibiotic pharmaceuticals in shaping the dissemination behaviours of antibiotic resistance genes (ARGs) in wastewater treatment systems remain poorly understood, and the influences of their transformation products have been overlooked. Here, we unveil more profound impacts of the metformin (MET) biotransformation product than the parent pollutant on the microbial community structure and ARG propagation of wastewater anaerobic sludge. The exposure to MET and its metabolic products guanylurea (GUA) at environmentally relevant concentrations both raised the methane production and resulted in up to 52.5% higher sludge ARGs abundance relative to the unexposed control. Especially, the GUA group showed up to 188-fold upregulation in several ARGs including bcrA, PmrF, acrB and mexF, enabled 3218-fold enrichment of plasmids from several bacteria. The underlying mechanisms were elucidated by integrated metagenomics, molecular dynamics simulations, and metabolic profiling analyses. MET and GUA were found to trigger coordinated cellular responses including disrupted glycerophospholipid metabolism, increased membrane permeability and broad metabolic reprogramming, which collectively boosted the ARGs dissemination. Overall, this work establishes a mechanistic link between micropollutant-induced microbial stress and ARGs propagation in anaerobic sludge, and advocates for re-evaluating the environmental risks of non-antibiotic pharmaceuticals and integrating resistance control into wastewater management framework.},
}

*Sewage/microbiology
Anaerobiosis
*Drug Resistance, Microbial/genetics
*Metformin/metabolism/pharmacology
*Bacteria/genetics/metabolism/drug effects
Anti-Bacterial Agents/pharmacology
*Drug Resistance, Bacterial/genetics
Biotransformation
Wastewater/microbiology
Water Pollutants, Chemical/metabolism

@article {pmid41361265,
year = {2025},
author = {Wang, C and Wang, C and Chen, S and Shi, K and Yu, J and Ding, Y and Yue, Y and Hua, Y and Wang, H and Chen, J},
title = {Global landscape of antibiotic resistance genes in the human gut microbiome metagenome-assembled genomes.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {33},
pmid = {41361265},
issn = {1471-2180},
support = {No.202524//the Scientific Research Program of the Bozhou University/ ; No. W2412100//International Cooperation and Exchanges NSFC-ASRT/ ; No. 42276137//National Natural Science Foundation of China/ ; No. 2022YFC2804205//National Key Research and Development Program of China/ ; No. 2022YFC2804104//National Key Research and Development Program of China/ ; },
abstract = {UNLABELLED: Antibiotic resistance poses a significant threat to human health, and the human gut microbiota serves as a major reservoir of antibiotic resistance genes (ARGs). In this study, we analyzed 149,515 metagenome-assembled genomes (MAGs) from human gut microbiomes and revealed marked geographic variations in the global distribution of gut-associated ARGs. Asia exhibits the highest diversity of ARGs. At the phylum level, Pseudomonadota was identified as the predominant ARG host among pathogenic bacteria, with its pathogenic strains frequently exhibiting high levels of multidrug resistant strains harboring ≥ 5 ARGs accounting for up to 88.5% and 79.1% in Africa and South America, respectively. Campylobacterota was also recognized as a potential high-risk ARG host phylum. Horizontal gene transfer (HGT) analysis revealed that ARG transmission predominantly occurred within the same phylum, with Bacillota being the most active donor, which was likely influenced by antibiotic selection pressure. Actinomycetota and Bacteroidota were identified as major recipients of interphylum HGT, indicating their greater capacity to acquire exogenous ARGs. Through the integration of deep learning and structural calculation, we also identified a potentially novel class of β-lactam resistance genes. This study provides a comprehensive global landscape of gut-associated resistomes, underscores the critical roles of public health infrastructure, antibiotic misuse, and HGT in shaping antimicrobial resistance (AMR), and offers methodological insights for the discovery of novel ARGs. Our findings highlight urgent challenges and provide a scientific basis for developing global AMR mitigation strategies.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-025-04586-0.},
}

@article {pmid41558472,
year = {2026},
author = {Baril, T},
title = {Evolution: Transposon traffic in the mycocosmos.},
journal = {Current biology : CB},
volume = {36},
number = {2},
pages = {R57-R59},
doi = {10.1016/j.cub.2025.11.062},
pmid = {41558472},
issn = {1879-0445},
mesh = {*DNA Transposable Elements/genetics ; *Fungi/genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Biological Evolution ; Genome, Fungal ; },
abstract = {Eukaryotes usually inherit genetic material from their parents, but occasional cross-species transfers can occur. A new study finds that these exchanges are surprisingly common in fungi, revealing an overlooked route for mobile elements to persist and impact host genomes.},
}

*DNA Transposable Elements/genetics
*Fungi/genetics
*Evolution, Molecular
*Gene Transfer, Horizontal
*Biological Evolution
Genome, Fungal

@article {pmid41556155,
year = {2026},
author = {Serwy, DM and Conde, MER and Alencar, ALC and Novaes, RLM and Lima-Junior, JDC and da Mota, FF and Carvalho-Assef, AP and Galvao, TC and Zahner, V},
title = {Genetic Diversity of Polymyxin Resistance Genes in Klebsiella pneumoniae Clinical Isolates.},
journal = {Molecular ecology},
volume = {35},
number = {2},
pages = {e70234},
doi = {10.1111/mec.70234},
pmid = {41556155},
issn = {1365-294X},
support = {421136/2023-5//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; E-26/210.228/2018//Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro/ ; 11E-26/210.982/2021//Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro/ ; //CAPES/ ; //Fundação Oswaldo Cruz, Fiocruz/ ; },
mesh = {*Klebsiella pneumoniae/genetics/drug effects ; *Genetic Variation ; *Polymyxins/pharmacology ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics ; Selection, Genetic ; Haplotypes ; },
abstract = {This study investigates the genetic diversity and evolutionary mechanisms driving polymyxin resistance in Klebsiella pneumoniae, a critical priority pathogen. By analysing mgrB, phoPQ and pmrAB genes in susceptible (PM-S) and resistant (PM-R) populations through neutrality tests (Tajima D, Fu & Li's D) we uncovered polygenic adaptation and positive selection as a key driver of resistance. High genetic diversity was observed across all loci, with mgrB insertions dominating PM-R populations. Negative Tajima and Fu & Li's D values and excess rare alleles revealed recent population expansions linked to the reintroduction of polymyxins in the 2010s. Positive selection via selective sweeps was detected in PM-R isolates, exemplified by the rapid spread of haplotype 27, which presents mgrB insertions, the major determinant of LPS modification pathway hyperactivation. The expansion of this haplotype suggests that horizontal gene transfer accelerates resistance dissemination. The elevated genetic diversity observed in the phoPQ and pmrAB systems among isolates harbouring mgrB alterations may reflect reduced adaptive fitness costs, enabling the preservation of genomic variability despite sustained selective pressures. Our results demonstrate that polymyxin resistance arises through polygenic adaptation and positive selection, combining de novo mutations, recombination and selection-driven sweeps. These dynamics threaten to exacerbate resistance in hospital environments, emphasising the need for genomic surveillance and alternative therapies. This study bridges molecular evolution and clinical epidemiology, offering insights into the resilience of K. pneumoniae and the ecological drivers of antimicrobial resistance.},
}

*Klebsiella pneumoniae/genetics/drug effects
*Genetic Variation
*Polymyxins/pharmacology
*Drug Resistance, Bacterial/genetics
Anti-Bacterial Agents/pharmacology
Bacterial Proteins/genetics
Selection, Genetic
Haplotypes

@article {pmid41352351,
year = {2026},
author = {Romeijn, J and Bañales, I and Seidl, MF},
title = {Extensive horizontal transfer of transposable elements shapes fungal mobilomes.},
journal = {Current biology : CB},
volume = {36},
number = {2},
pages = {355-369.e4},
doi = {10.1016/j.cub.2025.11.012},
pmid = {41352351},
issn = {1879-0445},
mesh = {*DNA Transposable Elements/genetics ; *Gene Transfer, Horizontal ; *Genome, Fungal ; *Fungi/genetics ; Genome Size ; Evolution, Molecular ; Phylogeny ; },
abstract = {Transposons impact eukaryotic genome size and evolution. Horizontal transfer of transposable elements (HTT) is important for their long-term persistence, but it has only been systematically studied in animals, and thus the abundance, impact, and factors that shape HTTs in lineages outside animals are unknown. Fungi are at least as ancient and diverse as animals and are characterized by extensive genome size variation caused by transposons. Here, we screened 1,348 genomes across fungal biodiversity, genome sizes, and lifestyles to detect extensive HTTs, which generated on average 7%-but up to 70%-of the transposon content in some taxa. We in total identified at least 5,906 independent HTTs, mostly involving Tc1/Mariner DNA transposons. While the majority of HTTs occur between closely related taxa, irrespective of their lifestyles, HTTs were particularly common in Mucoromycotina, Sordariomycetes, Dothideomycetes, and Leotiomycetes. Importantly, species lacking fungal-specific defense mechanisms against transposons, and those with gene-sparse and repeat-rich genomic compartments, are involved in a significantly higher number of HTTs, unveiling ecological and genomic factors shaping HTTs. Our findings thus illuminate the dynamic landscape of HTTs in fungi, providing the framework to further study the impact of HTTs on genome evolution and the processes that mediate transposon transfers within and between eukaryotic lineages.},
}

*DNA Transposable Elements/genetics
*Gene Transfer, Horizontal
*Genome, Fungal
*Fungi/genetics
Genome Size
Evolution, Molecular
Phylogeny

@article {pmid41553756,
year = {2026},
author = {van Hal, SJ and Jenkins, F and Hogan, TR and Ray, S and Kundu, RL and Marshall, HS and Bowden, R and Lahra, MM},
title = {Gene exchange between Neisseria meningitidis and Neisseria gonorrhoeae.},
journal = {Microbial genomics},
volume = {12},
number = {1},
pages = {},
doi = {10.1099/mgen.0.001623},
pmid = {41553756},
issn = {2057-5858},
mesh = {*Neisseria gonorrhoeae/genetics/isolation & purification/classification ; *Neisseria meningitidis/genetics/isolation & purification/classification ; Humans ; Phylogeny ; Whole Genome Sequencing ; Gonorrhea/microbiology ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Pharynx/microbiology ; },
abstract = {Genetic exchange between Neisseria meningitidis (NM) and Neisseria gonorrhoeae (NG) has not been well studied. This study aimed to investigate evidence of genetic exchanges between these two species. All coincident paired NM and NG isolates cultured from pharyngeal swabs collected from a sexual health clinic in Sydney in 2021 underwent whole-genome sequencing. A gene-by-gene analysis of the 47 NM-NG pairs identified 184 instances where the ancestry of the gene revealed intermixing between the two species. Incorporating the gene phylogenies demonstrated that these events occurred across a wide range of timeframes. At the nucleotide level, 91 genes were found where paired isolates harboured identical sequences. Notably, one instance of unequivocal recent gene transfer events between the paired pharynx isolates was observed. This work provides new insights into the evolutionary dynamics of these bacteria and highlights the importance of genetic exchange in populations with high rates of pharyngeal gonorrhoea. The clinical implications of such exchanges call for continued vigilance and research to address the challenges posed by these bacteria.},
}

*Neisseria gonorrhoeae/genetics/isolation & purification/classification
*Neisseria meningitidis/genetics/isolation & purification/classification
Humans
Phylogeny
Whole Genome Sequencing
Gonorrhea/microbiology
*Gene Transfer, Horizontal
Genome, Bacterial
Pharynx/microbiology

@article {pmid41414916,
year = {2026},
author = {Asim, M and Rizvi, SA and Haq, QMR},
title = {Antiplasmid systems: a novel strategy to combat antibiotic resistance.},
journal = {The Journal of antimicrobial chemotherapy},
volume = {81},
number = {1},
pages = {},
doi = {10.1093/jac/dkaf472},
pmid = {41414916},
issn = {1460-2091},
mesh = {*Plasmids/metabolism ; *Bacteria/drug effects/genetics ; *Drug Resistance, Bacterial ; Anti-Bacterial Agents/pharmacology ; Gene Transfer, Horizontal ; },
abstract = {Antibiotic resistance is a serious health threat of this century, responsible for millions of deaths annually due to the diminishing effect of currently used antibiotics. Bacteria become resistant through mutations or by the acquisition of genes conferring resistance. Determinants of resistance are often plasmids, which are small extrachromosomal DNA elements instrumental in disseminating antibiotic resistance genes (ARGs) through horizontal transfer (HGT). While plasmids may confer beneficial traits to bacteria, they also sometimes impose a fitness cost. To counter this, bacteria have evolved several defence mechanisms, such as prokaryotic Argonautes (pAgos), DNA defence module (DdmDE), ApsAB, Wadjet and Lamassu, which exhibit antiplasmid activity. The system restricts or degrades plasmid and phage DNA by various mechanisms, including abortive infection, replication interference or direct plasmid degradation. These antiplasmid systems offer the potential to specifically recognize and degrade the plasmid, rendering bacteria susceptible to antibiotics. This review highlights the in-depth understanding of these systems, including their structural diversity, from Argonaute-like proteins to SMC-based complexes, molecular mechanisms, origins and potential applications in combating plasmid-mediated antibiotic resistance. Furthermore, we have hypothesized two different ways of using the antiplasmid system to combat plasmid-borne drug resistance among bacterial pathogens.},
}

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

@article {pmid41547427,
year = {2026},
author = {Greff, B and Posgay, M and Lakatos, E and Varga, L},
title = {Colistin residues and colistin-resistant Enterobacteriaceae in agricultural soils: Sources, risks, and remediation strategies.},
journal = {Environmental research},
volume = {},
number = {},
pages = {123771},
doi = {10.1016/j.envres.2026.123771},
pmid = {41547427},
issn = {1096-0953},
abstract = {Polymyxins, including colistin, are critical last-line antibiotics, and their environmental dissemination raises One Health concerns. This review synthesizes current evidence on the occurrence, sources, environmental fate, and mitigation of colistin residues and colistin-resistant Enterobacteriaceae in agricultural soils, with emphasis on transmission pathways to crops and implications for food safety along the farm-to-fork continuum. Principal inputs from livestock manure, reclaimed wastewater, and wildlife are characterized. Resistance mechanisms, with a focus on plasmid-mediated mobile colistin resistance (mcr), are summarized. Although animal manure may be a significant source of colistin due to its low gastrointestinal absorption, soil concentrations are low, with bioavailability influenced by physicochemical parameters, including pH, clay content, cation exchange capacity, and organic matter content. Low desorption rates limit plant uptake; thus, the primary environmental risk arises from the selection and enrichment of colistin-resistant bacteria and mcr genes in the rhizosphere, as well as splash-mediated deposition of contaminated particles. In farm and arable soils, mcr-1 and mcr-3 have been identified as the dominant variants, with higher prevalence in livestock-associated environments. Their dissemination is primarily driven by horizontal gene transfer rather than clonal expansion, influenced by factors such as soil characteristics, heavy metals, soil treatments, and plant root exudates. Interventions are critically appraised, spanning veterinary stewardship and on-farm hygiene, physical processes, chemical approaches, and biological strategies, along with postharvest barriers that include Good Agricultural Practices and Hazard Analysis and Critical Control Points, washing and sanitization, and bacteriophage biocontrol. Major conclusions are that multi-barrier, context-specific programs can reduce environmental selective pressures and interrupt gene flow while maintaining agronomic viability, yet progress remains constrained by gaps in standardized surveillance (particularly for plant-based foods), and by the limited use of quantitative risk assessment and field-scale validation of remediation technologies. A One Health framework that integrates environmental monitoring with public-health endpoints is needed to guide proportionate policy and practice.},
}

@article {pmid41547328,
year = {2026},
author = {Kumar, RG and Dharumadurai, D},
title = {Unveiling the genetic blueprint of geosmin synthesis, secondary metabolite pathways, and functional genome analysis of Streptomyces rubrogriseus RKDTS3 from tilapia fish pond sediment.},
journal = {Computational biology and chemistry},
volume = {122},
number = {},
pages = {108900},
doi = {10.1016/j.compbiolchem.2026.108900},
pmid = {41547328},
issn = {1476-928X},
abstract = {Off-flavours such as geosmin and 2-methylisoborneol (MIB) are economically and sensorially problematic compounds in freshwater aquaculture. Although "geosmin" is produced by certain Streptomyces species living in lake sediments, we know very little about the genetic basis of this production or the biosynthetic precursors. Hence, we sequenced the draft genome of a Streptomyces rubrogriseus (RKDTS3), originally isolated from sediments in a tilapia pond near Tamil Nadu, India, to identify genes involved in producing geosmin and other secondary metabolites. The Illumina MiSeq-generated draft genome for RKDTS3 contains 5.32 Mb of sequence information, has a GC content of 71 %, and contains 6129 protein-coding genes, 61 tRNA genes, and one rRNA operon. The annotation of this genome indicated a significant number of metabolic genes required for productive biosynthetic pathways (as well as stress environment adaptation). There are 21 BGCs for producing various terpenoids, polyketides, nonribosomal peptide ligands (NRPBs); ribosomal peptide ligands (RiPPs); and siderophore compounds. The search for the biosynthetic cluster that produces geosmin and encodes the gene geoA identified a BGC that contained the KO K10187, determined using KofamKOALA, and provided strong evidence that the geosmin biosynthetic pathway is conserved and functional. A comparison of Streptomyces strains reveals 1994 core BGCs, along with a highly variable accessory genome that has adapted to various ecological environments. This strain has also acquired multiple copies of the CRISPR genome, three plasmids, and an incomplete prophage, indicating that it has undergone horizontal gene transfer, developed defence mechanisms to protect against phage, and has a dynamic genome. Overall, genome analysis revealed a GC-rich draft genome encoding 21 biosynthetic gene clusters, including a conserved geoA-containing terpene cluster responsible for geosmin biosynthesis, conserved core genome alongside a highly variable accessory genome, reflecting ecological adaptation in comparative genomics. Thus, the findings state the genomic origin of geosmin and secondary metabolite biosynthesis in S. rubrogriseus RKDTS3.},
}

@article {pmid41543305,
year = {2026},
author = {Liu, C and Hellemans, S and Kinjo, Y and Mikhailova, AA and Aumont, C and Weng, YM and Buček, A and Husnik, F and Šobotník, J and Harrison, MC and McMahon, DP and Bourguignon, T},
title = {Recurrent horizontal gene transfers across diverse termite genomes.},
journal = {Evolution; international journal of organic evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/evolut/qpag003},
pmid = {41543305},
issn = {1558-5646},
abstract = {Horizontal gene transfer (HGT), the transmission of genetic material across species, is an important innovation source in prokaryotes. In contrast, its significance is unclear in many eukaryotes, including insects. Here, we used high-quality genomes of 45 termites and two cockroaches to investigate HGTs from non-metazoan organisms across blattodean genomes. We identified 289 genes and 2,494 pseudogenes classified into 168 orthologous groups originating from an estimated 281 HGT events. Wolbachia represented the primary HGT source, while termite gut bacteria and the cockroach endosymbiont Blattabacterium did not contribute meaningfully to HGTs. Most horizontally acquired genes descended from recent and species-specific HGTs, experienced frequent duplications and pseudogenizations, and accumulated substitutions faster than synonymous sites of native protein-coding genes. Genes frequently transferred horizontally to termite genomes included mobile genetic elements and genetic information processing genes. Our results indicate that termites continuously acquired genes through HGT, and that most horizontally acquired genes are specific to restricted lineages. Overall, genes acquired by HGT by termites and cockroaches seemed generally non-functional and bound to be lost.},
}

