@article {pmid41136898,
year = {2025},
author = {Junier, T and Palmieri, F and Ubags, ND and Trompette, A and Koutsokera, A and Junier, P and Pagni, M and Neuenschwander, S},
title = {Prevalence of oxalotrophy in the human microbiome.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {954},
pmid = {41136898},
issn = {1471-2164},
support = {40B2-0_194701//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; GRS-064/18//Gebert Rüf Stiftung/ ; },
mesh = {Humans ; *Oxalates/metabolism ; *Microbiota/genetics ; Metagenome ; Gene Transfer, Horizontal ; *Bacteria/genetics/metabolism ; },
abstract = {BACKGROUND: Incomplete degradation of oxalate, a compound commonly found in the diet, can lead to disease in humans, particularly affecting the kidneys. The concentration of oxalate in the body depends on several factors, one of which is intestinal absorption-an aspect influenced by oxalotrophy among enteric bacteria. Despite its potential significance, oxalotrophy in the human microbiome remains poorly understood.

RESULTS: In this study, we conducted a systematic search for the co-occurrence of three key oxalotrophy genes-frc, oxc, and oxlT. We developed and validated specific conservation models for each gene and applied them to genomes and metagenomes associated with the human digestive tract, oral cavity, and lungs. Our analysis revealed that oxalotrophy, defined as the capacity to use oxalate as an energy source, is a rare metabolic trait predominantly confined to the gut. We also found evidence that this capacity can be acquired via horizontal gene transfer.

CONCLUSIONS: While oxalotrophy is relatively uncommon, the broader capacity for oxalate degradation is more widespread. Notably, the genes frc and oxc are frequently found in close proximity within genomes, suggesting a selective advantage for organisms possessing this capability. Incomplete degradation of oxalate, a compound commonly found in the diet, can cause disease in humans, particularly affecting the kidney. Its concentration in the body depends on several factors, one of which is intestinal absorption, which is itself affected by oxalotrophy among enteric bacteria. Oxalotrophy in the human microbiome is poorly known. In this study, we perform a systematic search for the simultaneous presence of the three oxalotrophy genes, namely frc, oxc and oxlT. Thanks to the construction and validation of specific conservation models for all three genes, we were able to search for oxalotrophy in genomes and metagenomes associated with the human digestive tract, oral cavity, and lungs. We report that oxalotrophy-the capacity to use oxalate as an energy source-is a rare metabolic trait, mostly confined to the gut, and also find evidence that it can be acquired by horizontal gene transfer. By contrast, the capacity for oxalate degradation is more widespread, and two genes responsible for it (frc and oxc) are almost always close together in the genome, suggesting selection pressure.},
}

Humans
*Oxalates/metabolism
*Microbiota/genetics
Metagenome
Gene Transfer, Horizontal
*Bacteria/genetics/metabolism

@article {pmid41136156,
year = {2026},
author = {Habib, I and Ibrahim Mohamed, MY and Lakshmi, GB and Ghazawi, A and Khan, M},
title = {Resident or transient? Whole-genome approach to tracking colistin-resistant Escherichia coli in the broiler chicken processing chain.},
journal = {Food microbiology},
volume = {134},
number = {},
pages = {104939},
doi = {10.1016/j.fm.2025.104939},
pmid = {41136156},
issn = {1095-9998},
mesh = {Animals ; *Colistin/pharmacology ; *Escherichia coli/genetics/drug effects/isolation & purification/classification ; *Chickens/microbiology ; *Anti-Bacterial Agents/pharmacology ; Whole Genome Sequencing ; Phylogeny ; *Drug Resistance, Bacterial/genetics ; Genome, Bacterial ; Plasmids/genetics ; *Meat/microbiology ; Escherichia coli Proteins/genetics ; Drug Resistance, Multiple, Bacterial/genetics ; Microbial Sensitivity Tests ; Food Contamination/analysis ; },
abstract = {This study presents a genome-informed surveillance model to investigate the persistence and spread of colistin-resistant Escherichia coli in broiler chicken processing. The study targeted a high-throughput poultry facility-previously linked to retail meat contamination by colistin-resistant E. coli and Salmonella-where 200 carcasses were sampled across ten production batches to assess the prevalence and genomic characteristics of antimicrobial-resistant strains within the processing line. We analyzed one E. coli isolate per carcass to characterize antimicrobial resistance (AMR), and utilized whole-genome sequencing (WGS) to delineate phylogeny, virulence, AMR determinants, and plasmid content. Colistin-resistant E. coli isolates were detected in all production batches and were confirmed in 10.5 % (21/200) of the carcasses, with all isolates carrying the mcr-1.1 gene. Notably, 57.1 % of these isolates also harbored a PmrB Y358N putative colistin resistance mutation. Phylogenetic analysis revealed substantial diversity, with 31 sequence types detected; however, six isolates belonging to ST162 were identified as a resident strains cluster, persisting over four months and from multiple farms and flocks. All colistin-resistant E. coli isolates were phenotypically multidrug-resistant (MDR), carrying 10-25 AMR resistance genes per genome, including ESBL genes such as blaCTX-M-55 (57.1 %). Virulence profiling showed a high prevalence of iron acquisition, serum resistance, and efflux-related genes, with an average of 22.5 putative virulence factors per isolate. Plasmidome analysis (n = 20 plasmids) revealed the dominance of IncI2 (60 %) and IncHI2-type replicons, with 90 % of plasmids predicted to be conjugative. Mobile genetic elements involved in horizontal gene transfer, such as MOBP relaxases and MPF-T systems, were prevalent (70 %), indicating a high potential for plasmid-mediated dissemination of AMR genes within the sampled isolates. This work offers a scalable model for processing facility-level AMR tracking and reinforces the value of WGS for industry-led food safety risk management, particularly for high-priority AMR determinants such as colistin resistance.},
}

Animals
*Colistin/pharmacology
*Escherichia coli/genetics/drug effects/isolation & purification/classification
*Chickens/microbiology
*Anti-Bacterial Agents/pharmacology
Whole Genome Sequencing
Phylogeny
*Drug Resistance, Bacterial/genetics
Genome, Bacterial
Plasmids/genetics
*Meat/microbiology
Escherichia coli Proteins/genetics
Drug Resistance, Multiple, Bacterial/genetics
Microbial Sensitivity Tests
Food Contamination/analysis

@article {pmid41136132,
year = {2026},
author = {Spaans, M and Winkler, LS and van den Broek, MA and Daran, JG},
title = {Diversity of α-acetolactate decarboxylase in the Saccharomycotina yeast subphylum: From discovery to brewing application.},
journal = {Food microbiology},
volume = {134},
number = {},
pages = {104903},
doi = {10.1016/j.fm.2025.104903},
pmid = {41136132},
issn = {1095-9998},
mesh = {Fermentation ; Phylogeny ; *Beer/microbiology/analysis ; *Carboxy-Lyases/genetics/metabolism ; Diacetyl/metabolism/analysis ; *Fungal Proteins/genetics/metabolism ; *Saccharomycetales/enzymology/genetics/classification ; Acetoin/metabolism ; Flavoring Agents/metabolism ; Lactates ; },
abstract = {Diacetyl, a vicinal diketone with a low sensory threshold, is a prominent off-flavour in beer, necessitating extended lagering to allow its reduction to non-flavour-active compounds. In brewing, bacterial α-acetolactate decarboxylases are commonly used to mitigate diacetyl formation by converting its precursor, α-acetolactate, directly into acetoin. Here, we report the first discovery and characterization of functional α-acetolactate decarboxylases enzymes of eukaryotic origin, specifically from yeasts within the Saccharomycotina subphylum. Using a homology-based search against fungal genomic databases, 29 candidate genes were identified across 18 yeast species from only three genera (Lipomyces, Dipodascus and Wickerhamiella) and classified into distinct phylogenetic groups. Phylogenetic analysis revealed both fungal and possible bacterial origins, suggesting evolutionary conservation and horizontal gene transfer events. Seven genes were heterologously expressed in Saccharomyces pastorianus lager brewing strains. Fermentation trials in both lab-scale septum flasks and E.B.C. tall tubes demonstrated that yeast-derived α-acetolactate decarboxylases significantly reduced diacetyl levels, with some performing comparably or superior to the benchmark Brevibacillus brevis enzyme. These strains also showed normal fermentation kinetics and produced beers with diacetyl concentrations below sensory thresholds, effectively eliminating the need for extended lagering. Our findings uncover a previously unrecognized enzymatic activity in budding yeasts and present yeast α-acetolactate decarboxylases as promising non-bacterial alternatives to improve process efficiency and sustainability in lager beer production.},
}

Fermentation
Phylogeny
*Beer/microbiology/analysis
*Carboxy-Lyases/genetics/metabolism
Diacetyl/metabolism/analysis
*Fungal Proteins/genetics/metabolism
*Saccharomycetales/enzymology/genetics/classification
Acetoin/metabolism
Flavoring Agents/metabolism
Lactates

@article {pmid41133644,
year = {2025},
author = {Zhu, X and Zou, A and Xianyu, Y},
title = {Bacterial membrane vesicles: from biogenesis to antibiotic resistance.},
journal = {Biomaterials science},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5bm01218j},
pmid = {41133644},
issn = {2047-4849},
abstract = {Bacterial membrane vesicles (MVs) are a heterogeneous group of lipid-bound structures produced by bacteria. Antibiotic stress aggravates the secretion of MVs that contributes to the development of bacterial antibiotic resistance. This review provides a focused, resistance-oriented perspective on the interplay between MVs and antibiotic resistance. We outline MV biogenesis, emphasizing the distinct formation mechanisms of Gram-negative and Gram-positive bacteria. We further focus on the secretion of MVs under antibiotic stress, highlighting pathways such as bacterial envelope stress, SOS response, and cell wall disruption. The pivotal role of MVs in bacterial antibiotic resistance is also elucidated, including neutralizing antibiotics, absorbing phages, and facilitating drug efflux, biofilm formation, and horizontal gene transfer. Current challenges and future prospects for elucidating MV-mediated mechanisms in antibiotic resistance are discussed.},
}

@article {pmid41130916,
year = {2025},
author = {Wadsworth, CB and Goytia, M and Shafer, WM},
title = {Commensal Neisseria and Antimicrobial-Resistant Gonorrhea.},
journal = {Annual review of microbiology},
volume = {79},
number = {1},
pages = {215-240},
doi = {10.1146/annurev-micro-022024-024306},
pmid = {41130916},
issn = {1545-3251},
mesh = {*Gonorrhea/microbiology/drug therapy ; Humans ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Gene Transfer, Horizontal ; *Neisseria gonorrhoeae/genetics/drug effects/physiology ; *Drug Resistance, Bacterial ; *Neisseria/genetics/drug effects/physiology ; Symbiosis ; },
abstract = {Alongside the crisis of antimicrobial-resistant gonorrhea is the threat of bystander selection on commensal Neisseria. As Neisseria species are permissive to gene flow across lineages, their evolutionary fates are irrevocably intertwined. Horizontal gene transfer (HGT) within the genus occurs through transformation and exchange of plasmids through conjugation. Both mechanisms of HGT threaten the long-term efficacy of antimicrobial treatments, with resistance passed between commensals and pathogens multiple times (e.g., mosaic penA and mtr alleles). Here, we underscore the importance of commensal Neisseria as a bubbling cauldron of adaptive solutions for pathogenic Neisseria, review the mechanisms of resistance harbored by commensals and transferred to the gonococcus, and discuss the impact of contemporary selective pressures on the future evolutionary trajectory of the genus. Ultimately, we believe that predicting the future efficacy of antimicrobials for the treatment of gonorrhea will only be successful if the commensal Neisseria are also considered.},
}

*Gonorrhea/microbiology/drug therapy
Humans
*Anti-Bacterial Agents/pharmacology/therapeutic use
Gene Transfer, Horizontal
*Neisseria gonorrhoeae/genetics/drug effects/physiology
*Drug Resistance, Bacterial
*Neisseria/genetics/drug effects/physiology
Symbiosis

@article {pmid41127838,
year = {2025},
author = {Li, X and Wei, L and Li, L and Huang, H and Chen, Y},
title = {Microbial Metabolites: An Underexploited Arsenal to Combat Antibiotic Resistance Dissemination.},
journal = {Environment & health (Washington, D.C.)},
volume = {3},
number = {10},
pages = {1121-1124},
pmid = {41127838},
issn = {2833-8278},
abstract = {The relentless global proliferation of antibiotic resistance genes (ARGs) poses a profound threat to public health and ecological stability. Unlike static chemical pollutants, ARGs propagate through horizontal gene transfer (HGT)(?)a dynamic biological process that facilitates the cross-taxa dissemination of resistance determinants among environmental, commensal, and pathogenic microbes. This ecological amplification of resistance undermines both clinical therapies and environmental resilience, rendering the understanding and control of ARG dissemination a critical challenge in the fight against antibiotic resistance.},
}

@article {pmid41125819,
year = {2025},
author = {Naseem, H and Haider, Z and Mannan, S and Rehman, SU},
title = {Genomic and physiochemical characterization of two lysogenic bacteriophages, ΦCP5(17) and ΦCP17(i), infecting Clostridium perfringens.},
journal = {Archives of virology},
volume = {170},
number = {11},
pages = {229},
pmid = {41125819},
issn = {1432-8798},
support = {110413//IDRC/ ; },
mesh = {*Clostridium perfringens/virology ; *Genome, Viral ; *Bacteriophages/genetics/isolation & purification/ultrastructure/classification/physiology ; Host Specificity ; Lysogeny ; Podoviridae/genetics/isolation & purification/ultrastructure/classification ; Sewage/virology ; Phylogeny ; Hydrogen-Ion Concentration ; Animals ; Temperature ; },
abstract = {Group A Clostridium perfringens is a major poultry pathogen that causes necrotic enteritis. The molecular similarity of its toxins to those of other bacterial species suggests the involvement of horizontal gene transfer through mobile genetic elements or bacteriophages. Lysogenic bacteriophages play an important role in bacterial evolution through horizontal gene transfer. In the present study, we examined and compared the physiochemical characteristics, genome sequences, and tail fiber proteins of two lysogenic bacteriophages infecting C. perfringens. Bacteriophages ΦCP5(17) and ΦCP17(i) were isolated from a sewage sample and tested for their stability at different temperatures and pH conditions, and in simulated gastric fluids. The genomes of these phages were sequenced, and their morphology was examined by electron microscopy. Both phages produced circular, hazy plaques on their host bacteria and were stable up to 60°C, exhibiting optimal activity at pH 7-8. Both bacteriophages were found to have a very narrow host range, with ΦCP17(i) exhibiting a slightly broader host range than ΦCP5(17). Both phages exhibited podovirus morphology and a genome size of 17.8 kb and 17.9 kb for ΦCP5(17) and ΦCP17(i), respectively. According to the ICTV classification system, ΦCP5(17) and ΦCP17(i) belong to the genus Brucesealvirus, family Guelinviridae, and class Caudoviricetes. These phages share 95.6% genomic nucleotide sequence identity, suggesting that they belong to the same species but differ at the subspecies level. Although ΦCP5(17) and ΦCP17(i) have similar morphological and genomic features, their tail fiber proteins differ in their predicted folding patterns. Nucleotide sequence analysis indicated the absence of toxin and antibiotic resistance genes. Both phages encode a SpoVG protein, whose functional role requires further investigation.},
}