@article {pmid41543069,
year = {2026},
author = {Finnegan, M and Rose, CJ and Hamet, J and Prat, B and Bedhomme, S},
title = {Hurdles to horizontal gene transfer: species-specific effects of synonymous variation and plasmid copy number determine antibiotic resistance phenotype.},
journal = {Microbiology (Reading, England)},
volume = {172},
number = {1},
pages = {},
doi = {10.1099/mic.0.001652},
pmid = {41543069},
issn = {1465-2080},
mesh = {*Gene Transfer, Horizontal ; *Plasmids/genetics ; *Escherichia coli/genetics/drug effects ; *Pseudomonas aeruginosa/genetics/drug effects ; *Acinetobacter/genetics/drug effects ; Anti-Bacterial Agents/pharmacology ; Phenotype ; *Drug Resistance, Bacterial/genetics ; Gene Dosage ; Gentamicins/pharmacology ; Species Specificity ; Codon Usage ; },
abstract = {Could codon composition condition the immediate success and the orientation of horizontal gene transfer? Horizontal gene transfer represents a change in the genome of expression of the transferred gene, and experimental evidence has accumulated indicating that the codon composition of a sequence is an important determinant of its compatibility with the translation machinery of the genome in which it is expressed. This suggests that codon composition influences the phenotype and the fitness conferred by a transferred gene and thus the immediate success of the transfer. To directly test this hypothesis, we characterized the resistance conferred by synonymous variants of a gentamicin resistance gene in three bacterial species: Escherichia coli, Acinetobacter baylyi and Pseudomonas aeruginosa. The strongest determinant of the resistance level conferred was the species in which the resistance gene was transferred, very likely because of important differences in the copy number of the plasmid carrying the gene. Significant differences in resistance were also found between synonymous variants within each of the three species, but more importantly, there was a strong interaction between species and variant: variants conferring high resistance in one species confer low resistance in another. However, the similarity in codon usage between the synonymous variants and the host genome only explained part of the phenotypic differences between variants in one species, P. aeruginosa. Further investigation of alternative explanations did not reveal common universal mechanisms across our three bacterial species. We conclude that codon composition can be a determinant of post-horizontal gene transfer success. However, there are multiple paths leading from synonymous sequence to phenotype, and sensitivity to these different paths is species-specific.},
}

*Gene Transfer, Horizontal
*Plasmids/genetics
*Escherichia coli/genetics/drug effects
*Pseudomonas aeruginosa/genetics/drug effects
*Acinetobacter/genetics/drug effects
Anti-Bacterial Agents/pharmacology
Phenotype
*Drug Resistance, Bacterial/genetics
Gene Dosage
Gentamicins/pharmacology
Species Specificity
Codon Usage

@article {pmid41382045,
year = {2025},
author = {Alalade, OM and Ameh, JB and Abdullahi, IO and Whong, CMZ and Atta, HI},
title = {Antibiotic resistance profiles and genetic characterization of Salmonella enterica from water supplies in Kaduna State, Northwest Nigeria.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {23},
pmid = {41382045},
issn = {1471-2180},
abstract = {BACKGROUND: Communities across Kaduna State, Nigeria, depend on diverse water sources, and the presence of Salmonella enterica is particularly concerning when the bacteria are resistant to antibiotics and possess resistance genes. The One Health approach recognizes that water quality, antimicrobial resistance patterns, and human health are closely linked, yet significant knowledge gaps exist regarding both the resistance patterns and the underlying genetic mechanisms of Salmonella in local drinking water sources of Kaduna state. This study aimed to determine the phenotypic antibiotic susceptibility patterns and detect some resistance genes in Salmonella enterica isolated from various drinking water sources in Kaduna State.

METHODOLOGY: Five hundred sources of water used for drinking in six selected Local Government Areas of Kaduna state were sampled from 2014 to 2015. The samples were processed using standard bacteriological methods to isolate and identify Salmonella species, followed by molecular confirmation through 16 S rRNA gene sequencing. The consensus sequences of the isolates were subjected to BLAST in the GenBank of the National Center for Biotechnology Information (NCBI). The isolates were subjected to antibiotic susceptibility tests and investigation of some resistance genes were assessed.

RESULTS: Six isolates (1.2% isolation rate) were obtained from various sources and were identified as Salmonella enterica. The sequences were submitted to the NCBI GenBank and have been assigned accession numbers. Four (66.7%) of the isolates were resistant to tetracycline, nalidixic acid and sulfamethoxazole-trimethoprim, while 2 (33.3%) were pan-susceptible. One isolate was resistant to three (3) different classes of antibiotics. Antibiotic resistance genes –tetA and sul1 were both detected in two isolates, obtained from treated pipe borne and well water respectively. The genes detected correlate with the phenotypic resistance observed.

CONCLUSION: Antibiotic-resistant Salmonella enterica in drinking water poses a critical One Health threat, linking human, animal, and environmental health risks. The correlation between resistance genes and phenotypic patterns indicates antibiotic misuse in the study area at the time, creating reservoirs for multidrug-resistant pathogens and horizontal gene transfer. Urgent implementation of multi-sectoral One Health surveillance, strict antibiotic regulation, improved water treatment, antimicrobial stewardship programs, and rapid response protocols is essential across Kaduna state and Nigeria.},
}

@article {pmid41535901,
year = {2026},
author = {Muhee, A and Pandit, A and Jan, S and Khan, IS and Hassan, N and Bhat, RA and Yatoo, MI},
title = {Whole genome sequencing reveals environmental pathogen misidentification and potential for cross-phylum antimicrobial resistance gene transfer in bovine mastitis: a pilot genomic study.},
journal = {BMC veterinary research},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12917-025-05280-z},
pmid = {41535901},
issn = {1746-6148},
}

@article {pmid41534774,
year = {2026},
author = {Huang, Y and Sun, Y and Jiang, C and Zeng, X and Wu, Y and Yan, Z and Wang, J and Zhou, H and Chen, G and Wu, Y and Dong, N},
title = {Characterization of tmexCD2-toprJ2-carrying carbapenem-resistant Raoultella ornithinolytica from hospital sewage in Zhejiang Province of China, 2022-2023.},
journal = {Journal of global antimicrobial resistance},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jgar.2026.01.002},
pmid = {41534774},
issn = {2213-7173},
abstract = {OBJECTIVE: Hospital wastewater serves as a critical source of antimicrobial resistance genes (ARGs), particularly those associated with opportunistic pathogens like Raoultella ornithinolytica. This study aimed to characterize carbapenem-resistant R. ornithinolytica (CR-ROR) isolates carrying the tmexCD2-toprJ2 gene cluster from hospital sewage in Zhejiang province, China.

METHODS: Wastewater samples collected from four hospitals in Zhejiang Province were screened for carbapenem-resistant isolates. Whole-genome sequencing using the Illumina platform, combined with bioinformatic analysis, was performed to investigate phylogenetic relationships, associated ARGs, and the structural features of plasmids in tmexCD2-toprJ2-positive CR-ROR isolates.

RESULTS: Five genetically distantly related tmexCD2-toprJ2-positive CR-ROR isolates were identified. All exhibited multidrug-resistant (MDR) phenotypes and carried various ARGs, including carbapenemase genes such as blaKPC-2, blaNDM-1, and blaIMP-4. Genomic analysis revealed that tmexCD2-toprJ2 was plasmid-borne and frequently flanked by mobile genetic elements (MGEs), suggesting a high risk of horizontal gene transfer.

CONCLUSIONS: The presence of tmexCD2-toprJ2-carrying CR-ROR in hospital sewage underscores the role of wastewater as a potential environmental reservoir for clinically resistant genes. Ongoing surveillance of hospital effluents is crucial for tracking the dissemination of high-risk antimicrobial resistance determinants and informing timely public health interventions.},
}

@article {pmid41534337,
year = {2026},
author = {Huang, X and Ni, Y and Ma, Z and Xie, Z and Ding, Z and Xu, H and Wei, H and Jin, Q and Zhou, R},
title = {Polymer type and aging drive the selective enrichment of antibiotic resistance genes and pathogens in microplastics biofilms.},
journal = {Water research},
volume = {292},
number = {},
pages = {125364},
doi = {10.1016/j.watres.2026.125364},
pmid = {41534337},
issn = {1879-2448},
abstract = {Microplastics (MPs) biofilms are critical vectors for antibiotic resistance in aquatic environments. In this study, in situ incubation coupled with metagenomic sequencing was employed to investigate microbial colonization patterns, antibiotic resistance gene (ARG) profiles, and mobile genetic element (MGE) dissemination characteristics of biofilms on MPs surfaces of different polymer types and aging states within a unique wetland ecosystem. Results demonstrated that microorganisms preferentially colonized the hydrophobic surface of conventional polypropylene (PP) over biodegradable polylactic acid (PLA). Aging treatments further enhanced MP-microbe interactions. Microbial community analysis revealed selective enrichment of microbial communities in MPs biofilms, including clinically relevant pathogens such as Acinetobacter baumannii. Notably, despite showing lower microbial colonization, PLA enriched a higher abundance of priority antibiotic-resistant pathogens and high-risk ARGs, which further amplified following environmental aging. Co-occurrence network analysis identified seven key MGEs strongly correlated with multiple ARGs and exhibited the highest abundance on PLA-derived biofilms, indicating a high potential for horizontal gene transfer mediating the propagation of antibiotic resistance. Furthermore, Enterobacteriaceae were identified as critical co-hosts of ARGs and MGEs within the plastisphere, potentially playing a central role in maintaining antibiotic resistance. Our findings highlight a significant ecological threat from biodegradable and aged MPs in amplifying antibiotic resistance.},
}

@article {pmid41533650,
year = {2026},
author = {Vincent, AG and Quispe, IAF and Majdi, M and Dice, LT and Harbison, SA and Lenaghan, SC and DeBruyn, JM and Occhialini, A},
title = {Risk assessment of plant-to-bacterium transgene flow associated with novel small synthetic genome (mini-synplastome) platforms for plastid genetic engineering.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiag002},
pmid = {41533650},
issn = {1574-6941},
abstract = {Novel cutting-edge technologies for plastid genetic engineering have a great potential in agriculture. Genetic engineering of the plastid genome (plastome) can be performed using both conventional homologous recombination (HR) vectors, and novel episomal platforms that rely on synthetic plastomes (mini-synplastomes) to express transgenes from a non-integrating plasmid. Evaluating the potential risk of horizontal gene transfer (HGT) is an important step for regulatory approval of environmental release of these novel genetic engineering tools. In particular, the endosymbiotic origin of plastids from a prokaryotic progenitor may increase the probability of HGT to the environmental microbial community. In this study, the naturally competent soil bacterium Acinetobacter baylyi has been used to test the probability of plant-to-bacterium HGT under laboratory conditions. While plant-to-bacterium HGT can be detected in vitro as a low probability event, the mini-synplastome does not show an increased HGT compared to conventional transformation platforms. After a comprehensive evaluation of mini-synplastome elements affecting plasmid persistence in bacteria (plastid origin of replications, plastomic regions containing rRNA genes, and regulatory elements for transgene expression), optimized mini-synplastome (Gen3) platforms with no residual activity in bacteria and with undetectable HGT were characterized. This study represents a valuable resource for designing mini-synplastome transformation platforms with improved environmental biosafety in agriculture.},
}

@article {pmid41532756,
year = {2026},
author = {Begmatov, S and Rakitin, AL and Beletsky, AV and Mardanov, AV and Ravin, NV},
title = {Plasmids of the multidrug-resistant Citrobacter portucalensis KOS1-1 strain isolated from a wastewater treatment plant harbor antibiotic resistance genes and gene clusters involved in carbon metabolism.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0203825},
doi = {10.1128/spectrum.02038-25},
pmid = {41532756},
issn = {2165-0497},
abstract = {The growing interest in multidrug-resistant (MDR) Citrobacter species stems from their epidemiological significance and their potential to harbor antibiotic resistance genes (ARGs), with mobile genetic elements playing a central role in their dissemination. Wastewater treatment plants play an important role in the formation of such MDR strains due to the high rate of horizontal gene transfer in these environments. In this study, we isolated the MDR strain KOS1-1 of Citrobacter portucalensis from wastewater, sequenced its genome, and characterized its ARG content and plasmid profile. This strain was resistant to ampicillin, cefazolin, cefaclor, cefatrizine, ciprofloxacin, kanamycin, streptomycin, spectinomycin, erythromycin, chloramphenicol, tetracycline, sulfamethoxazole, and trimethoprim. The KOS1-1 strain harbored five low copy number plasmids ranging in size from 77,569 to 289,033 bp. Genome analysis revealed the presence of multiple ARGs both on the chromosome and on plasmids, conferring resistance to β-lactams, quinolones, aminoglycosides, macrolides, sulfonamides, trimethoprim, phenicols, and tetracyclines. Many of these genes were associated with pseudo-composite transposon-like structures, emphasizing the role of mobile elements in ARGs dissemination. Plasmids harbored a bacterial cellulose biosynthesis operon and genes involved in mannose/fucose metabolism that could facilitate biofilm formation and a glycerol dissimilation gene cluster. Bacterial cellulose production was confirmed using electron and atomic force microscopy. Homologus gene clusters were identified on various plasmids of Enterobacteriales, suggesting their distribution via horizontal gene transfer. The presence of plasmids carrying ARGs and adaptive accessory genes increases the competitive fitness of C. portucalensis KOS1-1.IMPORTANCEAntimicrobial resistance represents a silent epidemic that has emerged as a critical global concern in recent years, underscoring the need for further research in this field. This study aimed to isolate and characterize multidrug-resistant bacteria from municipal wastewater, a huge reservoir of antibiotic resistance genes and resistant strains, from which they became disseminated into the environment. The isolated Citrobacter portucalensis strain KOS1-1 exhibits resistance to multiple antibiotics, arsenate, and mercury. It harbors five megaplasmids containing most of the resistance genes, along with laterally acquired bacterial cellulose biosynthesis operon and genes associated with mannose/fucose metabolism, which may facilitate biofilm formation. These plasmids may not only confer a selective advantage to host strains but also promote transfer of resistance determinants in high-density microbial communities of activated sludge at wastewater treatment plants. This work contributes to the understanding of the mechanisms of dissemination of bacterial resistance and virulence factors in municipal wastewater environments.},
}

@article {pmid41532636,
year = {2026},
author = {Jangra, M and Travin, DY and Kaur, M and Hackenberger, D and Koteva, K and Polikanov, YS and Wright, GD},
title = {An Acetyltransferase Conferring Self-Resistance of the Producer to Lasso Peptide Antibiotic Lariocidin.},
journal = {ACS infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsinfecdis.5c00885},
pmid = {41532636},
issn = {2373-8227},
abstract = {The soil microbiome, a reservoir of antibiotic-producing bacteria, also harbors resistance determinants encoded within antibiotic biosynthetic gene clusters (BGCs). Studying self-resistance mechanisms, which have evolved in producers to protect against their own toxic metabolites, provides critical insights into the evolution of resistance and the potential vulnerabilities of new antibiotics and can facilitate the production of natural products in heterologous hosts. Here, we describe the self-resistance mechanism to lariocidin (LAR), a recently discovered lasso peptide antibiotic that inhibits the ribosomal machinery and exhibits antibacterial activity against key pathogens. We identified and characterized an N-acetyltransferase enzyme (LrcE) encoded within the LAR BGC that mediates self-resistance in LAR-producing Paenibacillus sp. M2. LrcE is a member of the GCN5-related N-acetyltransferase (GNAT) superfamily and performs site-specific acetylation of LAR at a critical lysine residue. This modification disrupts ribosomal binding, thereby reducing LAR's antibacterial activity. Using in silico modeling, we predicted a conserved acetyl-CoA-binding motif and an LAR-binding region on LrcE. Bioinformatic analysis revealed LrcE homologues in environmental but not clinically relevant pathogens, suggesting a limited risk of horizontal gene transfer and, therefore, supporting the further development of LAR as a next-generation antibiotic.},
}

@article {pmid41531091,
year = {2026},
author = {Wu, XX and Li, YQ and Huang, CH and Zhu, L},
title = {[Influencing Factors and Mechanisms of Antibiotic Resistance Gene Enrichment by Microplastics in the Environment].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {47},
number = {1},
pages = {629-639},
doi = {10.13227/j.hjkx.202412243},
pmid = {41531091},
issn = {0250-3301},
mesh = {*Microplastics/analysis ; *Drug Resistance, Microbial/genetics ; *Environmental Pollutants/analysis ; Environmental Monitoring ; *Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; Bacteria/genetics/drug effects ; Genes, Bacterial ; },
abstract = {In recent decades， the misuse of antibiotics has contributed to a significant rise in antibiotic resistance among bacteria. Antibiotic resistance genes （ARGs）， carried by antibiotic-resistant bacteria and considered to be emerging pollutants， are primarily responsible for this phenomenon. ARGs have been extensively detected in various environmental media， including the atmosphere， soil， water， and sediments. Microplastics （MPs）， defined as plastic fragments with diameters less than 5 mm， pose a considerable threat due to their ease of ingestion by organisms， leading to adverse effects on ecosystems and human health. Moreover， microplastics exhibit a high affinity for organic pollutants， facilitating their migration through adsorption and desorption processes. The surfaces of microplastics can harbor bacterial pathogens and ARGs， thereby influencing the occurrence and dissemination of ARGs in the environment. Although numerous publications have reported the role of microplastics in the transmission of ARGs across diverse environments， there remains a gap in understanding the specific effects of microplastics on the accumulation and horizontal gene transfer of ARGs， including MPs types and surface characteristics， along with the underlying mechanisms. This review provides an overview of the ARGs enrichment by microplastics in various environment media and highlights how the type and surface characteristics of microplastics impact the concentration and subsequent spread of ARGs， while also clarifying the underlying mechanisms through which microplastics facilitate the horizontal transfer of ARGs. The review also outlines prospective research directions concerning microplastics and ARGs， offering valuable insights for the management and control of emerging pollutants.},
}

*Microplastics/analysis
*Drug Resistance, Microbial/genetics
*Environmental Pollutants/analysis
Environmental Monitoring
*Drug Resistance, Bacterial/genetics
Gene Transfer, Horizontal
Bacteria/genetics/drug effects
Genes, Bacterial

@article {pmid41522440,
year = {2025},
author = {Nusrat, S and Aliyu, M and Zohora, FT},
title = {Mechanisms of antimicrobial resistance: From genetic evolution to clinical manifestations.},
journal = {AIMS microbiology},
volume = {11},
number = {4},
pages = {1007-1034},
pmid = {41522440},
issn = {2471-1888},
abstract = {Antimicrobial resistance (AMR) is a significant global health challenge that threatens the effectiveness of antibiotics and other antimicrobial agents. Here, we examined the molecular mechanisms that contribute to bacterial resistance, including alterations at target sites, enzymatic inactivation, efflux pump overexpression, and biofilm formation. Key resistance determinants, such as bla CTX-M-15, bla NDM-1, mecA, and erm genes, mediate enzymatic degradation and target modification, thereby diminishing antibiotic potency. Clinically significant pathogens, including Escherichia coli, Pseudomonas aeruginosa, Klebsiella pneumoniae, Staphylococcus aureus, and Enterococcus faecium, exemplify a broad spectrum of resistance and frequently acquire these traits through horizontal gene transfer (HGT), facilitated by plasmids, integrons, and transposons. The propensity for biofilm formation further augments bacterial persistence by impeding antimicrobial penetration and fostering intra-community genetic exchanges. The clinical ramifications of AMR are profound, contributing to elevated morbidity and mortality, extended hospitalization, and increased rates of therapeutic failure, all of which exert significant strain on the healthcare system. The economic consequences are equally severe, with escalating healthcare expenditures and substantial projected losses to the global gross domestic product (GDP). Addressing these challenges necessitates the adoption of advanced approaches, including genomic surveillance, antimicrobial stewardship, novel inhibitors targeting resistance pathways, immuno-antibiotics, and bacteriophage therapy. This review underscores the need to integrate molecular diagnostics and a One Health perspective to monitor and contain resistance across human, animal, and environmental reservoirs. A comprehensive understanding of the molecular and epidemiological aspects of AMR is essential for driving advancements in diagnostics, therapeutics, and policies, thereby ensuring global health protection.},
}

@article {pmid41521939,
year = {2026},
author = {Chen, G and Du, H and Cao, Z and Wu, Y and Zhang, C and Zhou, Y and Ao, J and Sun, Y and Yuan, Z},
title = {QuickProt: A Fast and Accurate Homology-Based Protein Annotation Tool for Non-Model Organisms to Advance Comparative Genomics.},
journal = {Molecular ecology resources},
volume = {26},
number = {2},
pages = {e70097},
doi = {10.1111/1755-0998.70097},
pmid = {41521939},
issn = {1755-0998},
support = {U22A20534//National Natural Science Foundation of China/ ; KJRC2023C38//Innovational Fund for Scientific and Technological Personnel of Hainan Province/ ; },
mesh = {Animals ; *Genomics/methods ; *Molecular Sequence Annotation/methods ; *Computational Biology/methods ; Phylogeny ; Xenopus/genetics ; Perciformes/genetics ; },
abstract = {The rapid growth of genome sequencing has outpaced the development of efficient annotation tools, especially for species lacking transcriptome data. To address this challenge, we present QuickProt, a fast, accurate and user-friendly homology-based protein annotation tool. QuickProt constructs a non-redundant gene model by aligning homologous proteins from closely related species, offering an accurate and cost-effective solution suitable for large-scale comparative genomic studies. Benchmarking against BRAKER2 and GALBA across reference genomes demonstrated that QuickProt offers high specificity and dramatically improved runtime, while maintaining competitive annotation accuracy. To demonstrate its utility, we applied QuickProt to diverse genomes, including a non-model teleost (Epinephelus bruneus), two tetraploid Xenopus species and 11 Rutaceae plants. Across these datasets, QuickProt supported robust phylogenetic reconstruction, identification of conserved orthologs and detection of biologically functional genes, pathways, and chromosomal evolution mechanisms, regardless of genome ploidy. Notably, it revealed a potential horizontal gene transfer event between groupers and Vibrio, and uncovered conserved modules involved in volatile oil biosynthesis and oil gland development in citrus. With its scalability and minimal computational demands, QuickProt provides a powerful platform for genome annotation and evolutionary inference. As the number of sequenced genomes continues to expand, QuickProt is a useful tool for accelerating comparative genomics and functional exploration across the tree of life.},
}

Animals
*Genomics/methods
*Molecular Sequence Annotation/methods
*Computational Biology/methods
Phylogeny
Xenopus/genetics
Perciformes/genetics

@article {pmid41520435,
year = {2026},
author = {Wu, H and Shen, J and Zhang, H and Fang, Q and Zhu, T and Yuan, J and Shen, Q and Xue, C},
title = {Fusarium oxysporum f. sp. niveum invasion promotes Pseudomonas-driven antibiotic resistance gene enrichment.},
journal = {Journal of hazardous materials},
volume = {503},
number = {},
pages = {141084},
doi = {10.1016/j.jhazmat.2026.141084},
pmid = {41520435},
issn = {1873-3336},
abstract = {The dissemination of antibiotic resistance genes (ARGs) in agricultural soils poses a growing threat to ecosystem health and food security, highlighting the need to identify key environmental drivers. Although soil-borne phytopathogens disrupt microbial communities, their specific impact on ARG dynamics remains poorly understood. In this study, we examined how Fusarium oxysporum f. sp. niveum (FON) invasion changes soil ARG profiles. Our results indicate that increasing FON loads heighten the abundances of soil ARGs, virulence factor genes (VFGs), and mobile genetic elements (MGEs). This invasion significantly transformed rhizosphere bacterial communities by enriching Pseudomonas populations. We further identified Pseudomonas-driven mechanisms that involve functional adaptations such as SOS response activation and enhanced biofilm formation. Genomic features, including vertically inherited ARGs (e.g., mexF/T/W, bacA) and horizontal gene transfer (HGT) elements tnpA transpositions, along with ecological interactions such as growth-supporting metabolic exchanges, collectively fueled ARG enrichment and dissemination. Pseudomonas strains exhibited prevalent multidrug resistance (MDR) and further promoted the enrichment of antibiotic-resistant bacteria (ARB) through growth - supporting metabolic interactions. An analysis of 689 Pseudomonas genomes from diverse habitats revealed that nearly all genomes contain multiple ARGs, VFGs, and MGEs, suggesting that Pseudomonas proliferation significantly contributes to ARG dissemination. Our findings establish FON load as a critical driver of resistome dissemination by selectively enriching multi-resistant Pseudomonas reservoirs and activating key resistance-enhancing mechanisms within these reservoirs. These results offer mechanistic insights for managing antimicrobial resistance risks in agroecosystems.},
}

@article {pmid41520282,
year = {2026},
author = {Yin, Q and Gupta, S and Muller, E and Almeida, A},
title = {The human gut microbiome in enteric infections: from association to translation.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2612836},
doi = {10.1080/19490976.2026.2612836},
pmid = {41520282},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome ; Bacteria/genetics/classification/isolation & purification ; Host-Pathogen Interactions ; Animals ; },
abstract = {Enteric infections remain a leading global cause of morbidity, mortality and economic loss, increasingly compounded by the rise of antimicrobial resistance. The gut microbiome - spanning bacteria, archaea, fungi, protists and viruses - is now recognized as an important mediator that shapes susceptibility to infection, pathogen expansion and disease severity through mechanisms such as colonization resistance, resource competition and immune modulation. Conversely, the gut microbial community can facilitate enteric infection through other processes such as cross-feeding and horizontal gene transfer. In this review, we synthesize correlative and mechanistic evidence currently available on microbiome-pathogen interactions; outline host, environmental and socioeconomic modifiers that affect disease risk across the life course; and evaluate current clinical applications. We highlight key limitations in the field and identify priority areas for future research to refine causal models of microbiome-pathogen ecology and enable targeted diagnostics and therapeutics for preventing and managing enteric infections.},
}

Humans
*Gastrointestinal Microbiome
Bacteria/genetics/classification/isolation & purification
Host-Pathogen Interactions
Animals

@article {pmid41520089,
year = {2026},
author = {Adhvaryu, S and Kiskova, J and Piknova, M and Farkasova, V and Buchtikova, I and Kourilova, X and Kizovsky, M and Benesova, M and Samek, O and Obruca, S and Pristas, P},
title = {Genome sequence of Halovibrio sp. HP20-59 as a promising polyhydroxybutyrate producer.},
journal = {Applied microbiology and biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00253-025-13647-3},
pmid = {41520089},
issn = {1432-0614},
support = {VVGS-PF-2023-2545//Pavol Jozef Safarik University in Kosice/ ; LM2023050//MEYS CR/ ; VEGA-1/0779/21//Ministry of education, research, development and youth of the Slovak republic/ ; },
abstract = {Since plastics pose the greatest threat to humanity, it is essential to find an economic and sustainable solution to combat environmental pollution. In this study, the ability of polyhydroxyalkanoates (PHA) production by the halophilic bacterium Halovirbrio sp. HP20-59 in the presence of different carbon sources was examined. The strain showed a selective substrate preference, with the highest PHA production (reaching up to 73% of cell dry weight) in the presence of galactose, while fructose, arabinose, glycerol and xylose resulted in lower accumulation. Phylogenetic analysis based on the 16S rRNA gene sequence and whole-genome sequencing confirmed the HP20-59 strain as a novel species within the Oceanospirillales order. Draft genome showed a size of 4,165,370 bp with a GC content of 55.1% and a complete set of pha genes. The comparative analysis of the phaC gene identified a 638 amino acid-long class I poly(R)-hydroxyalkanoic acid synthase, showing 91% similarity to Halovibrio variabilis and 89% similarity to species within the Vreelandella genus, suggesting a possible horizontal gene transfer of the pha gene cluster. These findings highlight the unique genetic and metabolic characteristics of Halovibrio sp. HP20-59, making it a promising candidate for industrial PHA production and a valuable resource for research on sustainable biopolymers. KEY POINTS: The first study of PHB production by the halophilic Halovibrio spp.The highest level of PHB production observed using glucose, galactose, and sucrose.phaCAB operon possibly acquired by horizontal gene transfer from Vreelandella sp.},
}

@article {pmid41518812,
year = {2026},
author = {Wang, M and Masoudi, A and Wang, C and Wu, C and Yu, Z and Liu, J},
title = {Urban habitat types modulate soil contamination and bacterial functional traits through antibiotic resistance genes and metal(loid) interactions.},
journal = {Journal of hazardous materials},
volume = {503},
number = {},
pages = {141092},
doi = {10.1016/j.jhazmat.2026.141092},
pmid = {41518812},
issn = {1873-3336},
abstract = {Urban soils are important reservoirs for contaminants, including metal(loid)s and antibiotic resistance genes (ARGs), posing threats to ecosystem function and public health. However, the variation in these contaminants across urban habitat types remains poorly understood. This study integrated shotgun metagenomics, 16S rRNA sequencing, quantitative PCR, and multivariate modeling to investigate the co-distribution of ARGs, metal(loid)s, and bacterial functional traits across six urban habitat types: afforestation areas, croplands, orchards, parks, ruderals, and semi-natural remnants. Our findings revealed habitat-specific contamination patterns, with croplands and orchards showing the highest ARG risks and strong co-selection signals mediated by mobile genetic elements (MGEs) and biocide/metal resistance genes (BMRGs). In contrast, ruderals and remnants exhibited significantly lower ARG abundances (<1.2 × 10[4] copies/g) and metal(loid) concentrations (Cd < 0.05 mg/kg and Pb < 10 mg/kg), as well as nearly 50 % fewer plasmid-associated ARGs, indicating reduced horizontal gene transfer potential. Integrative modeling identified functional genes and BMRGs as the most consistent drivers of MGE dynamics, while MGEs showed limited direct influence on ARGs, suggesting that mobility alone may not explain the spread of resistance in urban soils. Metagenomic analyses linked ARG profiles to disruptions in bacterial functions essential for nutrient cycling and ecosystem services, indicating that resistance risks in urban soils are closely tied to declines in functional capacity. A substantial overlap in ARGs between orchard soils and fruits underscored the potential for soil-to-human transmission. These results provide a cross-habitat framework that links contaminant profiles, resistance mobilization, and functional consequences in urban soils.},
}

@article {pmid41518806,
year = {2026},
author = {Li, YK and Fu, GY and Rong, Z and Chen, JQ and Ding, ZH and Zhang, ZX and Jian, HH and Shu, WS and Wu, YH and Xu, XW},
title = {Unique ecological functions of viral communities potentially influence microbial adaptability in deep-sea ferromanganese nodule deposits.},
journal = {Journal of hazardous materials},
volume = {503},
number = {},
pages = {141083},
doi = {10.1016/j.jhazmat.2026.141083},
pmid = {41518806},
issn = {1873-3336},
abstract = {Ferromanganese nodule deposits represent unique deep-sea habitats characterized by metal-rich environments. However, the composition and ecological functions of viral communities inhabiting the regions remain poorly understood. Here, we investigated the composition, distribution patterns, and potential ecological roles of viral community in both sediments and nodules from ferromanganese nodule deposits. Our results indicated that viral community distribution was influenced by sediment depth, habitat type, and microbial community. Furthermore, viruses may enhance the environmental adaptability of microbial hosts by encoding auxiliary metabolic genes, thereby indirectly influencing the biogeochemical cycles of carbon, phosphorus, and sulfur. Notably, viral genomes in ferromanganese nodule deposits contained a high frequency of metal resistance genes (MRGs). At the viral operational taxonomic unit (vOTU) level, the proportion of MRG- encoding vOTUs was 2.46-67.50 times higher in deep-sea habitats than in other marine environments, suggesting potential horizontal gene transfer of MRGs between hosts in sediments and ferromanganese nodules. Laboratory experiments confirmed that some virus-encoded MRGs could significantly enhance microbial metal resistance. Overall, this study provides a comprehensive characterization of viral communities in ferromanganese nodule deposits, highlighting their role in microbial adaptation and providing valuable insights for environmental impact assessments of deep-sea mining.},
}

@article {pmid41518213,
year = {2026},
author = {Segawa, T and Yoshizumi, S and Toyonaga, H and Shiraishi, A and Sato, K and Yamabe, T and Takagi, M and Takagawa, M and Yokoyama, R and Itoh, T and Ono, E},
title = {Chromosome-scale Genome Assemblies of Two Allopolyploid Cuscuta Species Uncover Genomic Signatures of Parasitic Lifestyle and Polyploid Evolution.},
journal = {Plant & cell physiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/pcp/pcag002},
pmid = {41518213},
issn = {1471-9053},
abstract = {Dodders (Cuscuta spp.) are obligate parasitic plants that have lost a large portion of photosynthetic genes but gained host genes through parasitism-mediated horizontal gene transfer. Their genetic complexity of speciation is partly clarified in the genome level. Here, we report the de novo genome assemblies of two phylogenetically distinct dodders: C. campestris (2n = 4x = 60) and C. chinensis (2n = 4x = 60), which are classified into distinct section of subgenus Grammica. Relatively low completeness of eudicot Benchmarking Universal Single-Copy Orthologs genes (ca. 87%) indicated progressive gene loss after evolution of the parasitic lifestyle due to release from functional constraints. Comparative genomics analyses revealed that the genome size of each species differs significantly, despite having the same chromosome numbers and allopolyploidy via independent hybridization involving different ancient parents. Various genomic rearrangements have likely contributed to the genomic diversity of the two lineages, which partly share habitats, including (1) gene gain and loss events, (2) homoeologous recombination between two subgenomes, and (3) lineage-specific transposable elements dynamics. Our findings not only provide a genomic basis for surveying parental species for allopolyploidization but also enhance understanding of the unique speciation of parasitic dodders through these chromosomal events.},
}

@article {pmid41518206,
year = {2026},
author = {Zurita, J and Solís, MB and Sevillano, G and Herrera-Yela, A and Zurita-Salinas, C and Moreno, C and Romero, JJ and , },
title = {Clinical, microbiological and genomic characterization of carbapenem-resistant Gram-negative bacteria in bloodstream infection: A multi-center study in Ecuador.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxag008},
pmid = {41518206},
issn = {1365-2672},
abstract = {AIMS: To evaluate the diversity, prevalence, and phenotypic and genotypic characteristics of carbapenem-resistant gram-negative bacteria (CR-GNB) causing bloodstream infections, and assess the mechanisms driving their dissemination through a multi-center study in nine hospitals of Ecuador.

METHODS AND RESULTS: Between November 2021 and May 2022, 297 Gram-negative bacteria (GNB) were isolated from 273 patients across nine hospitals in Ecuador. Genotypic characterization of carbapenem-resistant GNB from blood cultures was performed by whole genome sequencing (WGS). CR-GNB accounted for 18.8% (56/297), predominantly Klebsiella pneumoniae (41.1%), followed by Enterobacter cloacae complex (16.1%), Acinetobacter baumannii (12.5%), and Pseudomonas aeruginosa (7.1%). CR-GNB showed high resistance to cephalosporins (80-95%), piperacillin-tazobactam (85.7%), ampicillin-sulbactam (91.1%), and ciprofloxacin (78.6%).Genomic analysis revealed carbapenemase genes blaKPC-2 (most frequent), blaNDM-1, and blaOXA-181 across high-risk clones (e.g., K. pneumoniae ST307, ST258, ST147; A. baumannii ST1187). Carbapenemase genes were plasmid-borne (IncA/C, IncM, IncN, IncF, IncHI2, IncX3, non-typeable) and associated with transposons (Tn4401, Tn125, Tn3). Also, blaVIM-2 in Pseudomonas spp. was plasmid- and chromosomally encoded.