*Clostridium perfringens/virology
*Genome, Viral
*Bacteriophages/genetics/isolation & purification/ultrastructure/classification/physiology
Host Specificity
Lysogeny
Podoviridae/genetics/isolation & purification/ultrastructure/classification
Sewage/virology
Phylogeny
Hydrogen-Ion Concentration
Animals
Temperature

@article {pmid41123117,
year = {2025},
author = {Pu, Q and Hao, Z and Zhang, Q and Zhang, K and Meng, B and Feng, X},
title = {Cadmium Elevates Methylmercury Levels in Rice Paddies via Microbial Adaptation and Biogeochemical Alterations.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c12718},
pmid = {41123117},
issn = {1520-5851},
abstract = {Methylmercury (MeHg) in rice poses significant health risks to populations with rice-based diets. While cadmium (Cd) contamination of paddy soils is widespread, its role in influencing MeHg accumulation in rice remains unclear. We combined a nationwide survey of 103 rice paddies with controlled pot and incubation experiments to examine how Cd affects MeHg in soils and rice grains. Soil geochemical parameters, microbial community composition, and horizontal gene transfer (HGT) of functional genes were analyzed to disentangle biological and geochemical mechanisms. Across field sites, Cd concentrations were positively associated with rice MeHg levels, independent of total Hg. Pot and incubation experiments confirmed that Cd exposure increased MeHg levels in soils and grains. This enhancement was mediated by both microbial and geochemical pathways: Cd reshaped microbial communities, promoted HGT that conferred Cd resistance to Hg-methylating bacteria, and altered soil redox potential and dissolved organic carbon, thereby creating conditions favorable for Hg methylation. Our findings reveal Cd as a previously overlooked driver of MeHg risk in rice agroecosystems. Given the co-occurrence of Cd and Hg pollution in global rice-growing regions, integrated management of multiple metals is needed to mitigate MeHg exposure through rice consumption.},
}

@article {pmid41120846,
year = {2025},
author = {Anik, TA and Islam, F and Uzzaman, R and Begum, SA and Akhter, H and Begum, A},
title = {Whole-genome sequencing and genomic characterization of a novel multi-drug resistant esxA-positive Staphylococcus haemolyticus DUEML1 (ST-184) isolated from a respiratory infection case: insights from panresistome analysis.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {677},
pmid = {41120846},
issn = {1471-2180},
abstract = {BACKGROUND: Staphylococcus haemolyticus is a coagulase-negative staphylococcal species and an opportunistic pathogen associated with hospital-acquired infections. The aim of this study was to use whole-genome sequencing (WGS) to characterize a novel multidrug-resistant (MDR) S. haemolyticus strain, DUEML1 (ST-184), isolated from a respiratory infection case in Bangladesh, and to place its resistome and virulence features in the context of global S. haemolyticus isolates.

METHODS: The isolate was obtained in pure culture from the tracheal aspirate of a 51-year-old male patient with respiratory infection, suggesting it was the primary causative agent. WGS was the primary method to analyze the genome of the isolated strain and subsequent in-silico analyses were performed to identify antimicrobial resistance genes, virulence factors, plasmid-associated genes, mobile genetic elements (MGEs), and prophages. Comparative pan-resistome analysis was conducted using 694 publicly available S. haemolyticus genomes retrieved from NCBI.

RESULTS: The isolate exhibited in vitro resistance to levofloxacin, ciprofloxacin, tetracycline, doxycycline, gentamicin, and trimethoprim-sulfamethoxazole, as determined by the disc diffusion test, and demonstrated the capacity for biofilm formation. Several antimicrobial resistance genes (ARGs) such as fosBx1, mgrA, norC, sdrM, sepA and two virulence genes, including esxA and cap8G were detected. To our knowledge, this is the first report of an esxA-positive S. haemolyticus isolate, recovered from a respiratory infection case in Dhaka, Bangladesh. Two plasmid-associated genes repUS23 and repUS46 were detected. Further analyses predicted 63 horizontal gene transfer (HGT) events and identified 147 MGEs, including integration/excision elements, recombination and repair-associated genes, and prophage-associated regions. With a new variant of arcC allele (arcC-38), the isolate was assigned to a novel ST-184. The PathogenFinder predicted a 93% probability that ST-184 is a human pathogen. A comparative analysis of 694 genome sequences identified a wide variety of ARGs, virulence factors, and plasmids in S. haemolyticus isolates from 35 different countries.

CONCLUSION: This study provides the first genomic characterization of a novel S. haemolyticus ST-184 isolate from Bangladesh, highlighting its multidrug-resistant nature and virulence potential. A limitation of this work is the lack of clinical treatment outcome data. Future research should include large-scale genomic surveillance to strengthen our understanding of the genomic architecture of S. haemolyticus.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-025-04406-5.},
}

@article {pmid41120633,
year = {2025},
author = {Feng, Y and Ding, J and Lin, Y and Cui, D and Li, K and Zheng, D and Cai, Z and Bell, SD and Wu, F},
title = {Serial innovations by Asgard archaea shaped the DNA replication machinery of the early eukaryotic ancestor.},
journal = {Nature ecology & evolution},
volume = {},
number = {},
pages = {},
pmid = {41120633},
issn = {2397-334X},
support = {32370003//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {The last eukaryotic common ancestor primarily inherited its core genetic system from archaea. However, it remains unclear when and how these essential machineries expanded their compositional and regulatory sophistication during eukaryogenesis. Here we combine statistical, phylogenetic, structural and biochemical approaches to examine the compositional diversity of the DNA replication machinery, that is, the replisome, across archaea and eukaryotes. We find that different lineages of Asgard archaea encode distinct replisome components with eukaryotic signatures, including a Baldrarchaeia-encoded DNA polymerase δ-like complex, a Sif/Wukong/Heimdallarchaeia-encoded primase complex and a Lokiarchaeales-encoded RFC clamp-loader complex. Copy number expansions driven by horizontal gene transfer probably contributed to the structural diversification of Asgard archaeal replisomes, including phylogenomic markers RfcS and Fen1, which were previously presumed to be transmitted vertically. Our analyses suggest that these distributed innovations were sequentially acquired by the early eukaryotic ancestor before the burst of gene duplications leading to the last eukaryotic common ancestor. By placing the captured events of gene gain and loss within the context of archaea-eukaryote evolution-as inferred from the phylogeny of concatenated single-copy replisome genes-we propose a hypothetical model for the emergence of the complex eukaryotic replisome.},
}

@article {pmid41117958,
year = {2025},
author = {Koech, N and Muoma, J and Banerjee, A and Okoth, P and Wekesa, C},
title = {Modular evolution and regulatory diversification of nodD-like LysR-type transcriptional regulators in α-Proteobacteria.},
journal = {Archives of microbiology},
volume = {207},
number = {12},
pages = {327},
pmid = {41117958},
issn = {1432-072X},
mesh = {*Bacterial Proteins/genetics/metabolism/chemistry ; *Transcription Factors/genetics/metabolism/chemistry ; *Gene Expression Regulation, Bacterial ; *Evolution, Molecular ; *Alphaproteobacteria/genetics/classification/metabolism ; Phylogeny ; Gene Transfer, Horizontal ; Genome, Bacterial ; Operon ; Symbiosis ; },
abstract = {The nodD gene encodes a LysR-type transcriptional regulator critical for nodulation gene expression in rhizobia, yet its evolutionary origin, structural plasticity, and regulatory reach beyond symbiosis remain incompletely resolved. Here we investigate the genomic organization, structural variation, and functional diversification of nodD and its homologs across α-proteobacteria with selected outgroups. Using orthogroup-based pangenome clustering, dated species trees, and gene-tree-species-tree reconciliation, we reconstruct the evolutionary trajectory of nodD, indicating emergence from ancient LTTRs deep in proteobacterial history. Reconciliation reveals widespread duplication and horizontal gene transfer (HGT), with several rhizobia showing notable duplication and exchange, and marine/non-rhizobial taxa contributing to a mosaic of nodD-like genes. Gene-neighborhood and operon analyses show conserved syntenic tendencies in classical rhizobia but extensive architectural divergence in free-living lineages, including frequent monocistronic anchors with extended upstream regions and, when polycistronic, enrichment for transporters and local metabolic enzymes within compact multi-regulator cassettes. Structural comparisons with AlphaFold and PyMOL confirm the canonical LTTR fold while uncovering species-specific deviations concentrated in effector-binding loops and interfaces. Motif discovery and genome-wide scanning identify targets involved in metabolism, stress responses, and transcriptional control, and network analysis reveals modular connectivity spanning core metabolism and accessory processes such as secondary metabolism, transport, and biofilm-associated functions. These findings portray nodD as a structurally conserved yet functionally flexible regulator repeatedly reshaped by duplication, HGT, and local genome context, extending nodD-like systems beyond symbiosis and broadening the regulatory landscape of bacterial LTTRs.},
}

*Bacterial Proteins/genetics/metabolism/chemistry
*Transcription Factors/genetics/metabolism/chemistry
*Gene Expression Regulation, Bacterial
*Evolution, Molecular
*Alphaproteobacteria/genetics/classification/metabolism
Phylogeny
Gene Transfer, Horizontal
Genome, Bacterial
Operon
Symbiosis

@article {pmid40970725,
year = {2025},
author = {Leng, J and Ferrandis-Vila, M and Oldenkamp, R and Mehat, JW and Fivian-Hughes, AS and Kumar Tiwari, S and Van der Putten, B and Trung Nguyen, V and Bethe, A and Clark, J and Singh, P and Semmler, T and Schwarz, S and Alvarez, J and Hoa, NT and Bootsma, M and Menge, C and Berens, C and Schultsz, C and Ritchie, JM and La Ragione, RM},
title = {Evidence of ESBL plasmid transfer and selective persistence of multiple host-associated Escherichia coli isolates in a chicken cecal fermentation model.},
journal = {Applied and environmental microbiology},
volume = {91},
number = {10},
pages = {e0082225},
doi = {10.1128/aem.00822-25},
pmid = {40970725},
issn = {1098-5336},
mesh = {Animals ; *Escherichia coli/genetics/drug effects/isolation & purification/enzymology ; Chickens/microbiology ; *Cecum/microbiology ; *beta-Lactamases/genetics/metabolism ; *Plasmids/genetics ; Cattle ; Swine ; Fermentation ; *Gene Transfer, Horizontal ; *Escherichia coli Infections/microbiology/veterinary ; Anti-Bacterial Agents/pharmacology ; },
abstract = {The guts of animals and humans harbor diverse microbial communities that are regularly exposed to bacteria originating from food, water, and their surroundings. Species such as Escherichia coli are adept at colonizing multiple hosts, along with surviving in the environment. By encoding pathogenic traits and transmissible forms of antimicrobial resistance (AMR), E. coli can also pose a zoonotic risk. Our understanding of the factors that govern host residency is limited. Here, we used a chicken cecal fermentation model to study survival and the AMR transfer potential of 17 host-associated extended-spectrum β-lactamase (ESBL)-producing E. coli isolates. Vessels containing chicken cecal contents were stabilized for 4 days before the addition of a cocktail comprising ESBL-producing E. coli obtained from human, cattle, pig, and chicken hosts. Consecutive sampling showed that pig and cattle-associated isolates persisted in most vessels, although the recovery of all isolates declined over time. Increasing the inoculum dose or adding ceftiofur helped to stabilize populations of ESBL E. coli within the vessels, although this did not result in outgrowth of resistant populations in all vessels. Sequencing revealed that most new ESBL-producing E. coli recovered during the study acquired a blaCTX-M-1 plasmid from a single ESBL E. coli included in the cocktail that lacked host-specific traits (generalist). Our data highlight that isolate-specific differences in the E. coli genome composition likely explain the persistence of specific clones and efficiency of plasmid transfer, both of which could impact the spread of AMR in complex communities.IMPORTANCEThere are few insights into how host-associated Escherichia coli behave within the gut environment of other hosts. E. coli isolates that are immigrants to the gastrointestinal system of humans and animals have the potential to transfer their resistance to other native bacteria. A better understanding of this process is needed to assess how the gastrointestinal environment could serve as a reservoir and a melting pot of new, multidrug-resistant E. coli isolates.},
}

Animals
*Escherichia coli/genetics/drug effects/isolation & purification/enzymology
Chickens/microbiology
*Cecum/microbiology
*beta-Lactamases/genetics/metabolism
*Plasmids/genetics
Cattle
Swine
Fermentation
*Gene Transfer, Horizontal
*Escherichia coli Infections/microbiology/veterinary
Anti-Bacterial Agents/pharmacology

@article {pmid41114150,
year = {2025},
author = {Chen, Z and Zhou, W and Wang, Z and Chen, Z and You, X and Gong, Y},
title = {Analysis of the mitochondrial genome of the Camellia sinensis cv. 'Zhuyeqi': multichromosomal structure, RNA editing sites, and evolutionary characterization.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1644130},
pmid = {41114150},
issn = {1664-462X},
abstract = {INTRODUCTION: Tea (Camellia sinensis) is a significant economic crop, and investigations into the structure and function of its mitochondrial genome are crucial for understanding the evolutionary history and genetic characteristics of this species. This study presents the first comprehensive analysis of the mitochondrial genome of the tea cultivar 'Zhuyeqi' (Camellia sinensis cv. 'Zhuyeqi'), aiming to elucidate its genomic structural features, gene composition, and evolutionary patterns. The findings provide a theoretical foundation for genetic breeding and molecular biology research in tea plants.

METHODS: High-throughput sequencing was employed to sequence the mitochondrial genome of 'Zhuyeqi'. Bioinformatics approaches were utilized for genome assembly and annotation. Various analytical strategies, including identification of RNA editing sites, codon usage bias analysis, repeat sequence recognition, calculation of non-synonymous substitution rates (Ka) and synonymous substitution rates (Ks), comparative genomics, and collinearity analysis, were applied to comprehensively analyze the structural features and evolutionary dynamics of the mitochondrial genome.

RESULTS AND DISCUSSION: The mitochondrial genome of 'Zhuyeqi' consists of one circular chromosome and six linear chromosomes, with a total length of 911,255 bp and a GC content of 46%. Genome annotation identified 77 functional genes, including 38 protein-coding genes (PCGs). The study revealed heterogeneously distributed introns within genes such as trnM-CAT (5 copies) and nad1/2/5/7. RNA editing analysis identified 556 C-to-U editing sites, notably enriched in ccmFn (38 sites) and ccmB (34 sites). Codon usage bias analysis indicated that leucine (Leu, 10%) and arginine (Arg, 7%) were the most frequently used amino acids. Repeat sequence analysis showed that dispersed repeats (780, 72%) dominated, with satellite DNA exhibiting significant distribution biases on chr1 (11) and chr3 (5). Ka/Ks analysis revealed that 37 PCGs were under varying selective pressures (0.09-2.70), with rps4 (Pi=0.09) and atp8 (Pi=0.09) showing exceptionally high variability, while rps19 (Pi=0) was completely conserved. Comparative genomics uncovered 66 homologous segments (25,656 bp) between the mitochondrial and chloroplast genomes, containing 27 intact genes such as trnA-UGC, confirming horizontal gene transfer events. Collinearity analysis demonstrated a high degree of conservation in genomic structures between 'Zhuyeqi' and closely related Camellia species. This study lays an important theoretical foundation for further elucidating the structural characteristics and evolutionary mechanisms of the tea plant mitochondrial genome.},
}

@article {pmid41112119,
year = {2025},
author = {Pandey, D and Gupta, I and Gupta, D},
title = {AmpC β-lactamases: A key to antibiotic resistance in ESKAPE pathogens.},
journal = {Cell surface (Amsterdam, Netherlands)},
volume = {14},
number = {},
pages = {100154},
pmid = {41112119},
issn = {2468-2330},
abstract = {BACKGROUND: AmpC β-lactamases (blaAmpC) are essential drivers of antimicrobial resistance (AMR) in ESKAPE pathogens, bacteria that cause hospital-acquired infections. Understanding AmpC enzymes is essential for uncovering resistance mechanisms and guiding antimicrobial strategies. We analyzed blaAmpC presence, genomic location, copy number, sequence variability, and evolutionary traits in ESKAPE pathogens.

RESULTS: We identified 1790 AmpC enzymes in 4713 complete genomes, classified into nine enzyme groups. Consistent with known taxonomic profiles, no class C β-lactamases were detected in Gram-positive bacteria (Staphylococcus aureus and Enterococcus faecium). Acinetobacter baumannii exhibited the highest occurrence of class C β-lactamases, with Enterobacter spp. showing the second highest prevalence, followed by Pseudomonas aeruginosa and Klebsiella pneumoniae. The largest enzyme group, ADC was restricted to A. baumannii; similarly, ACC, ACT, CMH, and MIR to Enterobacter spp.; and PDC and PIB to P. aeruginosa. Phylogenetic analysis showed divergence among some groups and closer evolutionary relationships in others. Functional Motif analysis revealed conserved catalytic residues across all groups except PIB. Instead of the canonical YXN and KTG motifs, PIB contains YST and AQG variants, respectively. Because of these variations, PIB's ability to bind cephalosporins decreases while enhancing their activity against carbapenems.

CONCLUSIONS: We identified 1790 AmpC enzymes in nine distinct groups across ESKAPE pathogens, with species-specific distribution patterns and notable absence in Gram-positive bacteria. The PIB enzyme group demonstrated unique motif variants (YST/AQG) conferring carbapenem resistance, while other groups maintained conserved catalytic motifs. Phylogenetic analysis revealed evolutionary divergence and horizontal gene transfer potential, emphasizing the need for targeted therapeutic approaches against AmpC-mediated resistance.},
}

@article {pmid41109624,
year = {2025},
author = {Bu, C and Chen, C and Zhang, W and Zhang, R and Yu, J and Hua, Y and Zeng, H and Han, Y and Jia, R and Zhao, Q and Ruan, Y and Ma, L},
title = {Antibiotics, antibiotic resistance genes, and environmental drivers: Assessment of resistance pollution along the Yangtze River Basin.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {386},
number = {},
pages = {127284},
doi = {10.1016/j.envpol.2025.127284},
pmid = {41109624},
issn = {1873-6424},
abstract = {Antibiotic resistance pollution presents a significant global health challenge. The present study systematically investigated the occurrence of 50 antibiotics in the dissolved, suspended particulate matter phases, and surface sediments at 30 locations across the Yangtze River Basin (YRB). Eleven extracellular and intracellular antibiotic resistance genes (eARGs and iARGs) in surface sediments were quantified using fluorescence-based real-time quantitative polymerase chain reaction. Additionally, key relationships between ARGs, antibiotic concentrations, mobile genetic elements, microbial communities, and environmental factors were explored. Results revealed high levels of antibiotic contamination in the dissolved phase, with the cumulative concentration of the 50 target antibiotics ranging 857-7560 ng/L across various sections of the YRB. While iARGs predominated in absolute abundance, eARGs showed higher relative abundance. Mechanistic of intI1-mediated horizontal gene transfer as the principal pathway for the dissemination of ARGs. Redundancy analysis revealed that antibiotic concentrations, environmental factors, and microbial communities collectively explained 57.69 % of the variation in ARGs distribution. Among these, environmental variables such as conductivity and dissolved oxygen indirectly promote the enrichment of ARGs by influencing microbial communities. This study provided a theoretical basis for developing targeted prevention and control strategies against antibiotic resistance pollution in this extensive and economically critical watershed.},
}

@article {pmid41105518,
year = {2025},
author = {Shaw, S and Pragasam, AK and Chowdhury, G and Samanta, P and Roy, D and Ghosh, D and Ramamurthy, T and Karia, J and Ninama, G and Miyoshi, S-i and Akeda, Y and Koley, H and Mukhopadhyay, AK},
title = {Genomic portrayal of emerging carbapenem-resistant El Tor variant Vibrio cholerae O1.},
journal = {Antimicrobial agents and chemotherapy},
volume = {},
number = {},
pages = {e0074025},
doi = {10.1128/aac.00740-25},
pmid = {41105518},
issn = {1098-6596},
abstract = {The escalating prevalence of carbapenem-resistant (CR) enteric pathogens elicits significant challenges to public health management and effective antimicrobial therapy. While carbapenem resistance is rare in Vibrio cholerae O1 (VC), the recent emergence of CR strains reveals a concerning shift in their antimicrobial resistance (AMR) landscape. This study aims to characterize the resistance mechanisms in newly identified El Tor CRVC isolated from cholera patients in Gujarat, India during 2019. Fifty VC isolates were screened for major virulence-associated genes along with the determination of their antibiotic resistance profiles using Kirby-Bauer disk diffusion and MIC assays. Whole-genome sequencing (WGS) was employed to investigate the underlying mechanisms of CR. All the isolates exhibited hypervirulent Haitian alleles of major virulence genes and AMR profiles of typical multidrug resistance (MDR). Strikingly, 12% (6/50) of them were resistant to carbapenems and other antibiotics. Molecular analysis revealed that these CR isolates were clonally related and harbored a 142 kbp IncA/C type conjugative mega-plasmid with several AMR encoding genes, including blaNDM-1, that can be easily transferred to other bacterial species and confer donor AMR patterns. The plasmid's competence for horizontal gene transfer presents a significant risk of dissemination to other enteric pathogens and thereby may complicate the treatment. This finding emphasizes the urgent need for enhanced genomic surveillance and robust antimicrobial stewardship programs aimed at curbing the spread of CRVC strains and mitigating their impact on cholera treatment and containment strategies.},
}

@article {pmid41104936,
year = {2025},
author = {Hauschild, K and Suzuki, M and Wolters, B and Tokuda, M and Yamazaki, R and Masumoto, M and Moriuchi, R and Dohra, H and Bunk, B and Spröer, C and Shintani, M and Smalla, K},
title = {The transferable resistome of biosolids-plasmid sequencing reveals carriage of clinically relevant antibiotic resistance genes.},
journal = {mBio},
volume = {},
number = {},
pages = {e0206825},
doi = {10.1128/mbio.02068-25},
pmid = {41104936},
issn = {2150-7511},
abstract = {UNLABELLED: Biosolids, widely used as organic fertilizers due to their high nutrient content, are significant reservoirs for antimicrobial-resistant bacteria (ARB) carrying transferable antimicrobial resistance genes (ARGs). This study investigated the transferability of ARG-containing plasmids of bacteria from biosolids originating from 12 German wastewater treatment plants (WWTPs) of varying sizes. Using exogenous plasmid captures with the recipient strain Escherichia coli CV601 gfp+, we collected 103 plasmids from 11 WWTPs. Characterization through DNA-based methods, including real-time PCR and Southern blot hybridization, revealed that the highest proportion of transconjugants harbored IncP (57%) and IncN (20%) plasmids. Complete sequencing of representative plasmids identified IncPβ, IncPε, IncQ2, IncN, and IncU plasmids carrying ARGs linked to mobile genetic elements (MGEs), including class 1 integrons, transposons, and IS elements (e.g., Tn402, IS26, and IS6100). These ARG-MGE complexes were integrated into specific plasmid regions, and similar plasmids were found across WWTPs and diverse geographic locations. The results underscore the role of WWTPs as hotspots for horizontal gene transfer, with biosolids serving as reservoirs for multi-resistant bacteria and resistance plasmids. This highlights the urgent need for improved biosolid management strategies to mitigate the release of ARGs and ARB into agricultural environments.

IMPORTANCE: This study emphasizes the critical role of wastewater treatment plants (WWTPs) in facilitating the horizontal transfer of ARGs through biosolids. As biosolids are routinely applied to agricultural soils, their load of clinically relevant ARG content and transferability pose risks to animal and human health through plant-associated bacteria or surface water. By identifying conserved ARG-MGE associations across diverse plasmid types and WWTPs, this work highlights the global and persistent nature of resistance dissemination. These findings underscore the urgent need for sustainable management practices to limit the spread of antimicrobial-resistant bacteria (ARB) and associated ARGs in agricultural ecosystems. Ensuring safe biosolid use will contribute to combating antimicrobial resistance gene connectivity from environmental to human- or animal-associated bacteria globally.},
}

@article {pmid41005125,
year = {2026},
author = {Cross, BJ and Partridge, SR and Sheppard, AE},
title = {Impacts of mobile genetic elements on antimicrobial resistance genes in gram-negative pathogens: Current insights and genomic approaches.},
journal = {Microbiological research},
volume = {302},
number = {},
pages = {128340},
doi = {10.1016/j.micres.2025.128340},
pmid = {41005125},
issn = {1618-0623},
mesh = {*Interspersed Repetitive Sequences/genetics ; *Gram-Negative Bacteria/genetics/drug effects ; Gene Transfer, Horizontal ; *Drug Resistance, Bacterial/genetics ; Genomics/methods ; Genome, Bacterial ; Anti-Bacterial Agents/pharmacology ; Humans ; *Genes, Bacterial ; Plasmids/genetics ; },
abstract = {Antimicrobial resistance threatens to take 10 million lives per year by 2050. It is a recognised global health crisis and understanding the historic and current spread of resistance determinants is important for informing surveillance and control measures. The 'inheritance' of resistance is difficult to track because horizontal transfer is common. Antimicrobial resistance genes (ARGs) spread rapidly between bacteria, plasmids and chromosomes due to different mobile genetic elements (MGEs). This movement can increase the range of species carrying an ARG, simplify acquisition of multi-resistance, or otherwise alter the selective advantage associated with carriage of the ARG. MGE activity is therefore a significant factor in understanding routes of ARG dissemination. Characterising the combinations of MGEs contributing to the movement of individual ARGs is crucial. Each MGE category has unique genetic characteristics, and distinct impacts on the location and expression of associated ARGs. Here, the ways in which MGEs can meaningfully associate with ARGs are discussed. Approaches for extracting information about MGE associations from bacterial genome sequences are also considered. Accurate and informative annotations of the genetic contexts of relevant ARGs provide crucial insight into the presence of MGEs and their locations relative to ARGs. Combining this genomic information with knowledge about relevant biological processes allows more accurate conclusions to be drawn about transmission and dissemination of ARGs.},
}

*Interspersed Repetitive Sequences/genetics
*Gram-Negative Bacteria/genetics/drug effects
Gene Transfer, Horizontal
*Drug Resistance, Bacterial/genetics
Genomics/methods
Genome, Bacterial
Anti-Bacterial Agents/pharmacology
Humans
*Genes, Bacterial
Plasmids/genetics

@article {pmid41102171,
year = {2025},
author = {Leu, AO and Woodcroft, BJ and McIlroy, SJ and Tyson, GW},
title = {Potential for aerobic hydrocarbon oxidation in archaea.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {9188},
pmid = {41102171},
issn = {2041-1723},
mesh = {Oxidation-Reduction ; *Hydrocarbons/metabolism ; *Archaea/metabolism/genetics/classification ; Aerobiosis ; Phylogeny ; Genome, Archaeal ; Metagenome ; Gene Transfer, Horizontal ; Mixed Function Oxygenases/genetics/metabolism ; },
abstract = {Over the last decade, there have been significant advances in our understanding of anaerobic hydrocarbon oxidation in archaea. However, the ability to oxidise hydrocarbons aerobically has been described in bacteria but not yet in archaea. Here, we provide evidence supporting potential aerobic hydrocarbon oxidation ability in archaea belonging to a novel order within the class Syntropharchaeia, which we propose to name Candidatus 'Aerarchaeales'. This order is represented by six metagenome-assembled genomes (MAGs) spanning three genera that are found in terrestrial and marine ecosystems. In particular, MAGs belonging to a newly defined genus, Ca. 'Aerovita', encode a copper monooxygenase complex with homology to bacterial hydrocarbon monooxygenases. The presence of genes encoding other oxygen-dependent enzymes, such as haem-copper oxygen reductase, indicates that Ca. 'Aerovita' may be capable of aerobic respiration. Our findings suggest that horizontal gene transfer between archaeal and bacterial domains facilitated the evolution of aerobic hydrocarbon-oxidizing archaea.},
}

Oxidation-Reduction
*Hydrocarbons/metabolism
*Archaea/metabolism/genetics/classification
Aerobiosis
Phylogeny
Genome, Archaeal
Metagenome
Gene Transfer, Horizontal
Mixed Function Oxygenases/genetics/metabolism

@article {pmid41101560,
year = {2025},
author = {Lu, J and Zhou, A and Wang, D and Wan, S and Yang, Y and Lv, N and Li, J and Wu, G},
title = {Convergence of genetic variants in MCR-1 and O-antigen conferring polymyxin resistance and fitness cost.},
journal = {Journal of global antimicrobial resistance},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jgar.2025.10.005},
pmid = {41101560},
issn = {2213-7173},
abstract = {OBJECTIVE: The emergence of multidrug-resistant bacteria threatens public health, alongside the wide spread of opportunistic pathogens with a diversity of their serotypes. The fitness cost and morphological variations might result from O-antigen diversity and lipid A modification, while these reconfiguration in lipopolysaccharide (LPS) confer polymyxin resistance.