CONCLUSIONS: Our findings demonstrate a high burden of CR-GNB, primarily due to K. pneumoniae and E. cloacae complex. Furthermore, the widespread distribution of blaKPC-2, blaNDM-1, and blaOXA-181 in high-risk clones, coupled with the frequent plasmid- and transposon-mediated mobilization of these genes, highlights the crucial role of horizontal gene transfer in the dissemination of resistance.},
}

@article {pmid41516370,
year = {2026},
author = {Krivoruchko, A and Nurieva, D and Ivshina, I},
title = {Extracellular Polymeric Substances Produced by Actinomycetes of the Genus Rhodococcus for Biomedical and Environmental Applications.},
journal = {International journal of molecular sciences},
volume = {27},
number = {1},
pages = {},
doi = {10.3390/ijms27010498},
pmid = {41516370},
issn = {1422-0067},
support = {122031400671-1//Ministry for Science and Higher Education of the Russian Federation/ ; 124020500028-4//Ministry for Science and Higher Education of the Russian Federation/ ; FSNF-2025-0013//Ministry for Science and Higher Education of the Russian Federation/ ; },
mesh = {*Rhodococcus/metabolism/chemistry ; *Extracellular Polymeric Substance Matrix/chemistry/metabolism ; Biodegradation, Environmental ; Biofilms/growth & development ; *Actinobacteria/metabolism ; },
abstract = {Extracellular polymeric substances (EPSs) produced by actinomycetes of the genus Rhodococcus play crucial roles in their ecological success, metabolic versatility, and biotechnological value. This review summarizes existing studies of Rhodococcus EPSs, emphasizing the biochemical composition, functional attributes, and practical significance of EPSs, as well as their importance in biomedicine, bioremediation, and other applications (food industry, biomineralization) with respect to the EPS chemical composition and biological roles. Rhodococcus species synthesize complex EPSs composed primarily of polysaccharides, proteins and lipids that, like in other bacteria, support cell adhesion, aggregation, biofilm formation, and horizontal gene transfer (and can prevent exogenous DNA binding) and are highly important for resistance against toxicants and dissolution/assimilation of hydrophobic compounds. EPSs produced by different species of Rhodococcus exhibit diverse structures (soluble EPSs, loosely bound and tightly bound fractions, capsules, linear and branched chains, amorphous coils, rigid helices, mushroom-like structures, extracellular matrix, and a fibrillar structure with a sheet-like texture), leading to variations in their properties (rheological features, viscosity, flocculation, sorption abilities, compression, DNA binding, and interaction with hydrophobic substrates). Notably, the EPSs exhibit marked emulsifying and flocculating properties, contributing to their recognized role in bioremediation. Furthermore, EPSs possess antiviral, antibiofilm, anti-inflammatory, and anti-proliferating activities and high viscosity, which are valuable in terms of biomedical and food applications. Despite extensive industrial and environmental interest, the molecular regulation, biosynthetic pathways, and structural diversity of Rhodococcus EPSs remain insufficiently characterized. Advancing our understanding of these biopolymers could expand new applications in biomedicine, bioremediation, and biotechnology.},
}

*Rhodococcus/metabolism/chemistry
*Extracellular Polymeric Substance Matrix/chemistry/metabolism
Biodegradation, Environmental
Biofilms/growth & development
*Actinobacteria/metabolism

@article {pmid41512751,
year = {2025},
author = {Zhao, Z and Wei, Y and Pan, X and Zhang, G and Luo, M and Wang, Y and Yi, G and Lei, Y and Sun, G and Li, R},
title = {Fishing boats as underestimated vectors for the transmission of high-risk genetic elements in nearshore ecosystems.},
journal = {Journal of hazardous materials},
volume = {503},
number = {},
pages = {140812},
doi = {10.1016/j.jhazmat.2025.140812},
pmid = {41512751},
issn = {1873-3336},
abstract = {Aquatic biofilms on anthropogenic surfaces have been increasingly recognized as key vectors for the cross-boundary transmission of microorganisms and genetic determinants between distinct ecosystems. Current research remains disproportionately centered on ballast water and large vessels, overlooking small fishing boats. This is despite the fact that these boats are common vectors moving between mariculture and nearshore zones, with hull biofilms that can form potential reservoirs for pathogenic and resistant bacteria. Here, we employ a range of genomics approaches to systematically evaluate how hull material (wood, iron, and foam) influences biofilm composition, function, and risk. The biofilm communities exhibit a high abundance of pioneer microorganisms, strong ecological competitiveness, and low metabolic overlap with native assemblages. Further analysis of antibiotic resistance genes (ARGs), virulence factors (VFs), and mobile genetic elements (MGEs) in biofilms, assembling 379 ARG-VF-MGE-carrying contigs into 50 metagenomic bins, highlighting a substantial potential for horizontal gene transfer (HGT) and pathogen dissemination mediated by fishing boats. Finally, considering their enhanced biofilm colonization potential and the abundance of high-risk genetic elements, iron-hulled boats are likely to serve as significant vectors for the dispersal of resistant and virulent microorganisms into sensitive coastal environments, thereby posing elevated ecological and health risks. Our findings underscore the critical role of hull material in shaping biofilm community assembly and function and identify fishing boats as a key vector for the dispersal of high-risk genetic elements in nearshore environments.},
}

@article {pmid41511523,
year = {2026},
author = {Ho, CL and Low, XZ and Lee, WK and Bothwell, JH},
title = {Genome-Wide Comparative and Phylogenetic Analysis of Putative Algal Carbohydrate Sulfotransferases.},
journal = {Journal of molecular evolution},
volume = {},
number = {},
pages = {},
pmid = {41511523},
issn = {1432-1432},
support = {FRGS/1/2021/STG01/UPM/01/1//Ministry of Higher Education Malaysia/ ; },
abstract = {Carbohydrate sulfotransferases (CHSTs) play a vital role in the production of sulfated polysaccharides (SPs) in algae by catalyzing the sulfation of carbohydrate moieties through the transfer of a sulfuryl group from the donor, 3'-phosphoadenosine 5'-phosphosulfate (PAPS). In the present study, putative algal CHSTs with a PF00685, PF03567. PF06990 and PF13469 domain were identified by HMMER search and Protein Basic Local Alignment Search Tool (BLAST) using the well-characterized human CHSTs as queries. Approximately half of the algal CHSTs that contained a PF00685 domain also possessed a PF13469 domain in an overlapping region. These CHSTs were structurally and phylogenetically distinct from algal CHSTs containing PF03567 or/and PF06990 domains. The PF00685/PF13469 domain is commonly found in Chlorophyta, while PF03567 and PF06990 domains are more prevalent in red algae and brown algae, respectively, reflecting the different types of SPs produced by these distinct phyla. Our phylogenetic analyses of algal CHSTs support the hypothesis of a polyphyletic origin, suggesting complex evolutionary histories involving both lineage-specific evolution and significant horizontal gene transfer (HGT) events between algae and organisms from other diverse taxa, including bacteria. In addition, the specificities of algal CHSTs for different carbohydrate moieties and site-specific sulfation patterns were inferred from the phylogenies of human CHSTs and the CHSTs from of algae with known SPs and chemical structures. This approach helps us to bridge the gap in knowledge, as a limited number of algal CHSTs have been biochemically characterized experimentally.},
}

@article {pmid41511467,
year = {2026},
author = {Priya, M and de Carvalho, LPS},
title = {Circumnavigating Antibiotic Mechanisms of Action and Resistance Research.},
journal = {Biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.biochem.5c00658},
pmid = {41511467},
issn = {1520-4995},
abstract = {Antibiotics have revolutionized human health by significantly reducing morbidity and mortality associated with bacterial infections. Antibiotics exert bactericidal or bacteriostatic effects through inhibition of cell wall synthesis and disruption of cell membrane integrity, inhibition of protein, nucleic acid synthesis, and other metabolic pathways. Despite their remarkable success since the mid-20th century, antimicrobial resistance (AMR) has emerged as a major global health concern, undermining current treatments and complicating infection management. Key drivers of AMR include the overuse and misuse of antibiotics in clinical settings as well as bacterial adaptations such as genetic mutations and horizontal gene transfer. Mechanistically, these changes can lead to enzymatic inactivation of antibiotics, modification of drug targets, changes in permeability, and active efflux of antimicrobial agents. As resistance rises, antibiotic discovery and development have lagged, creating an urgent need for novel therapeutic strategies and chemical scaffolds. This review examines the antibiotic mechanisms and antibiotic evasion strategies, highlighting genetic and omics approaches used to identify high-priority targets for future drug discovery.},
}

@article {pmid41510044,
year = {2025},
author = {Sarkar, J},
title = {Core genome expansion in Brevibacterium across marine provinces reveals genomic footprint for long-term marine adaptation.},
journal = {Iranian journal of microbiology},
volume = {17},
number = {6},
pages = {912-928},
pmid = {41510044},
issn = {2008-3289},
abstract = {BACKGROUND AND OBJECTIVES: Actinobacteria are ubiquitous across diverse environmental niches. Brevibacterium strains within this phylum are widely distributed in both marine and terrestrial ecosystems worldwide. Marine environments are defined by distinct physicochemical properties-high salinity, alkaline pH, fluctuating O levels, and dynamic nutrient availability-which set them apart from terrestrial habitats. The broad ecological range of Brevibacterium strains raises questions about genome-encoded metabolic features that have evolved to adapt in marine environments.

MATERIALS AND METHODS: Genomics of Brevibacterium strains from various marine provinces was analyzed, focusing on core genome and pan-genome structure.

RESULTS: Core genome and pan-genome derived phylograms reveal a distinct polyphyletic origin of marine strains, as evidenced by their phylogenetic proximity despite diverse species affiliations. Only 1.16% of gene clusters from the total nonredundant gene repertoire were part of the core genome. Core genome size is shaped by geographical distribution. Notably, when strains from localized regions are analyzed, the core genome expands, indicating specialized functional requirements of additional genes within that environment. In marine isolates, the core genome includes genes involved in nutrient uptake, osmoregulation, and resistance to sediment genotoxicity. Additionally, a marine province-specific core genome analysis reveals genomic adaptations essential for acclimatization across different environments, regardless of species-level taxonomy.

CONCLUSION: Microbial genome evolution is shaped by ecological niche differentiation. The emergence and spread of habitats driven by tectonic plate movements may contribute to province-specific genomic divergence in Brevibacterium. This hypothesis merits further investigation, particularly as genomic data from deeper, geologically stable environments such as marine sediments become more accessible.},
}

@article {pmid41507177,
year = {2026},
author = {Kortebi, M and Bourge, M and Le Bars, R and Van Dijk, E and Dorman, CJ and Bury-Moné, S and Boccard, F and Lioy, VS},
title = {Bacterial chromatin remodeling associated with transcription-induced domains at pathogenicity Islands.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {161},
pmid = {41507177},
issn = {2041-1723},
support = {ANR-20-CE35-005//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-24-INBS-0005 FBI (BIOGEN)//Agence Nationale de la Recherche (French National Research Agency)/ ; },
mesh = {*Genomic Islands/genetics ; *Bacterial Proteins/metabolism/genetics ; *Chromatin Assembly and Disassembly/genetics ; Gene Expression Regulation, Bacterial ; *Salmonella typhimurium/genetics/metabolism/pathogenicity ; *Transcription, Genetic ; Chromatin/metabolism/genetics ; DNA-Binding Proteins/metabolism/genetics ; Transcription Factors/metabolism/genetics ; Humans ; },
abstract = {The nucleoid-associated protein H-NS is a bacterial xenogeneic silencer responsible for preventing costly expression of genes acquired through horizontal gene transfer. H-NS silences several Salmonella Pathogenicity Islands (SPIs) essential for host infection. The stochastic expression of SPI-1 is required for invasion of host epithelial cells but complicates investigation of factors involved in SPI-1 chromatin structure and regulation. We performed functional genomics on sorted Salmonella populations expressing SPI-1 or not, to characterize how SPI-1 activation affects chromatin composition, DNA conformation, gene expression and SPI-1 subcellular localization. We show that silent SPIs are associated with spurious antisense transcriptional activity originating from H-NS-free regions. Upon SPI-1 activation, remodeling of H-NS occupancy defines a new chromatin landscape, which together with the master SPI-1 regulator HilD, facilitates transcription of SPI-1 genes. SPI-1 activation promotes formation of Transcription Induced Domains accompanied by repositioning SPI-1 close to the nucleoid periphery. We present a model for tightly regulated chromatin remodeling that minimizes the cost of pathogenicity island activation.},
}

*Genomic Islands/genetics
*Bacterial Proteins/metabolism/genetics
*Chromatin Assembly and Disassembly/genetics
Gene Expression Regulation, Bacterial
*Salmonella typhimurium/genetics/metabolism/pathogenicity
*Transcription, Genetic
Chromatin/metabolism/genetics
DNA-Binding Proteins/metabolism/genetics
Transcription Factors/metabolism/genetics
Humans

@article {pmid41507170,
year = {2026},
author = {Lyu, Y and Shi, Y and Song, K and Zhou, J and Chen, H and Li, XC and Yu, Y and Lu, H},
title = {Intergeneric chromosomal transfer in yeast results in improved phenotypes and widespread transcriptional responses.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-68164-8},
pmid = {41507170},
issn = {2041-1723},
abstract = {Interspecific genetic exchanges caused by natural hybridization or horizontal gene transfer can lead to enhanced phenotypes, which are often of interest for industrial applications and evolutionary research. However, transferring genetic materials between distantly related species, such as intergeneric yeasts, presents technical challenges. In this study, we establish a method to transfer individual chromosomes from Saccharomyces cerevisiae (Sc) into Kluyveromyces marxianus (Km), an emerging model for bioproduction. The Sc chromosome of interest is circularized, genetically modified to carry Km centromeres and replication origins, and transformed into Km via protoplast transformation. Using this method, we generate two synthetic strains, each containing a full set of Km chromosomes and either Sc chromosome I or III. The Sc chromosomes exhibit normal replication, segregation, and active transcription after the transfer. The synthetic strains display enhanced phenotypes in flocculation and salt tolerance, which is found to be caused by transgressive expression of FLO9 and SPS22 on the transferred Sc chromosomes, respectively. Transcriptomic analysis reveal that transgressive expression is prevalent among the transferred Sc genes, suggesting evolution of lineage-specific cis- and trans-regulatory interactions across a long evolutionary timescale. Our strategy has potential applications in optimizing cell factories, constructing synthetic genomes, and advancing evolutionary research.},
}

@article {pmid41503791,
year = {2026},
author = {Jin, J and Yao, G and Zhang, X and Zhang, T and Ye, H and Zhou, X and Yu, Y and Zhao, Y and Qin, Z and Chen, H and Bi, Y and Wang, X and Ren, X and Zhang, Y and Wang, Z and Zhang, Q},
title = {Gut virome dysbiosis contributes to premature ovarian insufficiency by modulating gut bacteriome.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2611645},
doi = {10.1080/19490976.2025.2611645},
pmid = {41503791},
issn = {1949-0984},
mesh = {Female ; Animals ; *Dysbiosis/microbiology/virology ; *Primary Ovarian Insufficiency/microbiology/virology/therapy ; *Gastrointestinal Microbiome ; Rats ; Humans ; Adult ; *Virome ; Fecal Microbiota Transplantation ; *Bacteria/genetics/classification/isolation & purification/virology ; Young Adult ; Feces/virology ; Ovary ; Rats, Sprague-Dawley ; },
abstract = {BACKGROUND: Premature ovarian insufficiency (POI) significantly impairs female fertility and poses substantial health risks; however, its pathogenesis is incompletely understood, and effective therapeutic interventions are limited. Although gut bacteriome has been closely associated with ovarian dysfunction, the role and therapeutic potential of gut viruses, which far outnumber bacteria, remain largely unexplored.

RESULTS: Therefore, we recruited 60 healthy reproductive-aged women and recently diagnosed POI patients and investigated these concerns using various techniques, including whole-genome shotgun sequencing of virus-like particle (VLP) and fecal virome transplantation (FVT) in CTX-induced POI rats. We found considerable interindividual variability in the gut virome. The virome of POI patients exhibited significant dysbiosis, characterized by a marked reduction in virulent phage, significant changes in predominant phages, and a notable increase in horizontal gene transfer of resistance genes and virulence factors. Furthermore, gut VLPs from the healthy reproductive-aged women significantly improved the condition of POI rats. Conversely, gut VLPs from POI patients markedly impaired the ovarian function and reproductive capacity of healthy rats. The above regulatory effect is primarily due to modulations of gut bacteriome, specifically the estrobolome, and intestinal barrier integrity, which subsequently affect hypothalamic-pituitary-ovarian axis hormone levels and regulate ovarian oxidative stress and inflammation, thereby influencing ovarian function.

CONCLUSIONS: Our findings demonstrate the critical roles of the gut virome in regulating ovarian function and provide new insights into the pathogenesis of POI. This study also underscores the therapeutic potential of the gut virome in improving ovarian dysfunction and female infertility including POI.},
}

Female
Animals
*Dysbiosis/microbiology/virology
*Primary Ovarian Insufficiency/microbiology/virology/therapy
*Gastrointestinal Microbiome
Rats
Humans
Adult
*Virome
Fecal Microbiota Transplantation
*Bacteria/genetics/classification/isolation & purification/virology
Young Adult
Feces/virology
Ovary
Rats, Sprague-Dawley

@article {pmid41499160,
year = {2026},
author = {Hai, Q and Li, D and Huang, T and Dang, X and Xu, J and Ma, Z and Zhou, Z},
title = {The Honeybee Gut Microbiome: A Novel Multidimensional Model of Antimicrobial Resistance Transmission and Immune Homeostasis from Environmental Interactions to Health Regulation.},
journal = {FEMS microbiology reviews},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsre/fuag001},
pmid = {41499160},
issn = {1574-6976},
abstract = {The honeybee gut microbiome has emerged as a model system in microbial ecology, valued for its structural stability and host specificity, and has garnered significant attention for elucidating universal principles of host-microbe interactions. This review advocates for the honeybee as a multidisciplinary model organism, highlighting the unique role of its gut microbiota in maintaining colony immune homeostasis, driving host co-evolution, unraveling the transmission mechanisms of antibiotic resistance genes (ARGs), and enhancing host adaptability to environmental stressors. By integrating multidimensional factors, including environmental gradients and apicultural practices, we construct an "Environment-Microbiota-Host Health" interaction framework to transcend the limitations of single-factor analyses. This framework provides a novel paradigm for the ecological containment of antimicrobial resistance, the conservation of pollinator resources, and microbiome-based engineering interventions. The review underscores the unique value of the honeybee model in unraveling social insect-microbe coevolution and resistance transmission dynamics, while also prospecting its application potential in developing novel antimicrobial peptides, designing probiotic formulations, and monitoring environmental resistance.},
}

@article {pmid41496435,
year = {2025},
author = {Sváb, D and Falgenhauer, L and Kotogán, E and Chakraborty, T and Tóth, I},
title = {Comparative genomic analysis of cyclomodulin-producing Escherichia coli strains of animal origin.},
journal = {International journal of medical microbiology : IJMM},
volume = {322},
number = {},
pages = {151690},
doi = {10.1016/j.ijmm.2025.151690},
pmid = {41496435},
issn = {1618-0607},
abstract = {Cytolethal distending toxin (CDT), a cyclomodulin and genotoxin produced by many Gram-negative bacteria including pathogenic Escherichia coli, disrupts the eukaryotic host cell cycle to facilitate bacterial colonization. In a survey of dairy cows in Hungary, 7 % of of sampled animal and farm environment isolates carried CDT-producing E. coli (CTEC). Whole genome sequencing (WGS) performed on six recent isolates and three historical CTEC strains revealed association with diverse pathotypes, including enteropathogenic- (EPEC) and necrotoxigenic- (NTEC) types, as well as several unclassified atypical strains. Four of the six strains isolated in this study carried plasmid encoding cdt-III+ NTEC, while a prophage based cdt-V allele was present in the remaining two strains which were of unknown pathotype. These isolates exhibited significant variability in their supplementary virulence genes (SVGs) content as well as in multiple prophage regions linked to virulence or fitness factors. They were phylogenetically distinct and comprised of only distantly related sequence types (STs) that include two novel STs. Several isolates also carried other genotoxic cyclomodulins such as the cytotoxic necrotizing factor (cnf), the cycle inhibiting factor (cif), and colibactin (polyketide synthase, pks) which is located on a genomic island, indicating multiple mechanisms for dysplastic damage of the eukaryotic host cells exist and highlight the role of horizontal gene transfer in the zoonotic and pathogenic potential of CTEC.},
}