METHODS: Herein, a multidrug-resistant Escherichia coli named EcE.CRE.COL was isolated from a patient suffering therapeutic laparoscope for liver cancer. Antibiotic susceptibility was measured by the VITEK 2 system. Whole genome sequencing found a chromosome, three plasmids (namely pEcE.CRE.COL015, pEcE.CRE.COL016 and pEcE.CRE.COL032, respectively). Comparative genomics was conducted to identify genetic determinants accounting for multi-drug resistance.

RESULTS: This isolate exhibited distinguishing resistance to carbapenems and polymyxin. Interestingly, pEcE.CRE.COL015 and pEcE.CRE.COL032 harbors blaNDM-5 and mcr-1, accounting for corresponding antimicrobial resistance, respectively. We consequently proposed an evolutionary pattern on the spread of mcr-1, of which transposon-like architecture could play a key role in the dissemination of polymyxin resistance driven by mcr-1. In addition, a novel serotype gene cluster related to defective O-antigen synthesis was determined, likely resulting from a genetic insertion. As a result, SDS-PGAE indicated LPS defectiveness in this isolate, suggesting a different charge in EcE.CRE.COL membrane surface.

CONCLUSION: Collectively, co-occurrence of plasmid-borne mcr-1 and blaNDM-5 was determined, and genetic variations in LPS biosynthesis genes might contribute to a synergistic change in bacterial surface charge and corresponding electrostatics to polymyxin.},
}

@article {pmid41092706,
year = {2025},
author = {Zhang, X and Yang, B and Zhang, H and Guo, X and Zhang, Y},
title = {Nicosulfuron-driven antibiotic resistance in corn silage: Effect and its mitigation by zinc oxide nanoparticles.},
journal = {Journal of hazardous materials},
volume = {499},
number = {},
pages = {140119},
doi = {10.1016/j.jhazmat.2025.140119},
pmid = {41092706},
issn = {1873-3336},
abstract = {Antibiotic resistance genes (ARGs) present in animal feed represent a significant threat to human health via the food chain, and pesticide application in crop production may further accelerate the ARGs dissemination. Corn silage, a primary forage for herbivorous livestock, has been shown to harbor diverse ARGs; however, the impact of pesticide-induced stress and potential mitigation strategies on ARG proliferation remains poorly understood. This study investigated the mechanistic link between nicosulfuron exposure and ARG dynamics in corn silage, as well as the mitigating effects of zinc oxide nanoparticles (ZnO NPs) on ARG under nicosulfuron exposure using metagenomic sequencing and high-throughput quantitative PCR. Nicosulfuron exposure increased (P < 0.05) ARG diversity and abundance, enriched (P < 0.05) ARG-hosting genera such as Pantoea, Escherichia, and Klebsiella, and intensified (P < 0.05) the correlation between ARGs and mobile genetic elements (MGEs). Additionally, it disrupted microbial metabolic pathways and elevated (P < 0.05) the ARG-associated risk index in corn silage. Conversely, ZnO NPs alleviated (P < 0.05) these effects by reducing the abundance of key ARGs-bacA, tetM, and ermB, enhancing microbial diversity, promoting beneficial genera such as Levilactobacillus and Companilactobacillus, and decreasing the complexity of ARG-MGE-microbe co-occurrence networks in corn silage under nicosulfuron exposure. Structural equation modeling indicated that there was a significant association between bacterial community and ARGs proliferation, and it had the strongest explanatory power for the variation in ARGs abundance, followed by MGEs. These findings underscore the ecological risks associated with nicosulfuron and demonstrate that ZnO NPs have the potential to mitigate ARGs dissemination in pesticide-contaminated silage. However, this potential does not qualify ZnO NPs as an effective strategy, and their role in promoting safer forage production still requires further evaluation.},
}

@article {pmid41088812,
year = {2025},
author = {Wang, YX and Hu, JJ and Hou, JJ and Yuan, XJ and Chen, WJ and Li, YJ and Gao, QL and Pan, Y and Lu, SP and Chen, Q and Hu, SR and Shao, ZJ and Xiong, CL},
title = {(Meta)transcriptomic Insights into the Role of Ticks in Poxvirus Evolution and Transmission: A Multicontinental Analysis.},
journal = {Biomedical and environmental sciences : BES},
volume = {38},
number = {9},
pages = {1058-1070},
doi = {10.3967/bes2025.062},
pmid = {41088812},
issn = {2214-0190},
mesh = {Animals ; *Poxviridae/genetics/physiology ; *Ticks/virology ; Phylogeny ; *Transcriptome ; *Evolution, Molecular ; *Poxviridae Infections/transmission/virology ; Genome, Viral ; },
abstract = {OBJECTIVE: Poxviruses are zoonotic pathogens that infect humans, mammals, vertebrates, and arthropods. However, the specific role of ticks in transmission and evolution of these viruses remains unclear.

METHODS: Transcriptomic and metatranscriptomic raw data from 329 sampling pools of seven tick species across five continents were mined to assess the diversity and abundance of poxviruses. Chordopoxviral sequences were assembled and subjected to phylogenetic analysis to trace the origins of the unblasted fragments within these sequences.

RESULTS: Fifty-eight poxvirus species, representing two subfamilies and 20 genera, were identified, with 212 poxviral sequences assembled. A substantial proportion of AT-rich fragments were detected in the assembled poxviral genomes. These genomic sequences contained fragments originating from rodents, archaea, and arthropods.

CONCLUSION: Our findings indicate that ticks play a significant role in the transmission and evolution of poxviruses. These viruses demonstrate the capacity to modulate virulence and adaptability through horizontal gene transfer, gene recombination, and gene mutations, thereby promoting co-existence and co-evolution with their hosts. This study advances understanding of the ecological dynamics of poxvirus transmission and evolution and highlights the potential role of ticks as vectors and vessels in these processes.},
}

Animals
*Poxviridae/genetics/physiology
*Ticks/virology
Phylogeny
*Transcriptome
*Evolution, Molecular
*Poxviridae Infections/transmission/virology
Genome, Viral

@article {pmid41086969,
year = {2025},
author = {Min, B and Xie, J and He, Y and Lin, R and Azari, M and Xie, L},
title = {Role of biofilm carriers in sulfamethoxazole removal and microbial adaptation strategies in integrated fixed-film activated sludge system.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133481},
doi = {10.1016/j.biortech.2025.133481},
pmid = {41086969},
issn = {1873-2976},
abstract = {Attached-growth biofilm processes using specific biofilm carriers are widely employed to enhance antibiotic removal. However, the relationship between antibiotic degradation, resistance risks and microbial adaptation strategies across different carriers is not yet fully understood. Hence, four common biofilm systems, including iron-carbon (Fe@C), granular activated carbon (GAC), ceramic (CE), and polyurethane (PU), were evaluated for sulfamethoxazole (SMX) removal and antibiotic resistance genes (ARGs) risks. GAC and Fe@C systems exhibited higher SMX removal performance, achieving removal efficiency > 99.0 % and 63.8 %, respectively, compared to other carriers (17.4-49.8 %). Moreover, GAC reduced ARGs by 34.8-47.7 % via inhibiting horizontal gene transfer, as demonstrated by a 50.6-74.5 % decrease in core MGEs (intI1_337old, IS6100, and tnpA-2). Conversely, Fe@C exacerbated ARGs accumulation. The high specific surface area and rich pore structure of GAC promoted the colonization of potential SMX-degrading bacteria, notably Thauera, and shaped a multifunctional biofilm system. GAC biofilms exhibited distinct advantages in signal transduction and biofilm formation pathways. Meanwhile, the adsorption capacity of the GAC carrier created a hotspot for SMX biodegradation. This study provides a comprehensive understanding of antibiotic removal and spread of ARGs through the biofilm process.},
}

@article {pmid41086015,
year = {2025},
author = {Sünderhauf, D and Winter, M and Ramshaw, J and Stevenson, EM and Vos, M},
title = {Seaweed exposure modulates Escherichia coli plasmid conjugation rate.},
journal = {Microbiology (Reading, England)},
volume = {171},
number = {10},
pages = {},
doi = {10.1099/mic.0.001622},
pmid = {41086015},
issn = {1465-2080},
mesh = {*Escherichia coli/genetics/physiology ; *Plasmids/genetics ; *Conjugation, Genetic ; *Seaweed/microbiology ; Ulva ; Gene Transfer, Horizontal ; Fucus ; },
abstract = {Seaweeds are a common and diverse component of coastal ecosystems and are known to be associated with Escherichia coli due to faecal pollution. As a biotic substrate, beach-cast seaweed may affect bacterial physiology and thereby horizontal gene transfer (HGT). Here, we test how the presence of three distinct senescing seaweed species affects E. coli plasmid conjugation. We allow the IncP plasmid pKJK5 to conjugate while supplying a substrate of Palmaria palmata (dulse), Ulva lactuca (sea lettuce) or Fucus serratus (serrated wrack). The three seaweed species induce distinct conjugative behaviours in E. coli: U. lactuca has no significant impact relative to a plastic control, the presence of F. serratus results in undetectable levels of conjugation and P. palmata promotes conjugation in a density-independent manner. This study highlights how biotic interactions can influence survival, HGT and antibiotic resistance in a human pathogen.},
}

*Escherichia coli/genetics/physiology
*Plasmids/genetics
*Conjugation, Genetic
*Seaweed/microbiology
Ulva
Gene Transfer, Horizontal
Fucus

@article {pmid40939716,
year = {2025},
author = {Zhang, H and Shao, Y and Li, T and Liu, W and Huang, Y and Jiang, Y and Wang, Z and Xiao, X},
title = {UV-aged biodegradable and non-biodegradable microplastics further enhance horizontal transfer of antibiotic resistance plasmids both in vitro and in intestinal flora.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {385},
number = {},
pages = {127111},
doi = {10.1016/j.envpol.2025.127111},
pmid = {40939716},
issn = {1873-6424},
mesh = {*Microplastics/toxicity ; *Plasmids ; Ultraviolet Rays ; *Gastrointestinal Microbiome/drug effects ; *Gene Transfer, Horizontal ; *Drug Resistance, Microbial/genetics ; },
abstract = {Microplastics is a well-known environmental contaminant that have raised concerns regarding their role in spreading antibiotic resistance genes (ARGs). This study investigates the effect of ultraviolet (UV) aging of 100 nm petroleum-based (polystyrene, PS) and bio-based (polylactic acid, PLA) microplastics on the horizontal transfer of multidrug resistance plasmids. Both PS and PLA significantly increase the frequency of horizontal spread of ARGs, and UV aging of both PS and PLA microplastics further enhance this frequency by 4- to 20-fold, implying that environmental elements, including UV radiation, may increase the ecological danger caused by microplastics. UV aging significantly alters the surface properties of both PS and PLA microplastics and disrupted the integrity of bacterial cell membranes. Moreover, UV-aged microplastics increased cellular uptakes and exacerbated oxidative stress in bacteria by elevating ROS levels and SOD activity. In addition, UV-aged microplastics improved bacterial energy metabolism, providing additional ATP for conjugation process. Finally, UV-aged microplastics aggravated oxidative stress and intestinal inflammation in gut which further promoted the plasmid conjugation rate in vivo by 3.5-fold. The findings not only draw attention to the important role of UV-aged microplastics in permitting ARG spread but also urge thorough risk assessments of degradation of microplastics on public health and ecosystems.},
}

*Microplastics/toxicity
*Plasmids
Ultraviolet Rays
*Gastrointestinal Microbiome/drug effects
*Gene Transfer, Horizontal
*Drug Resistance, Microbial/genetics

@article {pmid41082848,
year = {2025},
author = {Chu, W and Li, X and Li, P and Li, J and Wang, Z and Zhou, H and Yang, X and Chen, S and Zhou, M and Wang, S and Zheng, J and Chen, Y and Yu, Y and Tan, Z},
title = {Enhanced treatment of low C/N domestic wastewater in a membrane photobioreactor: Operational control of microalgal-bacterial symbiosis for synergistic pollutant and antibiotic resistance genes removal.},
journal = {Journal of environmental management},
volume = {394},
number = {},
pages = {127398},
doi = {10.1016/j.jenvman.2025.127398},
pmid = {41082848},
issn = {1095-8630},
abstract = {Conventional wastewater treatment technologies face significant limitations, including high CO2 emissions, poor resource recovery, and growing challenges from emerging contaminants such as antibiotics and their associated antibiotic resistance genes (ARGs), which pose serious risks to aquatic ecosystems and public health. In response to these challenges and within the framework of China's carbon neutrality goals, this study developed a microalgae-activated sludge membrane photobioreactor (MPBR) to enable synergistic pollutant removal and resource recovery from low carbon-to-nitrogen (C/N) domestic wastewater. Under the optimized internal circulation flow rate of 13.5 m[3]/d, the MPBR system achieved high removal efficiencies for ammonia nitrogen (NH4[+]-N, 99.48 %), total nitrogen (TN, 72.89 %), chemical oxygen demand (COD, 63.20 %), and total phosphorus (TP, 80.37 %). Simultaneously, ARGs and mobile genetic elements (MGEs) were reduced by approximately one log, attributed to two primary mechanisms: (1) suppression of ARGs in the sludge zone through the regulation of drug-resistant bacterial populations, and (2) inhibition of horizontal gene transfer in the microalgal zone via nitrogen-driven suppression of ARGs host bacteria, as well as enhanced microalgae-bacteria co-metabolism and community optimization. Furthermore, the optimization of microalgae photosynthesis and nitrogen cycling, along with microbial cooperation under anoxic conditions, supported efficient nutrient recovery while maintaining low-carbon operation. This study offers a novel, carbon-efficient strategy for integrating wastewater purification with ARGs risk mitigation, contributing to sustainable water management aligned with the circular economy and carbon neutrality objectives.},
}

@article {pmid41081360,
year = {2025},
author = {Shin, NR and Duncan, M and Adams, R and McKenna, DD},
title = {250 Million Years of Convergent Evolution and Functional Divergence of Glycoside Hydrolase Family 28 Genes in Xylophagous Beetles (Cerambycidae and Buprestidae): Insights Into Horizontal Gene Transfer, Gene Dynamics, Synteny and Adaptive Divergence.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e70131},
doi = {10.1111/mec.70131},
pmid = {41081360},
issn = {1365-294X},
support = {DEB1355169//National Science Foundation/ ; DEB2110053//National Science Foundation/ ; },
abstract = {Wood-feeding beetles harbour diverse gene families involved in plant cell wall degradation, including glycoside hydrolase family 28 (GH28) genes, which function as polygalacturonases. These genes are believed to have originated from microbial donors via horizontal gene transfers (HGT), followed by gene duplications. However, the evolutionary history of GH28 genes across independently evolved wood-feeding beetle lineages remains unclear. Here, we investigate the distribution, origin and diversification of GH28 genes in two xylophagous beetle groups, Cerambycidae: Lamiinae and Buprestidae: Agrilinae, which diverged over 250 million years ago. Phylogenetic analyses reveal that both groups possess GH28 genes most likely derived from ascomycete fungi, which are distinct from the 'ancestral-type' GH28 genes found in other Cerambycidae. Thus, Lamiinae and Agrilinae acquired similar 'new-type' GH28 genes via convergent HGT events. Comparative genomic analyses show conserved synteny around GH28 loci within each beetle subfamily, but not between them, consistent with independent acquisitions and endogenous retention. Subsequent lineage-specific duplications resulted in the expansion of GH28 gene copies, with protein structural modelling revealing divergent active sites and substrate-binding regions, suggesting functional differentiation and adaptation to distinct ecological contexts. Signatures of positive selection further support adaptive evolution of GH28 enzymes in both groups. Our findings demonstrate convergent acquisition and diversification of GH28 genes in distantly related xylophagous beetles, highlighting the roles of HGT, gene duplication and structural divergence in driving functional innovation. These results underscore how plant cell wall-degrading enzymes have contributed to trophic specialisation and the evolutionary success of specialised phytophagous beetles.},
}

@article {pmid40960772,
year = {2025},
author = {Li, Q and Zhang, LY and Zhou, YJ and Cui, HL and Ren, YJ and Gao, SH and Wang, AJ and Liang, B},
title = {Positive Contribution of Antimicrobial Biodegradation in Mitigating Conjugative Transfer of Antibiotic Resistance Genes.},
journal = {Environmental science & technology},
volume = {59},
number = {40},
pages = {21645-21656},
doi = {10.1021/acs.est.5c06928},
pmid = {40960772},
issn = {1520-5851},
mesh = {Biodegradation, Environmental ; *Drug Resistance, Microbial/genetics ; Gene Transfer, Horizontal ; Anti-Bacterial Agents ; Plasmids ; Drug Resistance, Bacterial/genetics ; Anti-Infective Agents ; },
abstract = {The evolution and spread of antimicrobial resistance (AMR) are common global challenge. However, little is known about the regulatory role and mechanisms of antimicrobial biodegradation processes in the transmission of antibiotic resistance genes (ARGs) in the environment. Here, we explored the effects of commonly used antimicrobials (chloramphenicol, sulfamethoxazole, triclocarban, trimethoprim, and parachlorometa-xylenol), their mixtures, and biodegradation processes on the conjugative transfer of plasmid-mediated ARGs from simple populations to complex communities. The findings show that antimicrobials can induce a series of reactions, including increased levels of reactive oxygen species, enhanced cell membrane permeability, and accelerated ATP synthesis, which in turn promote the horizontal transfer of ARGs. Importantly, antimicrobial biodegradation treatments significantly reduce the selective stress of antimicrobials, diminishing the transcription of key relevant genes and controlling the ARG conjugative transfer. Moreover, our findings emphasize the crucial role of antimicrobial biodegradation in reducing the abundance of high-risk pathogen microorganisms in actual community conjugative transference, thereby mitigating the negative health risks posed by antimicrobials. Our results highlight the positive contribution of antimicrobial biodegradation to impede the horizontal transfer of ARGs and provide a scientific basis for developing intervention strategies to manage and mitigate AMR development.},
}

Biodegradation, Environmental
*Drug Resistance, Microbial/genetics
Gene Transfer, Horizontal
Anti-Bacterial Agents
Plasmids
Drug Resistance, Bacterial/genetics
Anti-Infective Agents

@article {pmid41080529,
year = {2025},
author = {Stark, GF and Smith, LE and Truchon, AR and Martin, RM and Denison, ER and Wilhelm, SW},
title = {Microcystis plasmids: the unexplored portion of the mobilome and the presence of potential phage-like plasmids.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf154},
pmid = {41080529},
issn = {2730-6151},
abstract = {While resequencing Microcystis aeruginosa (PCC7806) and its nontoxigenic mutant (PCC7806 ΔmcyB), we discovered identical unreported plasmids in both strains. These strains were separated in culture over 25 years ago, resulting in sequence divergence among their chromosomes. RNA-seq data demonstrated these plasmids were transcriptionally active during chemostat growth. Moreover, in situ metatranscriptomes from Lake Erie revealed genes like those on the PCC7806 plasmid were expressed in the environment. As we investigated plasmids in Microcystis, we found that M. aeruginosa NIES-298 also had a putatively conserved plasmid, but with phage-like features. To gain an understanding of the ecological relevance of these plasmids, we examined Lake Erie metatranscriptomes and found that transcript abundance for predicted plasmid-like contigs was significantly higher than predicted virus-like contigs across the microbial community: this trend was also present when metatranscriptomic reads were mapped to Microcystis-infecting phage and Microcystis-specific plasmid genomes. Our observations demonstrate a potential ecological importance and stability of these extrachromosomal elements in Microcystis. Additionally, this work draws attention to the potential overlap between Microcystis plasmid and phage genomes, and how this may complicate molecular investigations.},
}

@article {pmid41080486,
year = {2025},
author = {Huang, YX and Lv, JM and Ding, CY and Zheng, XY and Liu, XJ and Chen, XN and Yu, SH and Meng, YF and Hu, HY and Wang, X},
title = {Genomic Evolution and Patterns of Horizontal Gene Transfer in Coccomorpha Species.},
journal = {Ecology and evolution},
volume = {15},
number = {10},
pages = {e72158},
pmid = {41080486},
issn = {2045-7758},
abstract = {As a significant group of agricultural and forestry pests, Coccomorpha warrants in-depth investigation into their environmental adaptation mechanisms. This study conducted a comparative genomic analysis using five published chromosome-level genomes of Coccomorpha species. Phylogenetic analysis revealed that the divergence times of these five species ranged from 333.18 to 84.22 million years ago (mya), with each having undergone two whole-genome duplication (WGD) events. The significantly expanded gene families in these species were predominantly enriched in antioxidant-related processes such as oxoacid metabolic process, organic acid metabolic process, and carboxylic acid metabolic process. Furthermore, 260 horizontal gene transfer (HGT) acquired genes were identified across these species, primarily originating from bacteria and archaea. These HGT-acquired genes were mainly involved in nutrient metabolism, suggesting their role in enhancing nutritional acquisition and metabolic flexibility. Through systematic identification of detoxification-related genes, ATP-binding cassette (ABC), carboxylesterases (COE), cytochrome P450, and UDP-glucuronosyltransferases (UGT) were identified as the major detoxification gene families in Coccomorpha, with significant variations in gene number and composition among different species. This study provides comprehensive insights into the genomic adaptations of Coccomorpha species, highlighting the roles of gene family dynamics, HGT, and detoxification mechanisms in their evolutionary success. These findings offer resources for understanding the molecular basis of Coccomorpha adaptation and provide references for developing targeted pest management strategies.},
}

@article {pmid41076908,
year = {2025},
author = {Chen, H and Yi, J and Li, Y and Li, X and Zhang, H and Yang, X and Zhong, H and Yu, G and Qiu, R and Chong, Y},
title = {Accumulation and translocation of antibiotic resistance genes in plants cultivated in hydroponic systems with nitrified biogas slurry.},
journal = {Journal of hazardous materials},
volume = {499},
number = {},
pages = {140092},
doi = {10.1016/j.jhazmat.2025.140092},
pmid = {41076908},
issn = {1873-3336},
abstract = {Hydroponic cultivation with biogas slurry supports nutrient recycling but raises biosafety concerns due to the dissemination of antibiotic resistance genes (ARGs). This study established a hydroponic system using nitrified biogas slurry to grow lettuce and cherry radish, and systematically investigated the accumulation of ARGs, mobile genetic elements (MGEs), high-priority human pathogenic bacteria (HPBs), and virulence factors (VFs) in plant tissues. ARGs predominantly accumulated in roots (0.16 ∼ 0.23 copies/16S rRNA), significantly higher than in leaves (0.01 ∼ 0.11 copies/16S rRNA), with sul1 consistently enriched in the rhizosphere. Filtration pretreatment significantly reduced ARG and MGE levels in cherry radish roots by 30.78 % and 39.43 %, respectively (p < 0.05). ARGs strongly correlated with MGEs (R[2] = 0.97, p < 0.0001), indicating horizontal gene transfer as the key dissemination pathway. Co-occurrence network analysis revealed synergistic enrichment of ARGs and MGEs with HPBs and VFs, highlighting Acinetobacter baumannii and Streptococcus pneumoniae as potential core hosts. These findings demonstrate that ARG accumulation and spread in plants are affected by slurry treatment, plant species, and tissue specificity. While filtration mitigates risks, persistent ARGs in roots necessitate further monitoring. This study informs safe reuse strategies for biogas slurry in agriculture.},
}

@article {pmid41076761,
year = {2025},
author = {Jin, Y and Ping, J and Huang, X and Dai, J and Wang, X and Wang, S},
title = {Nanoscale zero-valent iron coupled with microorganisms enhances the removal of organochlorine pesticides in groundwater: Insights from the role of cascading effects and horizontal gene transfer.},
journal = {Water research},
volume = {288},
number = {Pt B},
pages = {124745},
doi = {10.1016/j.watres.2025.124745},
pmid = {41076761},
issn = {1879-2448},
abstract = {Nanoscale zero-valent iron (nZVIs) represent a promising approach for the remediation of organic chlorine-contaminated groundwater. However, the interaction between nZVIs and indigenous dechlorinating microorganisms is complex, which may have unpredictable effects on the dechlorination of organic chlorine, necessitating further investigation. In this study, we investigated an abandoned pesticide factory in southwest China, combined with microcosm experiment to reconstruct the metabolic pathway of biological dechlorination, and quantified the functional contribution of dechlorination genes and microorganisms. The results showed that the combined treatment of nZVIs and microorganisms significantly enhanced the degradation efficiency of HCHs, DDTs, and their six isomers, achieving removal rates of up to 99 % for HCHs and 87.73 % for DDTs. The concentrations of Cl[-] and Fe[2+] had a direct positive effect on the enrichment of microbial communities harboring HCHs degradation genes. Haloalkane dehalogenase encoded by the dhaA gene was identified as a key enzyme in the degradation of β-HCH precursors, which not only promoted the growth of facultative dehalogenators (particularly Acidovorax and Methyloversatilis) but also enhanced overall dechlorination activity. Importantly, we successfully reconstructed 7 near-complete bacterial metagenome-assembled genomes (MAGs) carrying the dhaA gene, representing taxonomically diverse novel dechlorinating microorganisms. Additionally, nZVIs significantly increased the abundance of mobile genetic elements (MGEs), with 17 MGEs detected within scaffolds harboring dhaA in the 7 MAGs. Integrases and transposases were identified as key drivers facilitating the spread of dhaA. This finding was supported by the shift of dhaA-harboring hosts, and by the incongruent evolutionary patterns observed between the genome-based tree and the dhaA protein phylogenetic tree. To be specific, cascading effects and horizontal gene transfer synergistically promoted the proliferation of dechlorinating microbes, providing novel strategies for managing and remediating organic chlorine-contaminated ecosystems.},
}

@article {pmid41075842,
year = {2025},
author = {da Silva, ES and Martins, AS and Ribeiro, LFS and Cordeiro-Moura, JR and Rodrigues, DAS and Picão, RC and Starling, MCVM and Amorim, CC},
title = {Tackling CECs and antimicrobial resistant bacteria in hospital wastewater using biological and AOP hybrid technologies.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133462},
doi = {10.1016/j.biortech.2025.133462},
pmid = {41075842},
issn = {1873-2976},
abstract = {This study investigated the disinfection, and removal of contaminants of emerging concern (CECs) and antibiotic-resistant bacteria (ARB) from hospital wastewater (HWW) using biological treatment followed by the LED photo-Fenton (BIO + LED-PF) and LED photo-Fenton followed by biological treatment (LED-PF + BIO). BIO was conducted by the Zahn Wellens method, while the LED-PF was applied in a pulse width modulation reactor (20 mg L[-1] Fe[2+], 50 mg L[-1] H2O2, pH 2.8, 70 % duty cycle, 60 min). CECs removal exceeded 90 % using BIO + LED-PF and 71 % using LED-PF + BIO. Both treatments were efficient in removing targets CECs from non-spiked raw HWW achieving concentrations < 1 µg L[-1], except for trimethoprim (BIO + LED-PF). LED-PF + BIO removed 5 and 6 log10 units of total coliforms (TC) and Escherichia coli (MPN/100 mL), respectively, while BIO + LED-PF achieved 5 log10 units of removal of TC and E. coli (MPN/100 mL) elimination. Pathogens considered as "critical" priority by the World Health Organization detected in HWW by MALDI-TOF/MS (cephalosporin-resistant Enterococcus faecalis and E. coli and carbapenem-resistant Klebsiella pneumoniae) were eliminated by both strategies. Approximately 3 logs10 units of ARB were removed for both treatment strategies, yet bacterial regrowth was observed after the LED-PF + BIO (Staphylococcus warneri resistant to ciprofloxacin) and BIO (Citrobacter freundii resistant to ciprofloxacin with 2 log10 units), emphasizing antimicrobial resistance risks. This regrowth was attributed to biomass proliferation and horizontal gene transfer in organic-rich environments. BIO + LED-PF also suppressed ARB, yet regrowth was detected for ARB resistant to SME + TRI. Overall, BIO + LED-PF was the most effective treatment, showing the feasibility of application in-situ in hospitals.},
}

@article {pmid41075480,
year = {2025},
author = {Zhu, Y and Li, D and Zeng, H and Zhang, J and Li, B and Tang, X and Luo, Y and Li, S and Ding, F},
title = {Decoding anammox granulation: Microbial interactions promote granule formation and indirectly shape antibiotic resistance gene dissemination.},
journal = {Water research},
volume = {288},
number = {Pt B},
pages = {124746},
doi = {10.1016/j.watres.2025.124746},
pmid = {41075480},
issn = {1879-2448},
abstract = {The formation of anaerobic ammonium oxidation (anammox) granules plays a crucial role in biomass retention. However, the microbial interaction, metabolic regulation, and risks associated with the dissemination of antibiotic resistance gene (ARG) during granulation remain insufficiently understood. In this study, an anammox granulation reactor was established and analyzed through integrated physicochemical characterization and multi-omics approaches to investigate changes in sludge properties, microbial communities, metabolic gene expression, and ARG profiles throughout granulation process. The results showed that granule size was closely associated with sludge surface free energy and extracellular polymeric substance (EPS) content, particularly the protein content of tightly bound EPS, which exhibited a significantly positive correlation with granule mechanical strength in the stable phase. Members of Proteobacteria exhibited the most significant shifts during granulation and occupied multiple core nodes in the microbial interaction network, indicating their essential roles in sustaining system stability and functional coordination. Metabolic functional analysis revealed selective regulation of carbon metabolism gene expression, which preferentially provides precursors for amino acid and cofactor biosynthesis. Different microbial taxa displayed significant metabolic complementarity in the synthesis of amino acids and cofactors. ARG analyses revealed that granulation was accompanied by an enhanced potential for mobile genetic element mediated horizontal gene transfer of ARG, with antibiotic target replacement and antibiotic efflux as primary resistance mechanisms. These findings deepen the ecological understanding of anammox granulation and offer theoretical support for managing ARG propagation in engineered systems.},
}