@article {pmid41496236,
year = {2025},
author = {Huang, C and Huang, P and Zhang, Y and Bartlam, M and Wang, Y},
title = {Ecological filtering enhanced by smaller PBS biodegradable microplastics constrains ARG dynamics in the soil plastisphere.},
journal = {Environment international},
volume = {207},
number = {},
pages = {110030},
doi = {10.1016/j.envint.2025.110030},
pmid = {41496236},
issn = {1873-6750},
abstract = {Microplastics (MPs) are increasingly recognized as hotspots for antibiotic resistance genes (ARGs), yet the combined effects of polymer type and particle size on ARG dynamics in the soil plastisphere remain unclear. Here, we employed metagenomic assembly and binning to explore how MP polymer type and particle size jointly modulate ARG carrying frequencies (ACFs), mobility, and microbial hosts with polyethylene (PE), polystyrene (PS), and biodegradable polybutylene succinate (PBS) MPs across a size gradient (1000, 500, and 106 μm). PBS, PS, and PE plastispheres exhibited different size-related trends in ARG association, with PBS showing the strongest and most consistent decline in ACFs. Only PBS showed a corresponding reduction in ARG-MGE co-localization, suggesting size-dependent constraints on horizontal gene transfer. Distinct ARG combinations in ARG-Carrying Contigs (ACCs) also showed plastic-type selectivity, with complex resistance clusters absent in 106 μm PBS samples, potentially due to environmental constraints that limit the assembly or persistence of multigene resistance structures. Potential pathogens Enterobacter bugandensis and Stutzerimonas urumqiensis were markedly reduced in 106 μm PBS samples, a pattern not observed in PS or PE. Bacterial community analysis revealed that smaller PBS particles were associated with reduced richness, increased evenness, and more competitive interactions within co-occurrence networks. These features, together with the decline in ARG abundance and mobility, suggest that enhanced ecological filtering may occur in smaller biodegradable plastispheres, jointly limiting the persistence of resistance genes and their bacterial hosts. Together, our findings highlight the importance of considering both MP type and particle size in assessing plastisphere-associated ARG risks.},
}

@article {pmid41495279,
year = {2026},
author = {Berndt, H and Duarte, I and Repnik, U and Struwe, MA and Abukhalaf, M and Scheidig, AJ and Tholey, A and Gruber-Vodicka, HR and Leippe, M},
title = {An ancient lysozyme in placozoans participates in acidic extracellular digestion.},
journal = {Communications biology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s42003-025-09409-6},
pmid = {41495279},
issn = {2399-3642},
support = {INST 257/650-1 FUGG//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; INST 152/772-1 FUGG//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; INST 152/774-1 FUGG//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; INST 152/776-1 FUGG//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 261376515//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 5028/1-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 261376515//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
abstract = {Lysozymes are an essential part of immunity and nutrition in metazoans, degrading bacterial cell walls via the hydrolysis of peptidoglycan. Although various lysozymes have been reported for higher animals, the origin of animal lysozymes remains elusive as they seem to be lacking in all early branching phyla. In this study, we investigated a putative goose-type lysozyme (PLys, glycoside hydrolase family 23, GH23) of the placozoan Trichoplax sp. H2. We show that PLys is highly active and primarily produced by cells of the placozoan ventral epithelium. PLys contains a non-conserved cysteine-rich domain N-terminal of the GH23 lysozyme domain, which stabilizes the protein and is truncated during maturation. Using a pH-sensitive fluorescence reporter, we show that Trichoplax sp. H2 acidifies its temporary feeding grooves pulsatively during digestive events close to the optimum pH for PLys activity. To elucidate the evolutionary origin of the metazoan GH23 lysozyme family, we applied structure-based phylogenetics to show that the metazoan g-type GH23 lysozymes originated from a horizontal gene transfer event from bacteria to an early pre-bilaterian ancestor. GH23 lysozymes have then been retained and expanded in many phyla acting as first animal lysozyme and a key component in the antibacterial arsenal since early animal evolution.},
}

@article {pmid41489361,
year = {2026},
author = {Abdulqadir, HN},
title = {The plasmid-host fitness landscape: a new paradigm for predicting the fate of mobile resistance.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0198325},
doi = {10.1128/aem.01983-25},
pmid = {41489361},
issn = {1098-5336},
abstract = {The widespread persistence of antimicrobial resistance (AMR) plasmids presents a fundamental challenge to microbial evolution, known as the "plasmid paradox": if these plasmids cause fitness cost, why are they not eliminated by selection? The classical view, which imposed a fixed generic fitness cost, is insufficient to explain their epidemiological success. Here, we propose a new paradigm-the plasmid-host fitness landscape-a multi-dimensional model that takes into account the complex interplay between ecology and genetics. This landscape unfolds into three main axes. First, the host axis reveals that fitness costs often arise from host-dependent genetic conflicts, not a generic burden. Second, the time axis demonstrates that the fitness cost of any plasmid can be negated over time through plasmid or chromosome compensations, which leads to ameliorating initial costs and locking in resistance. Third, the environmental axis shows that the fitness cost of any plasmid can be affected by external factors like temperature and sub-inhibitory concentrations of antibiotics. These factors dynamically modulate the benefits and costs of plasmid carriage. By integrating the complex interplay between these dimensions, we argue that the plasmid fitness costs are not a fixed generic measurement, but rather a contingent trajectory across this landscape. This paradigm shifts the focus from static measurements to a dynamic, predictive science, providing a new foundation for assessing and managing the threat of mobile resistance.},
}

@article {pmid41488303,
year = {2025},
author = {Tsolakidou, PJ},
title = {CRISPR-Cas systems against carbapenem resistance: from proof-of-concept to clinical translation.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1725247},
pmid = {41488303},
issn = {1664-302X},
abstract = {Carbapenem-resistant Enterobacterales (CRE) pose a major global threat, driven by plasmid-borne carbapenemase genes such as bla KPC, bla NDM and bla OXA-48. CRISPR-Cas systems offer programmable strategies to selectively eliminate these resistance determinants. This mini-review summarizes recent advances in Cas9-based plasmid curing, RNA-targeting approaches such as Cas13a and Cas13d, and DNA-targeting Cas3-enhanced bacteriophage therapeutics that have entered early clinical evaluation. Particular attention is given to conjugative CRISPR-Cas9 plasmid systems, which enable targeted plasmid eradication without laboratory transformation and broaden the delivery toolbox beyond phage vectors. We further discuss major translational challenges, including delivery efficiency, phage host-range constraints, ecological risks of horizontal CRISPR dissemination, and off-target effects. Finally, we highlight emerging delivery platforms-outer membrane vesicles, lipid and polymeric nanoparticles, conjugative plasmids with containment circuits, and engineered live biotherapeutics-that may complement or overcome current limitations. Collectively, these developments illustrate the potential of CRISPR-based antimicrobials to augment traditional therapies through precise gene-level suppression of carbapenem resistance.},
}

@article {pmid41487187,
year = {2025},
author = {Adegoke, SC and Yawlui, ISY and LaJeunesse, D},
title = {Silica Nanoparticles Block Natural Genetic Transformation in Acinetobacter baylyi ADP1.},
journal = {ACS omega},
volume = {10},
number = {51},
pages = {62609-62620},
pmid = {41487187},
issn = {2470-1343},
abstract = {The prolonged and widespread use of antibiotics has driven the emergence of resistance to many commonly employed drugs, posing a growing global challenge that requires urgent measures to curb its spread. Once resistance develops, horizontal gene transfer facilitates the exchange of genetic materials among various bacterial species, often preceding vertical transmission. Previous work to control horizontal gene transfer and specifically natural transformation within a population of bacteria approached the problem by addressing the bacterial mechanisms required for transformation. In this study, we investigated the possibility of controlling horizontal gene transfer by limiting access to or the availability of environmental DNA to the bacteria. In this study, we investigated the impact of five different sizes of silica nanoparticles (SiO2NPs), 20, 80, 120, 200, and 500 nm, and three sizes of gold nanoparticles (AuNPs), 5, 20, and 200 nm, on the natural genetic transformation of Acinetobacter baylyi ADP1 (A. baylyi ADP1) using both circular and linear environmental DNA (pBTK501) carrying an ampicillin resistance cassette. Our findings reveal that SiO2NPs ranging from 120 to 500 nm consistently inhibited transformation events in both M9 and LB media. SiO2NPs effectively suppress the natural transformation of A. baylyi ADP1 in the presence of circular pBTK501 with a stronger effect on the linear pBTK501. The degree of inhibition was size-dependent, as the 500 nm SiO2NPs exhibited the strongest effect. The inhibitory effect of SiO2NPs was also found to be dose-dependent: increasing the pBTK501 concentration relative to the SiO2NPs diminished the inhibition, while a higher SiO2NP-to-pBTK501 ratio resulted in a stronger inhibition. Similarly, the 200 nm AuNPs also displayed a notable inhibitory effect on the natural transformation of A. baylyi ADP1. These results, taken together, appear to show the ability of nanoparticles to control natural transformations in A. baylyi ADP1. This size-dependent mechanism clearly defines a path to mitigate the spread of resistance evolution both at the hospital and community settings, which hitherto has not been given adequate consideration.},
}

@article {pmid41481463,
year = {2026},
author = {Sari, E and Enright, DJ and Ordoñez, ME and Allison, SD and Homyak, PM and Wilkins, MJ and Glassman, SI},
title = {Gene duplication, horizontal gene transfer, and trait trade-offs drive evolution of postfire resource acquisition in pyrophilous fungi.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {1},
pages = {e2519152123},
doi = {10.1073/pnas.2519152123},
pmid = {41481463},
issn = {1091-6490},
support = {DE-SC0023127//DOE | SC | Biological and Environmental Research (BER)/ ; 2022-67014-36675//USDA | National Institute of Food and Agriculture (NIFA)/ ; },
mesh = {*Gene Transfer, Horizontal ; *Gene Duplication ; Nitrogen/metabolism ; *Fires ; Carbon/metabolism ; Ascomycota/genetics/metabolism ; Soil Microbiology ; Evolution, Molecular ; Phylogeny ; *Fungi/genetics/metabolism ; Biological Evolution ; },
abstract = {Wildfires significantly alter soil carbon (C) and nitrogen (N), reducing microbial richness and biomass, while selecting for "fire-loving" pyrophilous microbes that drive postfire nutrient cycling. However, the genomic strategies and functional trade-offs (balancing gains in one trait with costs in another) underlying the traits that enable pyrophilous microbes to survive and thrive postfire are virtually unknown. We hypothesized that pyrophilous fungi employ specialized genomic adaptations for C and N cycling, with evolutionary trade-offs between traits governing aromatic C degradation, N acquisition pathways, and rapid growth. To test these hypotheses, we performed complementary comparative genomics, transcriptomics after pyrogenic organic matter amendment, and growth rate bioassays for 18 pyrophilous fungi from five Ascomycota (Eurotiales, Pleosporales, Sordariales, Coniochaetales, and Pezizales) and three Basidiomycota (Agaricales, Holtermanniales, and Geminibasidiales) orders isolated from burned soils. We found a dramatic trait trade-off between fast growth and number of genes responsible for aromatic C degradation, implying burned environments select for metabolically costly genes despite their evolutionary cost. We used the comparative genomics framework to evaluate genomic signatures of evolution and found that either gene duplication and somatic mutation, or recombination via sexual reproduction, were the primary drivers of fungal genomic variation in aromatic C degradation and N acquisition genes. Finally, we identified cross-kingdom bacterial to fungal horizontal gene transfer (HGT) as a secondary strategy producing novel aromatic C degradation genes. Overall, we found that trait trade-offs and genome evolutionary strategies are key drivers that may predict the persistence and contribution of pyrophilous fungi to global C and N cycling.},
}

*Gene Transfer, Horizontal
*Gene Duplication
Nitrogen/metabolism
*Fires
Carbon/metabolism
Ascomycota/genetics/metabolism
Soil Microbiology
Evolution, Molecular
Phylogeny
*Fungi/genetics/metabolism
Biological Evolution

@article {pmid41480148,
year = {2025},
author = {Lu, Z and Xia, R and Xu, A and Gu, J and Cai, H and Liu, Y and Koonin, EV and Li, M},
title = {Oxygen-adaptive plasticity of Asgard archaea dependent on terminal oxidase and globin.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.11.07.685452},
pmid = {41480148},
issn = {2692-8205},
abstract = {The oxygenation of ancient Earth is thought to have driven eukaryogenesis, beginning with the endosymbiosis of an aerobic alphaproteobacterium (proto-mitochondria) with an archaeal host. Given that the archaeal host likely evolved from within Asgard archaea (phylum Promethearchaeota), the metabolic traits of Asgard archaea could provide key insights into eukaryotic origins. Although Asgard archaea cultured to date are obligate anaerobes, their genomes encode oxygen-adaptive proteins, suggesting they might be oxygen-tolerant. Here, we demonstrate that some Asgard archaea, in particular, Hodarchaeales , the closest known relatives of eukaryotes, and Kariarchaeaceae , exhibit oxygen adaptation mediated by terminal oxidase and globin. Phylogenetic analysis reveals long-term vertical evolution of terminal oxidases in Asgard archaea, suggesting ancient adaptation to molecular oxygen. By contrast, globin was likely acquired by Asgard archaea via horizontal gene transfer from facultative aerobic Chloroflexales bacteria. Heterologous expression of the Asgard globin enhances aerobic growth of Haloarchaea and Escherichia coli in the presence of terminal oxidase-dependent electron transfer chain, suggesting that Asgard growth benefits from ambient oxygen. The Asgard globin gene is embedded in an oxygen-sensitive bidirectional promoter region, with one promoter driving oxygen-induced globin expression, and the other anaerobically activating expression of two enzymes, PdxS and PdxT, involved in a pyridoxal 5'-phosphate biosynthesis. The Asgard globin and promoter region exhibit high functional robustness across archaea and bacteria, and could contribute to the symbiosis between the Asgard and aerobic bacterial partners. These findings highlight the oxygen-adaptive plasticity of Asgard archaea and its potential contribution to eukaryogenesis.},
}

@article {pmid41308244,
year = {2026},
author = {Zou, C and Xu, C and Shang, Y and Yu, R and Shan, X and Schwarz, S and Li, D and Du, XD},
title = {Mechanism of horizontal transmission of tet(A)TIG multicopy structures in Escherichia coli of chicken origin.},
journal = {Veterinary microbiology},
volume = {312},
number = {},
pages = {110809},
doi = {10.1016/j.vetmic.2025.110809},
pmid = {41308244},
issn = {1873-2542},
mesh = {*Escherichia coli/genetics/drug effects ; Animals ; Plasmids/genetics ; *Chickens/microbiology ; *Gene Transfer, Horizontal ; Anti-Bacterial Agents/pharmacology ; Tigecycline/pharmacology ; *Escherichia coli Infections/veterinary/microbiology/transmission ; *Poultry Diseases/microbiology ; *Bacterial Proteins/genetics ; Antiporters ; },
abstract = {Tigecycline is a vital antimicrobial to treat bacterial infection. Our previous studies have demonstrated that a variant of the tet(A) gene, tet(A)TIG, can enhance Escherichia coli resistance to tigecycline through tandem amplification. However, the mechanism of tet(A) multicopy structure transfer remains unclear. In this study, we report the mechanism of tet(A)TIG multicopy structure transfer with the assistance of plasmid recombination. S1-PFGE shows that the transconjugant 573_16xJ53-TC1 (hereinafter referred to as the "TC1") carries two plasmids. Interestingly, the sizes of these two plasmids do not match any plasmids in donor strain E. coli 573_16. Whole genome sequencing showed that TC1 carries only one plasmid, named p573_16xJ53-TC1 (hereinafter referred to as the "pTC1"). Sequence alignment indicates that the tet(A)TIG multicopy structure was transferred from the donor strain to the recipient strain via plasmid p573_16-3, rather than its original p573_16-2. Genetic environment analysis indicated that the cross-plasmid transfer of the tet(A)TIG gene was mediated by the unconventional circularizable structure (UCS) formed by homologous recombination of its upstream and downstream ΔTnAs1. Conjugation experiments indicate that the hybrid plasmid pTC1 still retains the ability for horizontal transfer. The tet(A)TIG gene can cause cross-resistance to tetracycline and tigecycline, and its horizontal spread through different plasmids indicates a complex mode of transmission.},
}

*Escherichia coli/genetics/drug effects
Animals
Plasmids/genetics
*Chickens/microbiology
*Gene Transfer, Horizontal
Anti-Bacterial Agents/pharmacology
Tigecycline/pharmacology
*Escherichia coli Infections/veterinary/microbiology/transmission
*Poultry Diseases/microbiology
*Bacterial Proteins/genetics
Antiporters

@article {pmid41474711,
year = {2025},
author = {Patarapuwadol, S and Hintong, W and Nualnisachol, P and Wankaew, N and Kruasuwan, W and Sawaengwong, T and Laosena, P and Premsuriya, J},
title = {Whole-genome sequencing of Burkholderia glumae strains from Thailand reveals potential horizontal gene transfer with Burkholderia pseudomallei.},
journal = {PloS one},
volume = {20},
number = {12},
pages = {e0340071},
doi = {10.1371/journal.pone.0340071},
pmid = {41474711},
issn = {1932-6203},
mesh = {*Burkholderia/genetics/isolation & purification/classification ; *Gene Transfer, Horizontal ; Thailand ; *Burkholderia pseudomallei/genetics ; Phylogeny ; *Whole Genome Sequencing ; *Genome, Bacterial ; Oryza/microbiology ; Humans ; Polymorphism, Single Nucleotide ; Genetic Variation ; Plasmids/genetics ; },
abstract = {Burkholderia glumae is an emerging phytopathogen that causes bacterial panicle blight in rice and has been implicated in rare human infections. In Thailand, B. glumae and the human pathogen Burkholderia pseudomallei coexist in rice fields. Given the high genomic plasticity of Burkholderia species, including frequent genome rearrangements, variability in mobile genetic elements, and recombination events that facilitate horizontal gene transfer, there are concerns about the emergence of novel traits that may affect both plant and human health. In this study, we performed whole-genome sequencing and a comparative genomic analysis of 16 B. glumae strains isolated from rice fields across seven Thai provinces. Our phylogenomic analysis, based on core-genome single-nucleotide polymorphisms, revealed high genetic diversity and a polyclonal population structure, with evidence of a globally distributed clonal lineage. All isolates harbored plasmids and diverse prophage elements, which indicated extensive mobilome variability. A total of 572 putative horizontally transferred genes were identified. Most of these genes originated from unclassified or plant-associated Burkholderia species. Notably, two strains shared a chromosomal island that carried genes that were very similar to those found in B. pseudomallei. This genomic region contained genes associated with mobile genetic elements, phage defense, and a type VI secretion system, including genes that encode a PAAR domain-containing protein, a putative nuclease, and an immunity protein. Our findings highlight the genomic heterogeneity of B. glumae in Thailand and provide evidence of interspecies horizontal gene acquisition from human pathogenic B. pseudomallei. The presence of B. pseudomallei-derived genes in B. glumae chromosomes underscores the potential for genetic exchange in shared environmental niches, which could affect the evolutionary dynamics and pathogenicity of B. glumae. Hence, our findings also emphasize the critical need for environmental surveillance and genome-based monitoring to track emerging genomic combinations relevant to both plant and human health.},
}