@article {pmid41072318,
year = {2025},
author = {Hou, G and Zhou, W and Han, L and Qiao, M and Chen, G and Lou, Q and Shao, S and Chi, S and Zhuo, H and Zhai, W and He, T and Liu, M and Zhang, L and Ding, H},
title = {Ecotoxicological effects of rare earth mining drainage: Unraveling dual antibiotic resistance gene regulation and risk-abundance decoupling through microbial community restructuring.},
journal = {Ecotoxicology and environmental safety},
volume = {305},
number = {},
pages = {119198},
doi = {10.1016/j.ecoenv.2025.119198},
pmid = {41072318},
issn = {1090-2414},
abstract = {Large-scale mining of ion-adsorption rare earth elements (REEs) generates acidic mine drainage (AMD) laden with REEs and heavy metals (HMs), yet its cascading impacts on microbial community assembly and antibiotic resistance genes (ARGs) dissemination across multi-matrices remain poorly characterized. By integrating high-throughput sequencing, co-occurrence network analysis, and partial least squares path modeling (PLS-PM), we unraveled that mining-induced geochemical divergence between mining-impacted areas and adjacent watersheds acts as a dominant environmental filter, reshaping the microbial community assembly and ARGs endowment. Key findings were in three areas: (1) Pollution-driven microbial adaptation. Significant shifts in microbial composition fostered "alternative steady states" without altering richness and induced network polarization-simplification in mining water (degree/density reduced by about 50 %) versus complexification in mining soil (degree/connections increased by about 3-fold), with enhanced mutualistic interactions and a 3-fold reduction in keystone species complexity. (2) ARGs risk-abundance decoupling. Mining areas exhibited 2.6-fold higher ARGs health risks than watersheds (p = 0.019), despite comparable abundance levels (p > 0.05), necessitating a paradigm shift from quantitative surveillance to health risks monitoring. (3) Dual ARGs regulation. While acidic REEs co-contamination directly promoted ARGs proliferation via co-selection (pathway coefficient = 0.254), it concurrently mitigated overall ecological risks through host community restructuring and potential horizontal gene transfer suppression (total effects = -0.186). These findings elucidate the ecological trade-offs between microbial adaptive resilience and ARGs dissemination in mining-impacted ecosystems, while establishing a mechanistic framework for optimizing targeted remediation strategies and sustainable resource extraction protocols.},
}

@article {pmid41070998,
year = {2025},
author = {Akiti, BT and Kaya, G and Kennedy, SP and DasSarma, P and Vincze, T and Fomenkov, A and Roberts, RJ and DasSarma, S},
title = {Genome sequence and methylome of the extremely halophilic bacterium Salinibacter ruber strain M31[T] isolated from a crystallizer pond in Mallorca, Spain.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0085625},
doi = {10.1128/mra.00856-25},
pmid = {41070998},
issn = {2576-098X},
abstract = {Salinibacter ruber strain M31[T], an extremely halophilic bacterium, was isolated from a saltern crystallizer pond in Spain. Single-molecule real-time sequencing revealed a 3.6-Mbp genome with a single 3.55-Mbp circular chromosome and a 35.5-kbp plasmid. The highly acidic proteome includes a total of 2,962 proteins, some of which are archaeal-like.},
}

@article {pmid40983756,
year = {2025},
author = {Dong, S and Wang, S and Li, L and Yu, J and Zhang, Y and Xue, JY and Chen, H and Ma, J and Zeng, Y and Cai, Y and Huang, W and Zhou, X and Wu, J and Li, J and Yao, Y and Hu, R and Zhao, T and Villarreal A, JC and Dirick, L and Liu, L and Ignatov, M and Jin, M and Ruan, J and He, Y and Wang, H and Xu, B and Rozzi, R and Wegrzyn, J and Stevenson, DW and Renzaglia, KS and Chen, H and Zhang, L and Zhang, S and Mackenzie, R and Moreno, JE and Melkonian, M and Wei, T and Gu, Y and Xu, X and Rensing, SA and Huang, J and Long, M and Goffinet, B and Bowman, JL and Van de Peer, Y and Liu, H and Liu, Y},
title = {Bryophytes hold a larger gene family space than vascular plants.},
journal = {Nature genetics},
volume = {57},
number = {10},
pages = {2562-2569},
pmid = {40983756},
issn = {1546-1718},
mesh = {*Bryophyta/genetics/classification ; Phylogeny ; *Multigene Family ; *Genome, Plant/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Genes, Plant ; *Plants/genetics ; },
abstract = {After 500 million years of evolution, extant land plants compose the following two sister groups: the bryophytes and the vascular plants. Despite their small size and simple structure, bryophytes thrive in a wide variety of habitats, including extreme conditions. However, the genetic basis for their ecological adaptability and long-term survival is not well understood. A comprehensive super-pangenome analysis, incorporating 123 newly sequenced bryophyte genomes, reveals that bryophytes possess a substantially greater diversity of gene families than vascular plants. This includes a higher number of unique and lineage-specific gene families, originating from extensive new gene formation and continuous horizontal transfer of microbial genes over their long evolutionary history. The evolution of bryophytes' rich and diverse genetic toolkit, which includes new physiological innovations like unique immune receptors, likely facilitated their spread across different biomes. These newly sequenced bryophyte genomes offer a valuable resource for exploring alternative evolutionary strategies for terrestrial success.},
}

*Bryophyta/genetics/classification
Phylogeny
*Multigene Family
*Genome, Plant/genetics
Evolution, Molecular
Gene Transfer, Horizontal
*Genes, Plant
*Plants/genetics

@article {pmid41070122,
year = {2025},
author = {Ruiz, SE and Morandini, FN and Panzetta, ME and Lipari, FG and Irrazábal, MG and Toselli, R and Der Ohannesian, M and Amieva, C and Valdes, ME and Giraudo, FJ and Rollán, MDR and Amé, V and Sola, C and Saka, HA},
title = {Urban wastewater overflows as hotspots for dissemination of bacteria producing extended-spectrum β-lactamases and carbapenemases in the Suquía River, Argentina.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1669531},
pmid = {41070122},
issn = {1664-302X},
abstract = {Antimicrobial resistance (AMR) is a critical global challenge, yet the role of environmental dissemination of antibiotic-resistant bacteria remains underexplored, particularly in developing regions. This study investigated urban wastewater overflows from public streets as vectors for extended-spectrum-β-lactamase (ESBL)- and carbapenemase-producing Enterobacterales and Aeromonas in the Suquía River (Córdoba, Argentina). Sixty-two water samples were analyzed for coliform counts, antimicrobial susceptibility, and resistance genes. Horizontal gene transfer was assessed by conjugation. Sixty-five ESBL- and/or carbapenemase-producing isolates were recovered, including six carbapenemase producers subjected to whole-genome sequencing (WGS). Urban wastewater exhibited coliform levels >10[8] MPN/100 mL, while river counts increased 2-5 logs at urban and downstream sites compared to upstream, where no resistant strains were detected. ESBL- and/or carbapenemase-producers occurred in ~70% of wastewater and river samples, mainly Escherichia coli harboring blaCTX-M . Carbapenemase producers carried blaKPC-2 or blaNDM-1 in Enterobacter, Klebsiella, Citrobacter, and Aeromonas caviae. WGS revealed extensive resistomes, virulence genes, and plasmid replicons, including IncU and IncA/C2 linked to carbapenemases. Conjugation confirmed plasmid-mediated transfer of β-lactamase genes, and genetic context analysis identified clinically recognized transposons. Notably, Enterobacter kobei and Aeromonas caviae from the river carried blaKPC-2 on plasmidic contigs combining clinical and environmental elements, consistent with genetic exchange within aquatic ecosystems and transfer of clinically significant resistance determinants to species adapted for riverine survival. These findings identify urban wastewater overflows as AMR hotspots that facilitate the dissemination of multidrug-resistant bacteria and mobile resistance elements into urban and peri-urban aquatic environments, underscoring the need for integrated environmental AMR surveillance.},
}

@article {pmid41068737,
year = {2025},
author = {Debnath, PP and Chokmangmeepisarn, P and Papadopoulou, A and Coyle, NM and Baker-Austin, C and van Aerle, R and Bass, D and Tyler, CR and Rodkhum, C},
title = {Diversity and antimicrobial resistance among bacterial isolates from finfish aquaculture in Thailand.},
journal = {BMC veterinary research},
volume = {21},
number = {1},
pages = {595},
pmid = {41068737},
issn = {1746-6148},
support = {Second Century Fund (C2F) for postdoctoral fellowships//Chulalongkorn University/ ; FOOD_FF_68_201_3100_017//Chulalongkorn University, Bangkok, Thailand/ ; },
mesh = {Animals ; Thailand ; Aquaculture ; *Anti-Bacterial Agents/pharmacology ; Microbial Sensitivity Tests ; *Drug Resistance, Bacterial ; *Fishes/microbiology ; *Fish Diseases/microbiology/epidemiology ; *Bacteria/drug effects/isolation & purification ; Drug Resistance, Multiple, Bacterial ; Gram-Negative Bacteria/drug effects ; },
abstract = {BACKGROUND: Global aquaculture, has expanded rapidly, especially in Southeast Asia, with Thailand emerging as a leading producer. However, the sector faces economic losses from disease outbreaks and has problems with escalating antimicrobial resistance (AMR).

RESULTS: This study examined bacterial diversity and AMR in 695 moribund fish samples collected from regions across Thailand between 2018 and 2024, and spanning eight key finfish aquaculture species such as tilapia, Asian sea bass, snakeskin gourami, snakehead, walking catfish and carp species. Gram-negative bacteria (86.62% of isolates) were dominated by Vibrionaceae and Aeromonadaceae, while Gram-positive bacteria were primarily from Streptococcaceae, with notable species including A. veronii, V. vulnificus, S. agalactiae and S. suis. Antibiotic susceptibility testing was conducted with 29 antibiotics across nine different classes and the isolates were classified as wild-type (WT) or non-wild-type (NWT) based on their inhibition zone diameters. The results indicated high resistance levels, particularly against metronidazole, streptomycin, clindamycin, sulfonamide, and kanamycin. Multidrug resistance (MDR) was notably high in Aeromonas and Vibrio species. Antimicrobial resistance gene (ARG) analysis showed a high prevalence of beta-lactam, tetracycline, and fluoroquinolone resistance in Gram-negative bacteria, and resistance to beta-lactams, macrolides, fluoroquinolones, and peptides in Gram-positive bacteria. Antibiotic efflux was the predominant putatively detected resistance mechanism, accounting for 50-60% of ARGs. Identification of unique resistance gene families in Aeromonas spp. and V. vulnificus, including the SMR efflux pump and OXA beta-lactamase, emphasizes the adaptive strategies of these bacteria and the discovery of host-specific resistance mechanisms in S. suis, such as nutrient acquisition pathways, underscores the challenges of controlling and managing AMR in aquaculture systems. Mobile genetic elements (MGEs), particularly IS elements, were found to be widespread in all species, underscoring the significant role of horizontal gene transfer in the dissemination of resistance.

CONCLUSIONS: This study advocates for enhanced AMR surveillance, responsible antibiotic use, and species-specific monitoring to safeguard aquaculture and public health utilizing the one health approach.},
}

Animals
Thailand
Aquaculture
*Anti-Bacterial Agents/pharmacology
Microbial Sensitivity Tests
*Drug Resistance, Bacterial
*Fishes/microbiology
*Fish Diseases/microbiology/epidemiology
*Bacteria/drug effects/isolation & purification
Drug Resistance, Multiple, Bacterial
Gram-Negative Bacteria/drug effects

@article {pmid41068356,
year = {2025},
author = {Paillard, P and Rouger, Q and Thomet, M and Macé, K},
title = {Type IV secretion systems: from structures to mechanisms.},
journal = {The EMBO journal},
volume = {},
number = {},
pages = {},
pmid = {41068356},
issn = {1460-2075},
support = {ANR-22-PAMR-0005//Association Nationale de la Recherche et de la Technologie (ANRT)/ ; Tremplin-ERC VIRULENSSE//Association Nationale de la Recherche et de la Technologie (ANRT)/ ; },
abstract = {Bacterial conjugation is the fundamental process of unidirectional transfer of DNA from a "donor" cell to a "recipient" cell. It is the primary means by which antibiotic resistance genes spread among bacterial populations. Conjugation is mediated by a large molecular machinery termed Type IV secretion system (T4SS), embedded within the donor cell wall. In addition, some bacteria utilise T4SS to inject effector proteins into eukaryotic cells, modulating host functions to their advantage. In this review, we highlight how recent structural studies have substantially advanced our understanding of T4SS molecular mechanisms. We detail these mechanisms across four main sub-processes: assembly of the machinery, pilus biogenesis, donor-recipient cell contact, and substrate recruitment and secretion. By understanding the intricate workings of T4SS, we can gain valuable insights into bacterial evolution, virulence, and horizontal gene transfer, offering potential avenues for developing novel antibacterial strategies.},
}

@article {pmid41062968,
year = {2025},
author = {Han, S and Chen, Z and Liu, Q and Ding, Y and Wang, J and Liu, H and Zou, J and Hong, Z and Zhang, H and Yang, W and Zhang, L and Liu, H and Yuan, M},
title = {Identification and evolution of the plant sulfotransferase family.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {895},
pmid = {41062968},
issn = {1471-2164},
support = {C2024209006//the Natural Science Foundation of Hebei Province/ ; ZD-YG-202313-23//the Key research project of North China University of Science and Technology/ ; },
abstract = {UNLABELLED: Sulfotransferases (SOTs, EC 2.8.2.-), which catalyze sulfate conjugation reactions, are widespread across prokaryotes and eukaryotes. However, the origin, classification and evolution history of SOTs in plants are not as well understood as those in animals and bacteria. In this study, a systematic analysis of an array of sequenced genomes revealed that SOTs were ubiquitously distributed in green plants (Viridiplantae). Phylogenetic analysis classified plant SOTs into three subfamilies, including SULTs (soluble sulfotransferases), TPSTs (tyrosylprotein sulfotransferases), and NFSTs (nodulation factor sulfotransferase). Notably, CHSTs (carbohydrate sulfotransferases), abundant in animals, algae and bacteria, were not found in land plants. High-throughput screening algorithms, phylogenetic and gene structure analyses indicated that land plants might acquire NFSTs through horizontal gene transfer (HGT) from bacteria to green algae. In contrast to the low gene number of TPSTs and NFSTs in land plants, the number of SULTs varied greatly among species. The absence of SULTs resulted in a significantly reduced gene number of SOTs in Cucurbitaceae, whereas the recent expansion of SULTs, mainly driven by tandem duplication (TD), caused a significant increase in SOT gene number in Begoniaceae. The significant variation in the gene number of SULTs across species, along with their evolutionary branching patterns, indicated lineage-specific duplication or contraction of SULTs, which profoundly influenced the production of sulfated metabolites during the diversification of monocots and core eudicots. This study provided the first comprehensive phylogenetic, classification and evolutionary analysis of SOTs in green plants across a broad taxonomic range.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-025-12117-4.},
}

@article {pmid41068170,
year = {2025},
author = {Tsiklauri, R and Kobakhidze, S and Kotetishvili, M},
title = {Interactive networks of donors and recipients of the TetM gene and its evolutionary dynamics across the bacterial domain.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {35312},
pmid = {41068170},
issn = {2045-2322},
mesh = {*Evolution, Molecular ; *Bacteria/genetics ; Phylogeny ; Recombination, Genetic ; Humans ; *Bacterial Proteins/genetics ; Selection, Genetic ; },
abstract = {Identifying primary donors and recipients of the tetM gene is crucial for gaining a deeper understanding of the dynamics underlying the dissemination of resistance to tetracyclines in natural bacterial populations, including those of human and animal pathogens. This study modeled the major donor-recipient network of tetM, also providing important insights into the primary evolutionary mechanisms of this gene. The RDP4- and SplitsTree-embedded algorithms were used to detect genetic recombination events of tetM loci from different bacterial species and genera. FUBAR, MEME, and MEGA11 were employed to determine the evolutionary dynamics of this gene. A large tetM donor-recipient species network, exhibiting different bacterial genera, was determined based on the RDP4- and SplitsTree-generated inferences (P ≤ 3.75E-02; bootstrap and fit values ≥ 90 and ≥ 94.9 respectively). 3 sites were identified as undergoing episodic diversifying selection, while 42 sites were under pervasive negative selection for this gene, with a discrete Gamma distribution value of 0.0500. Notably, Streptococcus agalactiae, Streptococcus equinus, Streptococcus pyogenes, Streptococcus pneumoniae, Enterococcus faecalis, Enterococcus faecium, and Gardnerella vaginalis were suggested to be the predominant donors of tetM involved in inter-species and/or intergeneric recombination. Genetic recombination and pervasive negative selection were suggested to be the primary driving forces underlying the evolution of tetM.},
}

*Evolution, Molecular
*Bacteria/genetics
Phylogeny
Recombination, Genetic
Humans
*Bacterial Proteins/genetics
Selection, Genetic

@article {pmid41067449,
year = {2025},
author = {Yang, H and Cui, B and Zhou, D},
title = {Signaling role of 6-benzylaminopurine in enhanced biotreatment of saline wastewater: performance and mechanisms.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133455},
doi = {10.1016/j.biortech.2025.133455},
pmid = {41067449},
issn = {1873-2976},
abstract = {This study introduced the phytohormone 6-benzylaminopurine (6-BA) as a novel, economical, and eco-friendly bacterial signal molecule (SM), which overcame the cost and instability limitations of acyl-homoserine lactones (AHLs) in high-salinity wastewater treatment. 6-BA bound to histidine kinases in two-component systems (TCS) through hydrogen bonding, triggering downstream signal transduction and metabolic regulation. Under high-salinity stress, 6-BA promoted cellular integrity and ionic homeostasis, increasing live-cell counts by 113.7%. To mitigate phenol toxicity, 6-BA enhanced extracellular polymeric substance (EPS) functions and antioxidant systems, reducing reactive oxygen species (ROS) by 19.8%. 6-BA upregulated genes related to DNA replication, the TCA cycle, and fatty acid synthesis, thereby repairing membrane integrity. 6-BA also enriched degrading enzymes and improved phenol degradation, leading to approximately 20% increases in COD, TN, and TP removal. Crucially, 6-BA restructured the microbial community, reducing antibiotic resistance gene (ARG) host abundance by 27.9% and ARG-encoding plasmids by 32.8, which curtailed horizontal gene transfer risks. Additionally, 6-BA exhibited no observable ecotoxicity. This work proposed 6-BA signaling as a novel bioaugmentation strategy for enhanced remediation of high-salinity wastewater.},
}

@article {pmid41067299,
year = {2025},
author = {Feng, Y and Yuan, Q and Kang, Y and Zheng, M and Li, Z},
title = {Deciphering the mobility, pathogenic hosts, and co-selection of antibiotic resistance genes in untreated wastewater from three different hospitals.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {},
number = {},
pages = {105840},
doi = {10.1016/j.meegid.2025.105840},
pmid = {41067299},
issn = {1567-7257},
abstract = {OBJECTIVE: Antibiotic resistance genes (ARGs) in hospital wastewater pose significant environmental and public health risks, yet the co-selection mechanisms involving metal/biocide resistance genes (MRGs/BRGs) and the role of mobile genetic elements (MGEs) remain poorly characterized. This study aimed to comprehensively assess the abundance, mobility, pathogenic hosts, and co-selection patterns of ARGs, MRGs, and BRGs in untreated wastewater from three types of hospitals.

METHODS: Untreated wastewater samples from nine sources across three hospital types (general, traditional Chinese medicine, and dental) were analyzed using metagenomic sequencing and assembly. ARGs, MRGs, and BRGs were identified via the SARG and BacMet databases. ARG hosts, mobility, and MGE co-occurrence were analyzed using PlasFlow and MOB-suite, with risk levels evaluated alongside pathogenic bacteria databases.

RESULTS: A total of 1911 ARGs (222 subtypes), 1662 MRGs (167 subtypes), and 916 BRGs (139 subtypes) were detected. Tetracycline, multidrug, and β-lactam resistance genes were predominant, with 46.43 % of ARGs being plasmid-associated. Key pathogens including Klebsiella pneumoniae and Enterococcus spp. harbored high-risk ARGs such as KPC-2 and NDM-1. Notably, 76.2 % of ARGs in traditional Chinese medicine hospital wastewater were classified as high-risk. Significant co-occurrence of ARGs with MGEs (e.g., DDE recombinases) and MRGs/BRGs was observed, underscoring the role of horizontal gene transfer and co-selection.

CONCLUSION: Untreated hospital wastewater represents a significant reservoir of ARGs, with risks exacerbated by pathogenic hosts, MGE-mediated HGT, and metal/biocide co-selection. These findings underscore the urgent need for optimized wastewater treatment strategies to curb the spread of antibiotic resistance and inform future intervention efforts.},
}

@article {pmid41067103,
year = {2025},
author = {Wang, M and Liu, X and Wang, J and Hao, S and Sun, X},
title = {Three-dimensional synergistic mechanism ofphysical injury, microbiota dysbiosis, and gene transfer in the gut of Cipangopaludina cathayensisunder microplastics and roxithromycin exposure.},
journal = {Journal of environmental management},
volume = {394},
number = {},
pages = {127514},
doi = {10.1016/j.jenvman.2025.127514},
pmid = {41067103},
issn = {1095-8630},
abstract = {Microplastics (MPs) and antibiotics pose a combined threat to aquatic organisms by impairing gut health and promoting the spread of antibiotic resistance genes (ARGs). In this study, Cipangopaludina cathayensis was exposed for 28 days to polystyrene MPs, roxithromycin (ROX), and their combination to assess impacts on intestinal barrier integrity, microbiota composition, and ARG proliferation. MPs alone caused significant mucosal damage, villus atrophy, epithelial shedding, and reduced digestive enzyme activities. ROX exposure altered microbiota structure by increasing Bacteroidetes and reducing Firmicutes. Co-exposure (CM group) exacerbated epithelial injury and enzyme inhibition but partially restored balance through enrichment of SCFA-producing, anti-inflammatory bacteria. ARG levels in the CM group rose by over 1000 %, with notable increases in multidrug resistance genes (e.g., blaOXA10) and integrons (e.g., cIntI-1), mainly linked to Bacteroides and Proteobacteria. Transcriptomic data indicated oxidative stress and epithelial disruption under MPs, and upregulation of efflux and integron genes with ROX. Combined exposure triggered DNA repair and SOS pathways, facilitating horizontal gene transfer. These findings highlight a three-dimensional synergistic mechanism-physical damage, microbial dysbiosis, and gene transfer-that amplifies ARG dissemination and intestinal toxicity, underscoring the need to assess ecological risks of composite pollutants in freshwater systems.These processes form a self-reinforcing loop in which physical epithelial damage promotes microbial dysbiosis, which in turn facilitates ARG proliferation through increased permeability and immune disruption.},
}

@article {pmid41066873,
year = {2025},
author = {Hou, J and Liu, M and Li, Y and Li, L and Yao, Y and Xu, H and An, Y},
title = {Seed-borne and environmental transmission mechanisms drive diverse heavy metal-resistant plant growth-promoting bacteria (PGPB) in rice.},
journal = {Environment international},
volume = {204},
number = {},
pages = {109840},
doi = {10.1016/j.envint.2025.109840},
pmid = {41066873},
issn = {1873-6750},
abstract = {Heavy metal-resistant plant growth-promoting bacteria (PGPB) play a crucial role in mitigating heavy metal stress and reducing heavy metal accumulation in plants. However, the origins and transmission mechanisms of PGPB and their associated heavy metal resistance genes (MRGs) in plants remain unclear. To fill this knowledge gap, we collected rice and related environmental samples from heavy metal-contaminated paddy fields. The microbial DNA was recovered from these rice and environmental samples and then analyzed using shotgun metagenomics at the metagenome-assembled genomes (MAGs) level. As a result, 805 MRG-PGPB combinations were detected in rice tissues and related environments under heavy metal contamination conditions. Core MRG-PGPB combinations shared across seed-rice (42.46%) and environment-rice (13.34%) interfaces collectively constituted 55.80% of the detected combinations, demonstrating that environmental translocation and seed-borne vertical transmission jointly drive over half of MRG-PGPB colonization in rice systems. Subsequent source-tracking analysis indicated that PGPBs present in rice primarily originated from seeds, with a substantial proportion also attributed to translocation within rice tissues. Phylogenetic analysis of dominant MRGs further demonstrated the seed-borne vertical transmission of MRGs-PGPB, while simultaneously elucidating that MRGs harbored by PGPB in rice could also be acquired via horizontal gene transfer (HGT) from environmental or seed-borne MRG-PGPB, particularly from atmospheric microbes such as Methylophilus and Serratia. These findings provide valuable insights into harnessing PGPB to enhance rice resilience against heavy metal contamination, thereby contributing to improved food security and sustainable agricultural practices.},
}

@article {pmid41066555,
year = {2025},
author = {Macadangdang, BR and Wang, Y and Woodward, CL and Revilla, JI and Shaw, BM and Sasaninia, K and Varnum, GE and Makanani, SK and Berruto, C and Ahuja, U and Miller, JF},
title = {Targeted protein evolution in the gut microbiome by diversity-generating retroelements.},
journal = {Science (New York, N.Y.)},
volume = {390},
number = {6769},
pages = {eadv2111},
doi = {10.1126/science.adv2111},
pmid = {41066555},
issn = {1095-9203},
mesh = {*Gastrointestinal Microbiome/genetics ; *Retroelements/genetics ; Animals ; *Bacteroides/genetics/classification ; Mice ; Humans ; Female ; *Evolution, Molecular ; Germ-Free Life ; Gene Transfer, Horizontal ; *Bacterial Proteins/genetics ; Genetic Variation ; *Fimbriae Proteins/genetics ; },
abstract = {Diversity-generating retroelements (DGRs) accelerate evolution by rapidly diversifying variable proteins. The human gastrointestinal microbiota harbors the greatest density of DGRs known in nature, suggesting that they play adaptive roles in this environment. We identified >1100 distinct DGRs among human-associated Bacteroides species and discovered a subset that diversify adhesive components of type V pili and related proteins. We show that Bacteroides DGRs are horizontally transferred across species, display activity levels ranging from high to low, and preferentially alter the functional characteristics of ligand-binding residues on adhesive organelles. Specific variable protein sequences are enriched when Bacteroides strains compete with other commensal bacteria in gnotobiotic mice. Analysis of >2700 DGRs from diverse phyla in mother-infant pairs shows that Bacteroides DGRs are disproportionately transferred to vaginally delivered infants where they actively diversify. Our observations provide a foundation for understanding the potential roles of targeted genome plasticity in shaping host-associated microbial communities.},
}

*Gastrointestinal Microbiome/genetics
*Retroelements/genetics
Animals
*Bacteroides/genetics/classification
Mice
Humans
Female
*Evolution, Molecular
Germ-Free Life
Gene Transfer, Horizontal
*Bacterial Proteins/genetics
Genetic Variation
*Fimbriae Proteins/genetics

@article {pmid41065996,
year = {2025},
author = {Zhang, Y and Lin, Y and Ruan, Y and Yang, J and Holden, E and Felgate, H and Solsona, M and Liu, H and Liang, G and Jiang, H and Webber, MA and Zhuo, C},
title = {Pivotal plasmids drive the global spread of CTX-M-27 in Escherichia coli.},
journal = {Infection},
volume = {},
number = {},
pages = {},
pmid = {41065996},
issn = {1439-0973},
support = {82172318//the National Natural Science Foundation of China/ ; },
abstract = {The detection rate of CTX-M-27-producing E. coli has increased worldwide in recent years although relatively little is known about the strains and vectors responsible for this increased isolation.To explore the evolution of CTX-M-27-producing E. coli in the past 20 years at three levels; genetic structure of the blaCTX-M-27 locus, nature of carrying plasmids and types of host bacteria, we analysed 543 genomes of blaCTX-M-27-positive E. coli isolated globally from 2003 to 2020.Results indicated that hospitalised patients are a major reservoir of blaCTX-M-27 carrying isolates but there are a wide variety of other resistance genes, plasmid replicons and virulence factors carried by CTX-M-27-producing E. coli strains. There was a strong positive correlation between carriage of the blaCTX-M-27 gene and the highly virulent clone-ST131 E. coli. IncF-type plasmids were the most common vector of blaCTX-M-27 transmission with a subtype of F plasmids showing a tropism for specific sequence types of E. coli. The DNA transfer and replicon-stability regions of host plasmids showed evidence for significant evolution over time with deletion and truncation events associated with blaCTX-M-27-carrying plasmids being stably maintained in specific host sequence types. Moreover, recently isolated blaCTX-M-27-carrying plasmids were found to contribute to growth of host bacteria suggesting they have evolved to provide benefits to their host. IncF plasmids and the blaCTX-M-27 locus also showed evidence for co-evolution, in particular, "Bridge" co-integrate structures flanked by IS26 were found in this study in IncF plasmids.Together, our results illustrate that blaCTX-M-27 is present on various plasmids which are associated with epidemic host E. coli and it appears carriage of prevalent IncF blaCTX-M-27-carrying plasmids are beneficial for the host. Complex genetic structures are under evolutionary pressure which promote the wide spread of blaCTX-M-27 which is a global health threat.},
}