*Burkholderia/genetics/isolation & purification/classification
*Gene Transfer, Horizontal
Thailand
*Burkholderia pseudomallei/genetics
Phylogeny
*Whole Genome Sequencing
*Genome, Bacterial
Oryza/microbiology
Humans
Polymorphism, Single Nucleotide
Genetic Variation
Plasmids/genetics

@article {pmid41474525,
year = {2025},
author = {Unitt, A and Krisna, MA and Parfitt, KM and Jolley, KA and Maiden, MCJ and Harrison, OB},
title = {Neisseria gonorrhoeae LIN codes provide a robust, multi-resolution lineage nomenclature.},
journal = {eLife},
volume = {14},
number = {},
pages = {},
doi = {10.7554/eLife.107758},
pmid = {41474525},
issn = {2050-084X},
support = {BB/M011224/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 10.35802/218205/WT_/Wellcome Trust/United Kingdom ; 10.35802/214374/WT_/Wellcome Trust/United Kingdom ; },
mesh = {*Neisseria gonorrhoeae/genetics/classification ; Multilocus Sequence Typing/methods ; *Terminology as Topic ; Phylogeny ; Gonorrhea/microbiology ; Humans ; *DNA Barcoding, Taxonomic/methods ; },
abstract = {Investigation of the bacterial pathogen Neisseria gonorrhoeae is complicated by extensive horizontal gene transfer: a process which disrupts phylogenetic signals and impedes our understanding of population structure. The ability to consistently identify N. gonorrhoeae lineages is important for surveillance of this increasingly antimicrobial resistant organism, facilitating efficient communication regarding its epidemiology; however, conventional typing systems fail to reflect N. gonorrhoeae strain taxonomy in a reliable and stable manner. Here, a N. gonorrhoeae genomic lineage nomenclature, based on the barcoding system of Life Identification Number (LIN) codes, was developed using a refined 1430 core gene MLST (cgMLST). This hierarchical LIN code nomenclature conveys lineage information at multiple levels of resolution within one code, enabling it to provide immediate context to an isolate's ancestry, and to relate to familiar, previously used typing schemes such as Ng cgMLST v1, 7-locus MLST, or NG-STAR clonal complex (CC). Clustering with LIN codes accurately reflects gonococcal diversity and population structure, providing insight into associations between genotype and phenotype for traits such as antibiotic resistance. These codes are automatically assigned and publicly accessible via the https://pubmlst.org/organisms/neisseria-spp database.},
}

*Neisseria gonorrhoeae/genetics/classification
Multilocus Sequence Typing/methods
*Terminology as Topic
Phylogeny
Gonorrhea/microbiology
Humans
*DNA Barcoding, Taxonomic/methods

@article {pmid41474503,
year = {2025},
author = {Subramani, CB and Prasannakumar, MK and Kukreti, A and Channappa, M and Devanna, P and R, K and Patil, SS and J, H and S, S and Kagale, S},
title = {Enterobacter cloacae: a newly identified soft rot pathogen of radish with cross-species pathogenicity.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {1},
pages = {14},
pmid = {41474503},
issn = {1573-0972},
mesh = {*Plant Diseases/microbiology ; *Raphanus/microbiology ; *Enterobacter cloacae/genetics/pathogenicity/isolation & purification/classification ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; Virulence ; India ; DNA, Bacterial/genetics ; Host Specificity ; },
abstract = {Bacterial soft rot is a major vegetable disease of global significance, predominantly associated with Pectobacterium species; however, new reports indicate that novel, emerging pathogens are contributing to disease incidence. This study identified a novel pathogen, Enterobacter cloacae, as a causal agent of radish soft rot. Two isolates, RDH1 and RDH3, were isolated from 20 decaying radish taproots collected from Kolar, Karnataka, India, where a 12% disease incidence was recorded. Biochemical and physiological characterization, alongside comparison with E. cloacae ATCC 13047, confirmed the genus identity. Molecular analysis of 16S rRNA sequences revealed 99.56 and 99.87% similarity of RDH1 and RDH3, respectively, to known E. cloacae strains. Pathogenicity assay confirmed the pathogenicity of both isolates, and semi-quantitative assessment of plant cell wall degrading enzymes showed RDH1 producing clearance zones of 12.00, 10.33, and 8.00 mm, while RDH3 exhibited zones of 12.00, 10.00, and 7.67 mm, of pectin lyase, polygalacturonase, and cellulase, respectively. Host range assays on 10 vegetable crops revealed RDH3 as more virulent, particularly in radish, carrot, and cabbage, with the hypodermal syringe method showing broader infectivity compared to minimal infection via coir-enrichment seedling inoculation. Further, whole genome sequencing of RDH3 revealed a 4.8 Mb genome, 55% GC content, a single plasmid, and 99% ANI similarity to E. cloacae GGT036, containing T6SS, T4SS, ICEs, prophages, genomic islands, and 12 horizontal gene transfer events. These findings underscore the emerging role of E. cloacae in vegetable soft rot and highlight the need for further research on its pathogenic mechanisms and management strategies.},
}

*Plant Diseases/microbiology
*Raphanus/microbiology
*Enterobacter cloacae/genetics/pathogenicity/isolation & purification/classification
RNA, Ribosomal, 16S/genetics
Phylogeny
Virulence
India
DNA, Bacterial/genetics
Host Specificity

@article {pmid41474020,
year = {2025},
author = {Christie, PJ and Waksman, G and Berntsson, RP and Soler, N and Leblond-Bourget, N and Douzi, B},
title = {Type IV Secretion Systems: Reconciling Diversity Through a Unified Nomenclature.},
journal = {FEMS microbiology reviews},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsre/fuaf069},
pmid = {41474020},
issn = {1574-6976},
abstract = {Type IV secretion systems (T4SS) are versatile nanomachines responsible for the transfer of DNA and proteins across cell envelopes. From their ancestral role in conjugation, these systems have diversified into a superfamily with functions ranging from horizontal gene transfer to the delivery of toxins to eukaryotic and prokaryotic hosts. Recent structural and functional studies have uncovered unexpected architectural variations not only among Gram-negative systems but also between Gram-negative and Gram-positive systems. Despite this diversity, a conserved set of core proteins is maintained across the superfamily. To facilitate cross-system comparisons, we propose in this review a unified nomenclature for conserved T4SS subunits found in both Gram-negative and Gram-positive systems. We further highlight conserved and divergent mechanistic and architectural principles across bacterial lineages, and we discuss the diversity of emerging T4SSs whose unique structures and functions expand our understanding of this highly adaptable secretion superfamily.},
}

@article {pmid41473266,
year = {2025},
author = {Du, H and Xu, A and Feng, X and Huang, WC and Li, H and Liu, L and Li, Y and Zhang, S and Song, N and Appler, KE and Baker, B and Koonin, EV and Li, M and Liu, Y},
title = {Microcompartments in archaeal ancestors of eukaryotes: a bioenergetic engine that could have fuelled eukaryogenesis.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.11.08.687404},
pmid = {41473266},
issn = {2692-8205},
abstract = {Eukaryotic intracellular compartmentalization is a key innovation in the evolution of complex cellular life. While microcompartments enable metabolic specialization in many bacteria, to our knowledge, no analogous systems have been identified in Archaea. Here, we report the discovery of archaeal microcompartments (AMCs) in Hodarchaeales, an order within the phylum Promethearchaeati (Asgard archaea) that includes the closest known archaeal relatives of eukaryotes. Phylogenetic and structural analyses indicate that these catabolic AMCs, which are specialized for sugar-phosphate metabolism, were acquired by horizontal gene transfer from deep-rooted bacteria of the phylum Myxococcota. The shell pentamers of AMCs are fused to lysine/arginine-rich intrinsically disordered regions that capture cytosolic DNA, facilitating nutrient scavenging. Reaction-diffusion modelling predicts that enzyme colocalization and substrate channelling within AMCs can increase the NADH flux approximately 100-fold. Thus, the AMCs substantially boost energy production in the cell and might have primed the archaeal host for eukaryogenesis.},
}

@article {pmid41472774,
year = {2025},
author = {Dushayeva, LZ},
title = {Antimicrobial resistance in foodborne Escherichia coli and Salmonella spp. from animal-origin foods: Transmission pathways, global surveillance gaps, and alternative therapeutic strategies.},
journal = {Veterinary world},
volume = {18},
number = {11},
pages = {3288-3305},
pmid = {41472774},
issn = {0972-8988},
abstract = {Antimicrobial resistance (AMR) in enteric pathogens such as Escherichia coli and Salmonella spp. has emerged as a critical global health challenge affecting both human and animal populations. The widespread use of antibiotics in food-producing animals for therapeutic, prophylactic, and growth-promoting purposes has accelerated the selection and dissemination of resistant bacteria and resistance genes throughout the food chain. Animal-origin foods, including meat, milk, eggs, and fish, serve as important vehicles for the transmission of multidrug-resistant organisms and AMR genes to humans, representing a significant One Health concern. This review provides an overview of the occurrence, molecular mechanisms, and transmission pathways of AMR in E. coli and Salmonella isolated from animal-derived foods. Common resistance determinants include β-lactamase genes (blaTEM and blaCTX-M), tetracycline resistance genes (tetA and tetB), and plasmid-mediated quinolone resistance genes, which facilitate horizontal gene transfer through plasmids, integrons, and transposons. Global surveillance reports from World Health Organization's Global Antimicrobial Resistance Surveillance System, European Food Safety Authority, and World Organization for Animal Health reveal significant regional disparities, with limited monitoring capacity in Central Asia, Africa, and Latin America. Data from Kazakhstan indicate a high prevalence of multidrug-resistant E. coli and Salmonella in poultry, dairy, and cheese products, underscoring the urgent need for harmonized national surveillance and risk management strategies. The review also discusses alternative approaches to reduce antibiotic use in livestock production, including bacteriophage therapy, probiotics, phytogenic feed additives, vaccination, and nanotechnology-based interventions. While these strategies show promising results in laboratory and pilot studies, their practical application remains constrained by regulatory, economic, and field validation challenges. An integrated One Health strategy, combining surveillance, antimicrobial stewardship, and non-antibiotic interventions, is crucial to mitigating the dissemination of AMR along the farm-to-fork continuum. Strengthening laboratory networks, enhancing data sharing, and promoting collaboration among veterinary, environmental, and public health sectors will be crucial to safeguard food safety and global health security.},
}

@article {pmid41472034,
year = {2025},
author = {Barigelli, S and Koper, P and Petricciuolo, M and Firrincieli, A and Palusińska-Szysz, M and Federici, E},
title = {Unravelling the Genomic and Virulence Diversity of Legionella pneumophila Strains Isolated from Anthropogenic Water Systems.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41472034},
issn = {2076-2607},
support = {n.a.//University of Perugia, Environment and Safety Office/ ; 2022/47/D/NZ8/00258//Polish National Science Centre/ ; },
abstract = {Legionella pneumophila, a waterborne pathogen naturally present in freshwater and capable of colonizing artificial water systems, is responsible for Legionnaires' disease (LD), a severe form of pneumonia transmitted through inhalation of contaminated aerosols. Virulence of Legionella strains is affected by the plasticity of their genome, shaped by horizontal gene transfer and recombination events. Thus, contaminated water systems can host diverse Legionella populations with a distinct virulence potential. Here, we compare the genomic diversity of Legionella pneumophila strains isolated in water systems of academic buildings, together with their cytotoxicity and intracellular replication in THP-1-like macrophages. A six-year environmental surveillance revealed Legionella pneumophila contamination in 20 out of the 50 monitored sites, identifying five serogroups (sg) and 13 Sequence Types (STs). Phylogenetic investigations based on core genome multilocus sequence typing (cgMLST) and comparative genomics of representative isolates of each ST showed a broad diversity and a heterogeneous virulence repertoire, especially within the Dot/Icm and Lvh secretion systems. Following macrophage infection, a strain-dependent cytotoxicity and intracellular replication was observed, underlying significant pathogenic diversity within the same species and stage-dependent infection dynamics. Together, these results showed strain-specific genetic and phenotypic virulence traits to be considered during risk assessment in environmental surveillance.},
}

@article {pmid41472009,
year = {2025},
author = {Shirshikova, TV and Markelova, MI and Zhou, S and Bogomolnaya, LM and Sharipova, MR and Khilyas, IV},
title = {Nocardia mangyaensis NH1: A Biofertilizer Candidate with Tolerance to Pesticides, Heavy Metals and Antibiotics.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41472009},
issn = {2076-2607},
support = {24-24-00473//Russian Science Foundation/ ; },
abstract = {The extensive use of agrochemicals, heavy metals, and antibiotics in agriculture poses significant challenges to environmental sustainability and soil health. Plant growth-promoting bacteria (PGPB) offer a promising solution for sustainable agriculture; however, their selection requires careful evaluation of factors such as genome stability, metal tolerance, antibiotic resistance, and pesticide degradation capacity. This study characterizes the endolithic Nocardia mangyaensis NH1, focusing on its physiological and genomic features that enhance its potential as a biofertilizer in contaminated soils. Genomic analysis revealed a low number of antibiotic resistance genes with susceptibility to broad-spectrum antibiotics, minimizing the risk of horizontal gene transfer. The genome of N. mangyaensis NH1 contains two non-pathogenic genomic islands and prophage regions, with a CRISPR-Cas9 system. These findings highlight N. mangyaensis NH1 as a promising candidate for biofertilizers, combining pesticide and metal tolerance with genomic stability, thereby supporting sustainable agricultural practices and reducing environmental risks associated with agrochemical use.},
}

@article {pmid41471222,
year = {2025},
author = {Nass, NM and Zaher, KA},
title = {From Methylomes to CRISPR Epigenetic Editing: New Paths in Antibiotic Resistance.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {12},
pages = {},
doi = {10.3390/pathogens14121267},
pmid = {41471222},
issn = {2076-0817},
mesh = {*Gene Editing/methods ; *Epigenesis, Genetic ; *Bacteria/genetics/drug effects ; *CRISPR-Cas Systems ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Humans ; DNA Methylation ; *Epigenome ; *Drug Resistance, Microbial/genetics ; Gene Expression Regulation, Bacterial ; Epigenome Editing ; },
abstract = {Antibiotic resistance (AR) has long been interpreted through the lens of genetic mutations and horizontal gene transfer. Yet, mounting evidence suggests that epigenetic regulation, including DNA and RNA methylation, histone-like proteins, and small non-coding RNAs, plays a similarly critical role in bacterial adaptability. These reversible modifications reshape gene expression without altering the DNA sequence, enabling transient resistance, phenotypic heterogeneity, and biofilm persistence under antimicrobial stress. Advances in single-molecule sequencing and methylome mapping have uncovered diverse DNA methyltransferase systems that coordinate virulence, efflux, and stress responses. Such epigenetic circuits allow pathogens to survive antibiotic exposure, then revert to susceptibility once pressure subsides, complicating clinical treatment. Parallel advances in CRISPR-based technologies now enable direct manipulation of these regulatory layers. CRISPR interference (CRISPRi) and catalytically inactive dCas9-fused methyltransferases can silence or reactivate genes in a programmable, non-mutational manner, offering a new route to reverse resistance or sensitize pathogens. Integrating methylomic data with transcriptomic and proteomic profiles further reveals how epigenetic plasticity sustains antimicrobial tolerance across environments. This review traces the continuum from natural bacterial methylomes to engineered CRISPR-mediated epigenetic editing, outlining how this emerging interface could redefine antibiotic stewardship. Understanding and targeting these reversible, heritable mechanisms opens the door to precision antimicrobial strategies that restore the effectiveness of existing drugs while curbing the evolution of resistance.},
}

*Gene Editing/methods
*Epigenesis, Genetic
*Bacteria/genetics/drug effects
*CRISPR-Cas Systems
Anti-Bacterial Agents/pharmacology
*Drug Resistance, Bacterial/genetics
Humans
DNA Methylation
*Epigenome
*Drug Resistance, Microbial/genetics
Gene Expression Regulation, Bacterial
Epigenome Editing

@article {pmid41471176,
year = {2025},
author = {Bhowmik, S and Rivu, S and Bari, ML and Ahmed, S},
title = {Genome Mining of Cronobacter sakazakii in Bangladesh Reveals the Occurrence of High-Risk ST83 and Rare ST789 Lineages.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {12},
pages = {},
doi = {10.3390/pathogens14121220},
pmid = {41471176},
issn = {2076-0817},
support = {BIO-34//University Grant Commission, Bangladesh/ ; },
mesh = {Bangladesh/epidemiology ; Humans ; *Cronobacter sakazakii/genetics/isolation & purification/classification/pathogenicity ; *Genome, Bacterial ; *Enterobacteriaceae Infections/microbiology/epidemiology ; Virulence Factors/genetics ; Infant ; Food Microbiology ; Plasmids/genetics ; Infant, Newborn ; Whole Genome Sequencing ; Phylogeny ; Infant Formula/microbiology ; },
abstract = {Cronobacter sakazakii is a foodborne pathogen of major concern due to its link with severe neonatal infections through powdered infant formula (PIF). However, its genomic epidemiology in Bangladesh remains uncharacterized. We report the first whole-genome analysis of three isolates from PIF. Two isolates (S41_PIFM and S44_RUTF) belonged to ST83, a lineage repeatedly associated with neonatal meningitis, septicemia, and persistence in PIF production environments, while the third (S43_TF) represented ST789, a recently described and rare lineage of unknown pathogenic potential. Pan-genome and comparative analyses identified 39 virulence determinants, 19 antimicrobial-resistance genes, and diverse mobile genetic elements. ST83 isolates harbored plasmid replicons IncFII(pCTU2) and pESA2, while the ST789 isolate carried insertion sequence ISKpn34, indicating horizontal gene transfer potential. All strains encoded I-E CRISPR-Cas systems. The detection of globally recognized high-risk ST83 clones alongside the novel ST789 lineage highlights emerging public health risks. This study provides the first genomic insights into C. sakazakii in Bangladesh and underscores the urgent need for genomic surveillance and strengthened food safety monitoring to protect infant health in low- and middle-income countries.},
}

Bangladesh/epidemiology
Humans
*Cronobacter sakazakii/genetics/isolation & purification/classification/pathogenicity
*Genome, Bacterial
*Enterobacteriaceae Infections/microbiology/epidemiology
Virulence Factors/genetics
Infant
Food Microbiology
Plasmids/genetics
Infant, Newborn
Whole Genome Sequencing
Phylogeny
Infant Formula/microbiology

@article {pmid41469938,
year = {2025},
author = {Sanchez, AB and Lemes, CGC and Cordeiro, IF and Caneschi, WL and Barbosa, ÉF and de Paula, CH and da Silva, AK and Ribeiro, DF and de Matos, RC and de Matos, JP and Rocha, LCM and Damasceno, MRA and Garcia, CCM and Setubal, JC and de Mello Varani, A and Almeida, NF and Moreira, LM},
title = {Genomic characterization of Staphylococcus epidermidis Se252 isolated from the rhizosphere of a Brazilian endemic plant.},
journal = {BMC genomics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12864-025-12211-7},
pmid = {41469938},
issn = {1471-2164},
support = {LMM, NFA, JCS, AMV//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; LMM, NFA, JCS, AMV//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; LMM, NFA, JCS, AMV//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; LMM, NFA, JCS, AMV//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; APQ-02357-17//Fundação de Amparo à Pesquisa do Estado de Minas Gerais/ ; },
}

@article {pmid41468549,
year = {2025},
author = {Ye, L and Wu, Y and Guo, J and Wang, H and Cai, J and Chen, K and Dong, N and Yu, J and Chao, S and Zhou, H and Chen, G and Chen, S and Zhang, R},
title = {Elucidation of population-based bacterial adaptation to antimicrobial treatment by single-cell sequencing analysis of the gut microbiome of a hospital patient.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0163124},
doi = {10.1128/msystems.01631-24},
pmid = {41468549},
issn = {2379-5077},
abstract = {In this study, we used single-cell sequencing to analyze the gut microbiome of an adult male patient with acute cerebral hemorrhage undergoing antibiotic treatment. We identified 92 bacterial species, including 23 Firmicutes and one archaeon from Methanobacteriota, along with 69 unclassified strains. Single-cell sequencing effectively detected bacteria carrying antibiotic resistance genes (ARGs), particularly in unclassified species, and traced the evolution of these genes across diverse bacterial taxa. Notably, the cfr(C) gene was detected in 11 bacterial species following antimicrobial treatment, with mutation patterns characterized in Enterococcus faecalis, Klebsiella pneumoniae, Ruthenibacterium UN-1, and four unclassified species. In total, 29 ARG subtypes across eight types were identified in 13 known, five unknown, and 18 unclassified species, allowing us to trace their evolution routes. In addition, we detected a total of 309 horizontal gene transfer (HGT) events, in which several genes like folE and queE were frequently involved. The products of these genes are known to enhance the ability of the recipient bacterial strains to repair DNA damage and maintain genomic stability, especially following prolonged antibiotic treatment. Comparison between isolated strain genomes (IS-KP1) and single-cell analysis confirmed the presence of at least two K. pneumoniae strains in the patient, with one exhibiting a larger extent of involvement in ARG co-evolution. This strain was found to contain the cfr(C) and fosXCC genes, which were absent in IS-KP1. Klebsiella strains were also found to participate actively in HGT events. In conclusion, the study identified a wide range of ARGs and HGT events within the microbiome. The detection of K. pneumoniae strains with distinct ARG evolution patterns underscores the gut microbiome's adaptability to environmental changes. These findings facilitate the development of novel antimicrobial strategies by fine-tuning the gut microbiome composition.IMPORTANCEThis study highlights the power of single-cell sequencing to unravel the diversity and dynamics of the gut microbiome during antibiotic treatment in a patient with acute cerebral hemorrhage. By identifying antibiotic resistance genes (ARGs) in both known and unclassified bacterial species, we reveal the intricate evolution and horizontal transfer of resistance traits across taxa. The discovery of distinct ARG patterns, including the emergence of the cfr(C) gene in multiple species and its co-evolution in K. pneumoniae, underscores the gut microbiome's adaptability to antimicrobial pressures. These findings provide critical insights into the mechanisms driving resistance dissemination and offer potential pathways for developing precision microbiome-based therapies to combat antibiotic resistance.},
}

@article {pmid41467788,
year = {2025},
author = {Derriche, M and Nouvel, LX and Fauvet, C and Mach, N and Simon, E and Pot, G and Robert, H and Stella, A and de la Fe, C and Maillard, R and Torres-Puig, S and Arfi, Y and Citti, C and Baranowski, E},
title = {Nucleoside binding by a surface lipoprotein governs conjugative ICE acquisition in mycoplasmas.},
journal = {mBio},
volume = {},
number = {},
pages = {e0293925},
doi = {10.1128/mbio.02939-25},
pmid = {41467788},
issn = {2150-7511},
abstract = {Integrative and conjugative elements (ICEs) are major mediators of horizontal gene transfer in bacteria. However, the role of recipient cells in their acquisition has received little attention. Using the ruminant pathogens Mycoplasma agalactiae and Mycoplasma bovis as minimal models, we combined genome-wide transposon mutagenesis with high-throughput mating assays to identify recipient factors required for ICE acquisition. The surface lipoprotein P48 emerged as the primary determinant of ICE uptake in both species. Structural and functional analyses revealed that P48 is the substrate-binding component of an ABC transporter with nucleoside-binding capacity. A single-point mutation that abolished nucleoside binding drastically reduced ICE acquisition, demonstrating that P48-mediated nucleoside recognition is essential for conjugative transfer. However, ICE uptake did not require nucleoside transport, as inactivation of the transporter permease blocked nucleoside analog toxicity but not ICE invasion. Loss of P48 also triggered transcriptional activation of vestigial ICE genes, suggesting that surface recognition affects the intracellular state of the recipient. Remarkably, ICE transfer from recipient-derived donors was unaffected by P48 loss, underscoring its acquisition-specific role. Together, these results reveal a previously unrecognized, surface-exposed recipient factor critical for efficient ICE transfer in mycoplasmas and identify nucleotide binding as a central function in conjugation. By demonstrating that recipient-encoded functions can directly control ICE dissemination, this work challenges the donor-centric paradigm of bacterial conjugation and suggests new strategies to restrict horizontal gene flow in pathogenic and synthetic mycoplasmas.IMPORTANCEIntegrative and conjugative elements (ICEs) are mobile DNA elements that drive bacterial conjugation, a major process by which bacteria exchange genes. Although conjugation has been studied for decades, the focus has been almost exclusively on donor cells and the ICE itself, leaving the role of recipient cells largely overlooked. Using the wall-less ruminant pathogens Mycoplasma agalactiae and Mycoplasma bovis as minimal models, we discovered that a single recipient lipoprotein is required for efficient ICE uptake. Our data show that nucleoside recognition by P48, but not transport, is critical for conjugation, revealing an unexpected mechanistic link between nutrient sensing and gene acquisition. These findings shift the paradigm of conjugation from a donor-driven process to one jointly determined by donor and recipient functions. By identifying a recipient-encoded determinant of ICE transfer, this work opens new avenues to control horizontal gene flow in both pathogenic and engineered bacteria.},
}

@article {pmid41465500,
year = {2025},
author = {Gong, W and Cheng, X and Villena, J and Kitazawa, H},
title = {eDNA-Amyloid Synergistic Interactions in Bacterial Biofilms: A Hidden Driver of Antimicrobial Resistance.},
journal = {International journal of molecular sciences},
volume = {26},
number = {24},
pages = {},
doi = {10.3390/ijms262412075},
pmid = {41465500},
issn = {1422-0067},
support = {25K23670//Japan Society for the Promotion of Science KAKENHI/ ; },
mesh = {*Biofilms/drug effects/growth & development ; *Drug Resistance, Bacterial ; Anti-Bacterial Agents/pharmacology ; *Amyloidogenic Proteins/metabolism ; *Bacteria/drug effects/metabolism/genetics ; Humans ; *DNA, Bacterial/metabolism ; *Amyloid/metabolism ; Pseudomonas aeruginosa ; Bacterial Proteins/metabolism ; },
abstract = {Bacterial biofilms are critical contributors to chronic infections and antimicrobial resistance. Among the diverse extracellular matrix components, extracellular DNA (eDNA) and amyloid proteins have recently emerged as pivotal structural and functional molecules. Both individually contribute to biofilm stability and antibiotic tolerance, yet their cooperative roles remain underappreciated. This review aims to summarize current knowledge on the origins and functions of eDNA and amyloid proteins in biofilms, to highlight their molecular interactions, and to discuss how their synergistic effects promote biofilm-mediated resistance to antimicrobial agents. A comprehensive literature search was conducted using PubMed, Scopus, and Web of Science databases up to September 2025. Keywords included "biofilm", "extracellular DNA", "amyloid proteins", "matrix", and "antimicrobial resistance". Relevant original research and review articles were systematically screened and critically analyzed to integrate emerging evidence on eDNA-amyloid interactions in bacterial biofilms. Current studies demonstrate that eDNA originates primarily from autolysis, active secretion, and host-derived DNA, while amyloid proteins are produced by multiple bacterial species, including Escherichia coli (curli), Pseudomonas aeruginosa (Fap), Bacillus subtilis (TasA), and Staphylococcus aureus (phenol-soluble modulins). Both molecules independently strengthen biofilm integrity and provide protective functions against antimicrobial agents. Importantly, recent evidence shows that eDNA can act as a nucleation template for amyloid fibrillation, while amyloid fibers stabilize and protect eDNA from degradation, creating a dense extracellular network. This synergistic eDNA-amyloid assembly enhances biofilm robustness, impedes antibiotic penetration, sequesters antimicrobial peptides, protects persister cells, and facilitates horizontal gene transfer of resistance determinants. The interplay between eDNA and amyloid proteins represents a central but underexplored mechanism driving biofilm-mediated antimicrobial resistance. Understanding this cooperative network not only deepens our mechanistic insights into bacterial pathogenesis but also highlights novel therapeutic targets. Strategies that disrupt eDNA-amyloid interactions may offer promising avenues for combating persistent biofilm-associated infections.},
}

*Biofilms/drug effects/growth & development
*Drug Resistance, Bacterial
Anti-Bacterial Agents/pharmacology
*Amyloidogenic Proteins/metabolism
*Bacteria/drug effects/metabolism/genetics
Humans
*DNA, Bacterial/metabolism
*Amyloid/metabolism
Pseudomonas aeruginosa
Bacterial Proteins/metabolism

@article {pmid41465260,
year = {2025},
author = {Vladimirova, ME and Roumiantseva, ML and Saksaganskaia, AS and Kozlova, AP and Muntyan, VS and Gaponov, SP and Yurkov, AP and Zhukov, VA and Grudinin, MP},
title = {Mitogenome of Medicago lupulina L. Cultivar-Population VIK32, Line MlS-1: Dynamic Structural Organization and Foreign Sequences.},
journal = {International journal of molecular sciences},
volume = {26},
number = {24},
pages = {},
doi = {10.3390/ijms262411830},
pmid = {41465260},
issn = {1422-0067},
support = {agreement no. 075-15-2022-320, dated 20 April 2022//Ministry of Science and Higher Education of the Russian Federation/ ; },
mesh = {*Genome, Mitochondrial ; *Medicago/genetics/microbiology ; Phylogeny ; Symbiosis ; Open Reading Frames ; Mycorrhizae ; Gene Transfer, Horizontal ; },
abstract = {This study presents the complete assembly and analysis of the mitochondrial genome (mitogenome) of Medicago lupulina L. var. vulgaris Koch, cultivar-population VIK32, line MlS-1, which forms an effective symbiosis not only with arbuscular mycorrhiza but also with the root nodule bacteria Sinorhizobium meliloti. The assembly, generated using a hybrid sequencing approach, revealed sequences of putative horizontal origin. These include a highly conserved open reading frame (ORF), orf279, encoding a protein structurally homologous to maturase K, yet bearing remote similarity to bacterial reverse transcriptases and CRISPR-associated proteins. We also identified sequences homologous to mitovirus RNA-dependent RNA polymerases and a fragment of the chloroplast 23S ribosomal RNA (rRNA), suggesting historical gene transfers from viruses and plastids. This work establishes a foundation for investigating the role of mitochondrial genome variation in key plant's phenotypic traits, such as the enhanced responsiveness to arbuscular mycorrhiza observed in this agronomically valuable line.},
}

*Genome, Mitochondrial
*Medicago/genetics/microbiology
Phylogeny
Symbiosis
Open Reading Frames
Mycorrhizae
Gene Transfer, Horizontal

@article {pmid41465192,
year = {2025},
author = {Mikołajczuk-Szczyrba, A and Wnęk-Auguścik, K and Średnicka, P and Shymialevich, D and Jaroszewska, E and Wojtczak, A and Zapaśnik, A and Bucka-Kolendo, J and Cieślak, H and Nasiłowska, J},
title = {Genomic and Phenotypic Landscape of Antibiotic Resistance in Gut Lactic Acid Bacteria from Livestock Environments.},
journal = {Genes},
volume = {16},
number = {12},
pages = {},
doi = {10.3390/genes16121518},
pmid = {41465192},
issn = {2073-4425},
support = {agreement no. DRE.prz.070.1.2025//This research was funded by the Ministry of Agriculture and Rural Development of Poland/ ; },
mesh = {Animals ; *Livestock/microbiology ; Anti-Bacterial Agents/pharmacology ; *Lactobacillales/genetics/drug effects/isolation & purification ; *Gastrointestinal Microbiome/genetics/drug effects ; Phenotype ; Microbial Sensitivity Tests ; Whole Genome Sequencing ; Feces/microbiology ; Genome, Bacterial ; *Drug Resistance, Bacterial/genetics ; Genomics ; Plasmids/genetics ; },
abstract = {BACKGROUND/OBJECTIVES: The widespread use of antibiotics in livestock has raised concerns about commensal gut bacteria, such as lactic acid bacteria (LAB), acting as reservoirs for antimicrobial resistance. This study aimed to characterize the antibiotic resistance profiles of LAB isolated from livestock feces by combining phenotypic susceptibility testing with whole-genome sequencing (WGS) to identify antibiotic resistance genes (ARGs) and their genomic context.

METHODS: Four LAB strains from farm animal fecal samples were subjected to antibiotic susceptibility testing for 9 antibiotics (ampicillin, gentamicin, kanamycin, clindamycin, chloramphenicol, erythromycin, streptomycin, tetracycline, and vancomycin) using MIC determinations. WGS was performed on each isolate to detect ARGs using curated databases and to determine the chromosomal or plasmid location of these genes.

RESULTS: All four isolates exhibited phenotypic resistance to at least one antibiotic class, most frequently to aminoglycosides. However, discrepancies between phenotype and genotype were noted: resistance to aminoglycosides was common despite the absence of known aminoglycoside-resistance genes, suggesting intrinsic, uptake-related mechanisms. In contrast, one strain carried the chromosomal lsa(D) gene but remained susceptible to clindamycin. WGS revealed that all strains harbored the chromosomal van(T) gene, while one isolate carried three additional plasmid-borne ARGs-erm(B), cat(A), and tet(W)-conferring resistance to macrolide-lincosamide-streptogramin antibiotics, chloramphenicol, and tetracycline. Another strain encoded van(Y), lsa(D), and arr on its chromosome. The detection of multiple plasmid-located ARGs in a single LAB isolate highlights their potential for horizontal gene transfer.

CONCLUSIONS: This study provides a detailed phenotypic and genomic insight into antibiotic resistance in gut-derived LAB from livestock. The findings highlight that commensal LAB can harbor clinically relevant ARGs-sometimes on mobile genetic elements-without always expressing corresponding resistance phenotypes. Such LAB may serve as a hidden reservoir for antibiotic resistance, raising the risk of ARG dissemination through the food chain. These results underscore the importance of vigilant monitoring and genomic screening of LAB, especially those considered for use in foods or feed, to ensure they do not contribute to the spread of antimicrobial resistance.},
}

Animals
*Livestock/microbiology
Anti-Bacterial Agents/pharmacology
*Lactobacillales/genetics/drug effects/isolation & purification
*Gastrointestinal Microbiome/genetics/drug effects
Phenotype
Microbial Sensitivity Tests
Whole Genome Sequencing
Feces/microbiology
Genome, Bacterial
*Drug Resistance, Bacterial/genetics
Genomics
Plasmids/genetics

@article {pmid41463733,
year = {2025},
author = {Xin, R and Lin, H and Li, Z and Yang, F},
title = {Plasmid-Mediated Spread of Antibiotic Resistance by Arsenic and Microplastics During Vermicomposting.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {12},
pages = {},
doi = {10.3390/antibiotics14121230},
pmid = {41463733},
issn = {2079-6382},
support = {23JCYBJC00250//Tianjin Municipal Natural Science Foundation/ ; 42277033//National Natural Science Foundation of China/ ; Y2024QC28//Central Public-interest Scientific Institution Basal Research Fund/ ; 202401AT070304//Basic Research Foundation of Yunnan Province of China/ ; },
abstract = {Background: The efficiency of vermicomposting in reducing antibiotic resistance genes (ARGs) in dairy manure may be compromised by co-pollutants like arsenic (As) and microplastics. Specifically, plasmids serving as carriers and vectors of ARGs were largely distributed in this process. However, the impact of As and microplastics on plasmids carrying ARGs during vermicomposting is largely unknown. Methods: This study utilized a controlled experimental design and applied plasmid metagenomics to investigate the individual and combined effects of As and polyethylene terephthalate (PET) microplastics on plasmid-mediated ARG dynamics during vermicomposting. Results: We found that vermicomposting alone mainly enriched non-mobilizable plasmids, while PET microplastics selectively promoted conjugative and mobilizable plasmids, whereas As significantly increased all plasmid types. Moreover, both PET or As alone and combined exposure (PET and As) increased total ARG abundance, with their combination inducing synergistic ARG enrichment despite unchanged total plasmid abundance. Furthermore, co-occurrence network analysis combined with ARGs/plasmid ratio assessments demonstrated that As influences ARGs through co-selective pressure by enriching ARGs co-localized with As resistance genes (e.g., the ars operon) on plasmids while simultaneously promoting horizontal gene transfer (HGT) via activation of oxidative stress and SOS response pathways. In contrast, PET primarily facilitates ARG dissemination through a "metabolism-resistance" coupling strategy by enriching colonizing bacteria with PET-degrading capacity. Their co-exposure formed As-enrichment hotspots on PET microplastic surfaces, functioning as a "super-mixer" that selectively screened for superbugs carrying potent resistance mechanisms (e.g., blaOXA-50 and mdtB/mdtE). Conclusions: This study provides the first plasmidome-level evidence of synergistic ARG propagation by As and PET microplastics during vermicomposting, highlighting mobile genetic elements' critical role in co-pollutant risk assessments.},
}

@article {pmid41463701,
year = {2025},
author = {Kiatyingangsulee, T and Hein, ST and Prathan, R and Srisanga, S and Jeamsripong, S and Chuanchuen, R},
title = {Integrated Genetic Characterization and Quantitative Risk Assessment of Cephalosporin- and Ciprofloxacin-Resistant Salmonella in Pork from Thailand.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {12},
pages = {},
doi = {10.3390/antibiotics14121198},
pmid = {41463701},
issn = {2079-6382},
support = {POP6305030650 and POP6305030660//the Agricultural Research Department Agency (Public Organization)/ ; GCUGR1125652075D//the 90th anniversary of Chulalongkorn university/ ; N42A660897//National Research Council of Thailand (NRCT)/ ; 6271010031//the Second Century Fund (C2F) PhD scholarship/ ; },
abstract = {Background/Objectives: This study assessed the risk associated with third-generation cephalosporin- and fluoroquinolone-resistant Salmonella from pork consumption by integrating phenotypic resistance profiles with genetic data to characterize the risks and transmission pathways. Methods: Salmonella were isolated from raw pork meat samples (n = 793) collected from fresh markets and hypermarkets across Bangkok during 2021-2022, of which 150 were extended-spectrum β-lactamase (ESBL)-producing and 31 were fluoroquinolone-resistant isolates. Phenotypic and genotypic resistance profiles were characterized. Quantitative antimicrobial resistance risk assessment (AMR RA) was conducted using a dose-response model. Results: Salmonella spp. was detected in 42.75% of pork samples, with a higher prevalence in fresh markets (75.5%) than in hypermarket samples and with concentrations ranging from 1.3 to 180 MPN/g. Twenty-eight percent of isolates were ESBL producers, with ciprofloxacin and levofloxacin resistance observed in 5.3% and 3.0%, respectively. The blaCTX-M55 genes were located on conjugative plasmids. Whole genome sequencing revealed both vertical and horizontal gene transfer. IncHI2/N and IncC plasmids shared conserved backbones and resistance gene architectures, indicating horizontal dissemination of resistance genes. Phylogenomics suggested possible clonal transmission among pigs, pork, and humans. AMR RA estimated 88,194 annual illness cases per 100,000 people from ESBL-producing Salmonella and 61,877 from ciprofloxacin-resistant strain, compared with 95,328 cases predicted by QMRA from Salmonella contamination. Cooking pork at ≥64 °C for 3 min eliminated the risk in all scenarios. Sensitivity analysis identified initial contamination level and cooking temperature as key determinants. Conclusions: Raw pork meat consumption represents the highest risk, which can be mitigated by thorough cooking (>64 °C, ≥3 min), while integrating genomic data enhances AMR hazard identification, source attribution, and exposure assessment. Therefore, promoting well-cooked meat consumption and safe cooking practices, alongside the use of AMR genetic data to inform targeted interventions, is recommended.},
}

@article {pmid41461507,
year = {2026},
author = {Su, Q and Du, Y and Du, D and Zhang, TC},
title = {New insights into the anaerobic digestion of high carbon wastewater with ciprofloxacin: Methane production and ARGs inhibition.},
journal = {Journal of environmental sciences (China)},
volume = {161},
number = {},
pages = {612-621},
doi = {10.1016/j.jes.2025.05.037},
pmid = {41461507},
issn = {1001-0742},
mesh = {*Methane/metabolism ; *Wastewater/chemistry/microbiology ; *Ciprofloxacin ; Anaerobiosis ; *Waste Disposal, Fluid/methods ; *Water Pollutants, Chemical/analysis ; Anti-Bacterial Agents ; Drug Resistance, Microbial/genetics ; Carbon ; },
abstract = {Ciprofloxacin (CIP), as a quinolone antibiotic, has broad-spectrum antibacterial properties and can affect methanogenic performance in anaerobic digestion (AD). While previous studies focused on synthetic wastewater, the fate of CIP in real distillery wastewater (RDW) and its impact on microbial adaptation mechanisms remain unclear (such as biotransformation pathways, population dynamics, and the enzymes involved) in RDW is largely unclear. In this study, we investigated AD performance, metabolic pathways, and antibiotic resistance gene (ARG) dynamics using real wastewater spiked with CIP (0.3-2 mg/L). Results indicate that 0.5 mg/L CIP (631.83 mL CH4/g·VS) enhanced the methane yield by 6.67 % (592.34 mL CH4/g·VS in control), correlating with upregulated enzyme in glycosis, TCA cycle, and methanogenesis (F420 increased). With full use of short-chain acids, transient volatile fatty acid (VFA) inhibition (≤ 50 mg/L on Day 3) was overcome by Day 10. Metagenomics revealed CIP promoted the production of stress proteins (e.g., cysteine synthase activity doubled). Furthermore, CIP (0.3-1 mg/L) suppressed mobile genetic elements (MGEs) encoding horizontal gene transfer, including isfinder (15.15 %) and integrases (6.25 %), while ARG and virulence factor abundances remained unchanged versus control. This study firstly shows that low-dose CIP in RDW increases methanogenesis via metabolic adaptation without exacerbating ARG risks. MGE suppression implies that CIP may lessen the possibility of ARG diffusion in AD systems. These results offer vital information for improving AD performance in the treatment of wastewater contaminated by antibiotics and developing methods to strike a balance between antibiotic removal and ARG control.},
}

*Methane/metabolism
*Wastewater/chemistry/microbiology
*Ciprofloxacin
Anaerobiosis
*Waste Disposal, Fluid/methods
*Water Pollutants, Chemical/analysis
Anti-Bacterial Agents
Drug Resistance, Microbial/genetics
Carbon

@article {pmid41461481,
year = {2026},
author = {Qian, J and Bai, S and Wu, L and Geng, M and Chen, G and Jiang, F},
title = {Energy recovery from corn straw-based biochar@MIL-88A(Fe)-mediated anaerobic digestion of waste activated sludge under norfloxacin: Metabolism and antibiotic resistance gene fates.},
journal = {Journal of environmental sciences (China)},
volume = {161},
number = {},
pages = {350-359},
doi = {10.1016/j.jes.2025.07.034},
pmid = {41461481},
issn = {1001-0742},
mesh = {*Norfloxacin ; Sewage/microbiology/chemistry ; Zea mays/chemistry ; Anaerobiosis ; Charcoal/chemistry ; *Waste Disposal, Fluid/methods ; Anti-Bacterial Agents ; *Drug Resistance, Microbial/genetics ; Biodegradation, Environmental ; },
abstract = {Norfloxacin (NOR), a commonly detected antibiotic in waste activated sludge (WAS), remains understudied in anaerobic digestion (AD). This study investigated the effect of NOR on WAS AD, with corn straw-based biochar modified with MIL-88A(Fe) (BM) added to enhance energy recovery during digestion. Accumulated methane production was inhibited by 41.86 % in the BM-mediated digestion system under 1 mg/L NOR. Moreover, NOR induced the build-up of volatile fatty acids (VFAs), hindering methanogenic pathways subsequently. Microbial community structure was altered, with an enrichment of bacteria responsible for NOR degradation and a 13.20 % reduction in the abundance of hydrogenotrophic methanogens under antibiotic stress. Methanogenesis was inhibited with the expression of related genes and enzymes suppressed. The high enzymatic activities of cytochrome P-450 (CYP450) and acetate kinase contributed to the high NOR biodegradation efficiency (88.79 %). Twelve typical antibiotic resistant genes (ARGs) types, including multidrug, aminoglycoside, macrolides (MLs), etc., were examined in the AD system. The total abundance of ARGs type and subtype increased under NOR addition, implying ARGs removal was inhibited by NOR stress. Resistance to NOR exposure was primarily associated with antibiotic efflux and alterations in antibiotic target. Horizontal gene transfer (HGT) and vertical gene transfer (VGT) were the mechanistic routes for ARG evolution, with HGT inhibited and VGT promoted following NOR addition. The dominant genus Acinetobacter was the potential host for nearly all ARGs. This study advanced understanding of the impact of NOR on WAS digestion with BM mediation, providing new insights for optimizing WAS digestion.},
}

*Norfloxacin
Sewage/microbiology/chemistry
Zea mays/chemistry
Anaerobiosis
Charcoal/chemistry
*Waste Disposal, Fluid/methods
Anti-Bacterial Agents
*Drug Resistance, Microbial/genetics
Biodegradation, Environmental

@article {pmid41461451,
year = {2026},
author = {Xiao, S and Zheng, C and Yang, J and Zhang, W and Fang, H and Wu, X and Han, L},
title = {Responses and regulatory mechanisms of soil microbiome and antibiotic resistome to carbendazim and ZnO nanoparticles.},
journal = {Pesticide biochemistry and physiology},
volume = {217},
number = {},
pages = {106891},
doi = {10.1016/j.pestbp.2025.106891},
pmid = {41461451},
issn = {1095-9939},
mesh = {*Zinc Oxide/pharmacology/toxicity ; *Soil Microbiology ; *Microbiota/drug effects ; *Benzimidazoles/pharmacology ; *Carbamates/pharmacology ; Plasmids/genetics ; *Soil Pollutants ; *Fungicides, Industrial/pharmacology ; *Nanoparticles ; Bacteria/drug effects/genetics ; *Metal Nanoparticles ; *Drug Resistance, Microbial/genetics/drug effects ; Reactive Oxygen Species/metabolism ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Exogenous pollutants may alter the profile of antibiotic resistance genes (ARGs) in soil. Substantial application of a fungicide carbendazim (CBD) and ZnO nanoparticles (nZnO) in modern agriculture has led to serious combined pollution in soil. Here, the degradation characteristics of CBD, the diversity and abundance of ARGs and their dissemination and regulatory mechanisms were investigated in response to individual and combined applications of CBD and nZnO. CBD initially degraded fast and then slowly in soil, and nZnO slightly delayed the degradation of CBD. CBD and nZnO significantly changed the soil bacterial community structure. Meanwhile, CBD and nZnO significantly increased the abundance of ARGs, especially for multidrug and beta-lactam resistance genes. The relative abundance of plasmids significantly increased in CBD and nZnO treatments, and the elevation in soil ARG abundance was associated with the increase in plasmid-borne ARG abundance, suggesting that plasmid-mediated horizontal gene transfer might contribute to the dissemination of ARGs. Moreover, the intergenus and intragenus conjugative transfer frequency of plasmid RP4 in the CBD and nZnO treatments increased by up to 9.4-fold of the control. Additionally, the cell membrane permeability and intracellular reactive oxygen species content of recipient and donor bacteria in the CBD and nZnO treatments increased by up to 1.6-fold of the control, which facilitated plasmid-mediated conjugative transfer of ARGs. It is concluded that CBD and nZnO can alter soil microbiome and improve antibiotic resistome by accelerating conjugative plasmid-mediated ARGs propagation.},
}

*Zinc Oxide/pharmacology/toxicity
*Soil Microbiology
*Microbiota/drug effects
*Benzimidazoles/pharmacology
*Carbamates/pharmacology
Plasmids/genetics
*Soil Pollutants
*Fungicides, Industrial/pharmacology
*Nanoparticles
Bacteria/drug effects/genetics
*Metal Nanoparticles
*Drug Resistance, Microbial/genetics/drug effects
Reactive Oxygen Species/metabolism
Anti-Bacterial Agents/pharmacology

@article {pmid41459220,
year = {2025},
author = {Zhao, X and Qiao, J and Wang, Y and Xiong, H and Wang, R and Su, F and Guo, Z},
title = {Shotgun metagenomics reveals antibiotic resistome dynamics and metabolic specialization in fungal-dominated microbiomes.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1626799},
pmid = {41459220},
issn = {1664-302X},
abstract = {BACKGROUND: Metagenomics offers a culture-independent framework for comprehensively characterizing microbial communities by directly extracting and sequencing DNA from environmental samples. In this study, we employed high-throughput metagenomic sequencing to explore microbial communities inhabiting fungal-rich environments, emphasizing taxonomic composition, functional potential, and antibiotic resistance gene (ARG) dynamics.

METHODS: Six samples from two distinct groups (HFJ and QFJ) were subjected to Illumina-based shotgun sequencing, followed by rigorous quality control, taxonomic classification, KEGG-based functional annotation, and ARG identification via the CARD database. Comparative analysis revealed stark contrasts between the two groups.

RESULTS: HFJ samples were dominated by eukaryotic taxa, particularly Saccharomyces cerevisiae, and exhibited elevated carbohydrate metabolism, aligning with the ecological role of fermentative fungi. Conversely, QFJ samples displayed higher bacterial diversity, particularly Firmicutes and Proteobacteria, and were enriched in lipid and amino acid metabolism pathways. Striking differences were also observed in ARG profiles. QFJ samples harbored greater ARG abundance, particularly genes conferring resistance to beta-lactams, aminoglycosides, and tetracyclines, indicating higher resistance potential and possible horizontal gene transfer activity.

CONCLUSION: Our results reveal distinct microbial, functional and resistome profiles in fungal-rich versus bacterial-rich fermentation environments. Fungal dominance correlated with lower bacterial diversity and a reduced abundance of certain ARGs, whereas bacterial-rich samples exhibited higher diversity and ARG prevalence. These correlations generate the hypothesis that fungal dominance may suppress bacterial growth or ARG dissemination; however, causal relationships cannot be inferred from our cross-sectional data. The study highlights the potential of metagenomic surveillance to elucidate ecological niches that influence bacterial diversity and resistance dynamics.},
}

@article {pmid41455196,
year = {2025},
author = {Xia, R and Zhang, L and Li, G and Luo, W and Xu, Z},
title = {A small technology for big health: Blocking the potential spread of antibiotic resistomes from home composting of food waste by mature compost.},
journal = {Waste management (New York, N.Y.)},
volume = {211},
number = {},
pages = {115312},
doi = {10.1016/j.wasman.2025.115312},
pmid = {41455196},
issn = {1879-2456},
abstract = {Home composting is a popular lifestyle for onsite treatment and recycling of food and garden wastes, but potentially spreads antimicrobial resistance to affect human health. Thus, the dynamics of antibiotic resistomes during home composting and their control by mature compost were investigated. Results show that the relative abundance of antibiotic resistance genes (ARGs) decreased significantly at thermophilic stage and then increased at cooling stage. Integrative and conjugative elements (ICEs) located on chromosomes and mobilizable plasmids reduced at thermophilic stage to restrain horizontal gene transfer (HGT) events and relative abundance of ARG. Nevertheless, HGT events were driven by mobile genetic elements (MGEs) on chromosomes to rebound in relative abundance of ARG at cooling and mature stages. Mature compost could improve the control of antibiotic resistomes by reducing ARG and MGE hosts and blocking their HGT events. Specifically, mature compost significantly accelerated microbial metabolisms and increased composting temperature to sterilize ARG hosts and thus vertical gene transfer events during thermophilic stage. Thus, the rebound in relative abundance of ARG was effectively inhibited to increase their overall removal by 8.3% - 14.9%, particularly for high-risk ones. These results propose a simple but pragmatic strategy to mitigate significant antimicrobial resistance risks from home composting to safeguard environmental and public health.},
}

@article {pmid41455408,
year = {2025},
author = {Fridrich, A and Irwin, NAT},
title = {Cross-kingdom gene transfer as a driver of land plant evolution.},
journal = {Current opinion in plant biology},
volume = {89},
number = {},
pages = {102850},
doi = {10.1016/j.pbi.2025.102850},
pmid = {41455408},
issn = {1879-0356},
abstract = {Land plant evolution has been marked by bursts of novelty, often underpinned by extensive genomic innovation. A key mechanism driving these changes is horizontal gene transfer (HGT), the process by which genes move between species and even across taxonomic kingdoms. HGT can accelerate evolutionary change through the rapid introduction of new genes yet its importance in plant biology is only beginning to be understood. Here, we review the functional contributions of HGT during the origin and diversification of land plants. We discuss the occurrence of HGT throughout plant evolution and its impact on the origin of defining traits from cell walls to developmental programs. Beyond ancient contributions, HGT continues to drive the emergence of lineage-specific innovations. Recently acquired bacterial and fungal genes make complex functional contributions to processes including stress response, pathogen defence, and development across plant phylogeny. These observations suggest that HGT was, and continues to be, a major force shaping plant evolution, exemplifying the potential significance of HGT in eukaryotic biology more broadly.},
}

@article {pmid41448087,
year = {2025},
author = {Yi, J and Li, Z and Han, X and Li, J and Liu, H and Zhu, L and Wang, M},
title = {Metformin drives the antibiotic resistome in activated sludge by reshaping microbial communities and promoting horizontal gene transfer.},
journal = {Journal of hazardous materials},
volume = {501},
number = {},
pages = {140887},
doi = {10.1016/j.jhazmat.2025.140887},
pmid = {41448087},
issn = {1873-3336},
abstract = {Aerobic granular sludge (AGS) serves as a major reservoir and dissemination hotspot for human bacterial pathogens (HBPs) and antibiotic resistance genes (ARGs). Metformin (MET) as an emerging contaminant, which exacerbates antibiotic resistance and poses a problem for the stable operation of the activated sludge process in wastewater treatment plants. However, the specific mechanisms underlying the effects of MET stress on microbial communities and ARGs propagation in activated sludge remain poorly understood. In this study, we employed metagenomic analysis to investigate the effects of MET exposure, under a composite antibiotic background, on microbial community dynamics and resistome profiles in AGS systems and interpreted these effects from the perspectives of energy metabolism and community competition. Our findings demonstrate that MET exposure significantly enriched HBPs and multidrug resistance-related ARGs. Co-occurrence network analysis further identified that, among all sludge samples, 27 high-risk HBPs were strongly correlated with ARGs, virulence factor genes, and mobile genetic elements. Additionally, MET was also found to enhance ATP production in specific HBPs, conferring a competitive edge that facilitates ARG accumulation. Furthermore, the natural transformation and conjugation experiments further demonstrated the key role of MET in promoting horizontal gene transfer. In summary, this study underscores the role of MET in exacerbating the ecological risk of antibiotic resistance in AGS systems by concurrently enriching pathogenic bacteria and facilitating the horizontal transfer of ARGs, thereby highlighting the potential environmental impacts of MET as a pervasive contaminant on the propagation of resistance within wastewater treatment ecosystems.},
}

@article {pmid41448015,
year = {2025},
author = {Amirfard, KD and Amarasiri, M and Sano, D},
title = {Energy allocation trade-offs among conjugative transfer, biofilm formation, and heavy metal resistance: a dynamic energy budget theory perspective.},
journal = {Water research},
volume = {291},
number = {},
pages = {125216},
doi = {10.1016/j.watres.2025.125216},
pmid = {41448015},
issn = {1879-2448},
abstract = {Plasmid-mediated bacterial conjugation is a significant driver of antimicrobial resistance (AMR) dissemination in the environment, particularly within surface-attached biofilms, where spatial proximity facilitates gene exchange. Environmental stressors, such as heavy metals, can influence both the structural development of biofilms and the frequency of conjugation, imposing metabolic burdens that force bacteria to reprioritize their energy use. In this study, we used a simplified Dynamic Energy Budget (DEB)-based modeling framework to evaluate energy allocation in a single-strain bacterial population exposed to varying concentrations of zinc oxide (ZnO; 0-0.1 g/L). The model incorporates substrate assimilation, reserve dynamics, and energy partitioning toward growth, maintenance, metal resistance, biofilm formation, and conjugation. Experimental data were collected every 12 h for 48 h, including total organic carbon (TOC, mg/L), biomass (CFU/mL), intracellular adenosine triphosphate (ATP, mol/mL), conjugation frequency (transconjugants/donor), and biofilm density (OD550). Ordinary Differential Equation (ODE)-based simulations over 60 h showed that at 0.1 g/L ZnO, reserve energy and substrate declined approximately 3.1- and 1.9-fold, respectively (vs around 5- and 2.9-fold in control), indicating reduced depletion. Discrete-time-point flux models revealed conjugation demanded 17% of total energy at 36 h under 0.01 g/L ZnO, and 10% under 0.1 g/L at 60 h, while energy allocated to biofilm formation remained ≤ 3% under the highest ZnO concentration. Overall, the model reveals key trade-offs in bacterial energy allocation and provides mechanistic insight into how metal stress may shape biofilm formation and conjugation dynamics. Its modular and data-driven structure offers a basis for understanding microbial adaptation and AMR propagation in metal-contaminated environments.},
}