@article {pmid41065715,
year = {2025},
author = {Feng, Y and Wicke, S},
title = {Systemic organellar genome reconfiguration along the parasitic continuum in the broomrape family (Orobanchaceae).},
journal = {Plant & cell physiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/pcp/pcaf131},
pmid = {41065715},
issn = {1471-9053},
abstract = {The transition from autotrophy to heterotrophy in parasitic plants disrupts organellar coordination and presents a unique opportunity to examine the coevolution of cellular genomes. Using the Broomrape family (Orobanchaceae) as a model, we analyzed mitochondrial and plastid genome evolution across 30 species representing the full spectrum of parasitic lifestyles. We show that plastid genome reduction is correlated with mitogenomic expansion, revealing a striking inverse relationship between genome compaction and inflation. Mitogenome enlargement in parasitic taxa is driven by the accumulation of horizontally and intracellularly transferred DNA, proliferation of short repeats, and integration of unique sequences with no detectable homology. Across the family, plastid-derived mitochondrial sequences (MTPTs) are consistently more similar in GC content to plastomes than to mitogenomes, and in several holoparasites, 'ghost' MTPTs preserve regions now lost from plastomes, indicating integration before plastome reduction. Relaxed selection in ATP synthase and ribosomal genes contrasts with intensified selection on components of electron transport and cytochrome c maturation, reflecting functional reconfiguration of mitochondrial respiration in parasitic plants. RNA editing, intron loss, and frameshift insertions further reshape gene structure, particularly in obligate parasites. Together, our findings suggest that parasitism initiates a systemic genomic feedback loop in which relaxed selection and disrupted maintenance mechanisms affect even distant genomic compartments. This study provides a comprehensive evolutionary framework for multi-compartment genome remodeling in parasitic plants and highlights the dynamic interplay between lifestyle specialization and organelle genome evolution.},
}

@article {pmid41065417,
year = {2025},
author = {Lamoureux, A and Elvira-Matelot, E and Porteu, F and Laplane, L},
title = {Revisiting Clonal Evolution Through the Light of Retrotransposons.},
journal = {BioEssays : news and reviews in molecular, cellular and developmental biology},
volume = {},
number = {},
pages = {e70078},
doi = {10.1002/bies.70078},
pmid = {41065417},
issn = {1521-1878},
support = {//CNRS MITI, 80 Prime/ ; //CNRS 80 Prime program/ ; 2021-1-EMERG-54-CNRS DR 5-1//Cancéropôle IDF/ ; INCa-DGOS-Inserm-ITMO Cancer_18002//SIRIC/ ; //McDonnell Foundation/ ; Equipe labellisée EL2020//Ligue Nationale Contre le Cancer/ ; },
abstract = {The clonal evolution model provides a framework for understanding the evolution of cancer cells. According to this model, cancer cells accumulate genetic mutations over time, and these mutations are passed down to their descendants, leading to genetic diversity within the tumor. Some of these mutations confer selective advantages, causing certain lineages of cancer cells (clones) to dominate and expand. However, this model is rooted in certain conceptual assumptions, which we propose to revisit by considering the potential involvement of retrotransposons in cancer initiation and progression. In recent years, it has become evident that transposable elements, particularly retrotransposons, play a significant role in driving cancer transformation and progression. We first review how current knowledge about retrotransposon activity aligns with the clonal evolution model by highlighting its ability to modulate cancer cell fitness. We then take a forward-looking perspective to explore additional ways retrotransposons may also influence clonal dynamics beyond the current model.},
}

@article {pmid41064843,
year = {2025},
author = {Herawati, O and Bejo, SK and Zakaria, Z and Zubaidah Ramanoon, S},
title = {Impact of antibiotic use on Escherichia coli resistance in goats: A longitudinal cohort study in Selangor, Malaysia.},
journal = {Veterinary world},
volume = {18},
number = {8},
pages = {2479-2486},
pmid = {41064843},
issn = {0972-8988},
abstract = {BACKGROUND AND AIM: Antibiotic resistance (ABR) in food animals poses a significant threat to public health under the One Health framework. In Malaysia, Escherichia coli is a key indicator organism for antimicrobial resistance (AMR) surveillance. However, limited data exist on the resistance profiles of E. coli in goats, particularly in relation to antibiotic usage. This study aimed to evaluate the effect of antibiotic use on the temporal development of ABR in E. coli isolated from goat farms in Selangor.

MATERIALS AND METHODS: A prospective cohort study was conducted on two goat farms: one with a documented history of antibiotic use (Farm 2) and one without (Farm 1). A total of 60 goats (30/farm) were followed for 3 months, with fecal samples collected monthly. E. coli isolates were identified and subjected to antimicrobial susceptibility testing using the Kirby-Bauer disk diffusion method. Data were analyzed using Chi-square tests, logistic regression, and Cox proportional hazards modeling.

RESULTS: A significant association was found between antibiotic use and the presence of ABR E. coli (odds ratio = 5.82; 95% confidence interval [CI]: 1.12-30.20; p < 0.05). The highest resistance was observed in Farm 2 (96.74%) compared to Farm 1 (57.14%). A hazard ratio of 1.74 (95% CI: 1.03-2.94) indicated increased risk over time. Resistance was detected against critically important human antibiotics, including ciprofloxacin, ampicillin, chloramphenicol, and tetracycline. Notably, resistance to meropenem, an antibiotic not approved for veterinary use, was detected in both farms, suggesting possible environmental or interspecies transmission.

CONCLUSION: This study confirms that antibiotic use in goat farming significantly influences the development of ABR in E. coli. The detection of resistance in farms without antibiotic use underscores the need to investigate other contributing factors, such as environmental residues and horizontal gene transfer. These findings support policy recommendations to restrict antibiotic use in livestock and highlight the urgency for comprehensive AMR surveillance and intervention strategies.},
}

@article {pmid41064643,
year = {2025},
author = {de Oliveira, AM and de Castro, CP},
title = {Perspectives in clinical microbiology for combating multi-drug resistant bacterial infections.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1695284},
pmid = {41064643},
issn = {2235-2988},
mesh = {Humans ; *Drug Resistance, Multiple, Bacterial ; *Bacterial Infections/diagnosis/microbiology/drug therapy/therapy ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; *Bacteria/drug effects ; Bacteriophages ; Phage Therapy ; Antimicrobial Peptides/therapeutic use ; },
abstract = {Multidrug-resistant bacterial infections are a major global threat, exacerbated by globalization and poor sanitation. Bacteria develop resistance through mechanisms like enzymatic degradation, efflux pumps, and horizontal gene transfer. Rapid diagnostics and artificial intelligence are crucial for overcoming the limitations of traditional culture methods. Combating this issue requires novel therapeutic strategies, such as bacteriophages, antimicrobial peptides, and microbiome-based therapies. Ultimately, proper antibiotic use, increased research, and global multidisciplinary cooperation are essential to address this complex challenge.},
}

Humans
*Drug Resistance, Multiple, Bacterial
*Bacterial Infections/diagnosis/microbiology/drug therapy/therapy
*Anti-Bacterial Agents/therapeutic use/pharmacology
*Bacteria/drug effects
Bacteriophages
Phage Therapy
Antimicrobial Peptides/therapeutic use

@article {pmid41064044,
year = {2025},
author = {Herold, L and Fitzgerald, BG and Leclercq, GME and Sorbara, MT},
title = {Strain-level variation controls nutrient niche occupancy by health-associated Anaerostipes hadrus.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf163},
pmid = {41064044},
issn = {2730-6151},
abstract = {Nutrient niche access by the gut microbiota impacts community assembly and dynamics, the production of host-benefiting short-chain fatty acids (SCFAs), and pathogen inhibition through colonization resistance. Furthermore, deciphering if and how niche access varies on a strain level will be important as individual strains of gut microbes are selected for inclusion in new live biotherapeutic products. Despite this, for many gut anaerobes, nutrient niche occupancy and impacts of strain variation remain unknown. Here, we examined nutrient niches of Anaerostipes hadrus (AH), a butyrate-producing member of the Lachnospiraceae family. We found that AH isolates encode a carbohydrate metabolism gene repertoire that is distinct from other Lachnospiraceae. Furthermore, tested AH isolates show variation in carbohydrate-related genes between strains and large numbers of genes associated with horizontal gene transfer events. Functionally, we demonstrate that AH isolates exhibit strain-specific patterns of nutrient niche access that can be associated with the gain, loss, and disruption of gene clusters enabling specific carbohydrate metabolism. This strain-specific carbohydrate use drives variable SCFA production. Unexpectedly, strains exhibit differential preferences for carbohydrates, which alter SCFA profiles in environments with multiple possible nutrient niches available. Furthermore, when strains of AH interact in an environment with multiple nutrient niches available, strain-strain interactions result in varying SCFA profiles that extend beyond the additive effects of individual strain behavior. Altogether, these results demonstrate the importance of evaluating strain-level variation in the design of future live biotherapeutic products.},
}

@article {pmid41063607,
year = {2025},
author = {Bernabeu, M and Manzano-Morales, S and Gabaldón, T},
title = {Phylogeny-aware simulations suggest a low impact of unsampled lineages in the inference of gene flow during eukaryogenesis.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evaf190},
pmid = {41063607},
issn = {1759-6653},
abstract = {The topologies of gene trees are broadly used to infer horizontal gene transfer events and characterize the potential donor and acceptor partners. Additionally, ratios between branch lengths in the gene tree can inform about the timing of transfers relative to each other. Using this approach, recent studies have proposed a relative chronology of gene acquisitions in the lineage leading to the last eukaryotic common ancestor (LECA). However, a recognised caveat of the branch-length ratio method are potential biases due to incomplete taxon sampling resulting in so-called "ghost" lineages. Here, we assessed the effect of ghost lineages on the inference of the relative ordering of gene acquisition events during eukaryogenesis. For this, we used a novel simulation framework that populates a dated Tree of Life with plausible "ghost" lineages and simulates their gene transfers to the lineage leading to LECA. Our simulations suggest that a substantial majority of gene acquisitions from distinct ghost donors are inferred with the correct relative order. However, we identify phylogenetic placements where ghost lineages would be more likely to produce misleading results. Overall, our approach offers valuable guidance for the interpretation of future work on eukaryogenesis, and can be readily adapted to other evolutionary scenarios.},
}

@article {pmid41061540,
year = {2025},
author = {Zhang, L and Gao, X and Li, G and Xu, Z and Luo, W},
title = {Metagenomic insights to effective elimination of resistomes in food waste composting by lime addition.},
journal = {Journal of hazardous materials},
volume = {499},
number = {},
pages = {140065},
doi = {10.1016/j.jhazmat.2025.140065},
pmid = {41061540},
issn = {1873-3336},
abstract = {Food waste contains abundant resistomes, including antibiotic and heavy metal resistance genes (ARGs and MRGs), which pose risks to the environment and human health. Composting can be used for food waste treatment, but it fails to effectively eliminate these resistomes. Thus, this study investigated the performance of lime to regulate the dynamics and mobility of ARGs and MRGs in food waste composting by metagenomics. Genome-resolved analysis was further conducted to identify the ARGs and MRGs hosts and their horizontal gene transfer (HGT) events. Results showed that lime addition at 1 % (wet weight) could significantly promote temperature and pH increase to sterilize hosts, particularly pathogen bacteria (e.g. Acinetobacter johnsonii and Enterobacter cloacae), thus reducing the abundance of resistomes by more than 57.1 %. This sterilization notably reduced the number of mobile ARGs and MRGs driven by mobile genetic elements (MGEs). The contribution of MGEs located on chromosomal sequences to horizontally transfer ARGs and MRGs was significantly higher than that on mobilizable plasmids. Further analysis indicated that the reduced resistomes by lime was mainly attributed to effective sterilization of hosts rather than decreased HGT diversity. Thus, this study provides valuable insights into use lime as a low-cost control of resistomes in waste recycling.},
}

@article {pmid41060691,
year = {2025},
author = {Gao, F and Colles, FM and Ko, S and Luo, J and Sheppard, SK and Chen, M},
title = {Genomic epidemiology and the evolution of erm(B)-mediated macrolide resistance in Campylobacter.},
journal = {Microbial genomics},
volume = {11},
number = {10},
pages = {},
doi = {10.1099/mgen.0.001528},
pmid = {41060691},
issn = {2057-5858},
mesh = {*Campylobacter/genetics/drug effects/isolation & purification/classification ; *Macrolides/pharmacology ; Humans ; *Anti-Bacterial Agents/pharmacology ; Phylogeny ; Animals ; *Campylobacter Infections/epidemiology/microbiology ; *Drug Resistance, Bacterial/genetics ; China/epidemiology ; *Methyltransferases/genetics ; Genome, Bacterial ; Microbial Sensitivity Tests ; *Bacterial Proteins/genetics ; Gene Transfer, Horizontal ; Poultry/microbiology ; Evolution, Molecular ; },
abstract = {Campylobacter is a major foodborne bacterial pathogen that has become increasingly resistant to clinically important antimicrobials. Of particular concern is the emergence of erm(B)-mediated macrolide resistance, which has been increasingly documented across Campylobacter isolates from diverse ecological reservoirs. In this study, we investigated the genomic characteristics and epidemiology of erm(B)-carrying clinical Campylobacter isolates from Shanghai, alongside a globally representative dataset of all publicly available strains. Among clinical isolates obtained from a diarrhoeal outpatient surveillance programme between 2020 and 2023 in Shanghai, China, 16% (80/500) were erythromycin-resistant, with 23.8% (19/80) testing positive for erm(B). The genomes of these isolates were sequenced to identify erm(B) gene alleles. Phylogenetic analyses, pairwise comparisons of core and accessory genomes and examination of shared alleles revealed horizontal gene transfer as the predominant mechanism driving the transmission of erm(B) between isolates from various sources. Poultry was identified as a key reservoir for human infections caused by erm(B)-positive Campylobacter isolates. Comparative pangenome analyses of erm(B)-positive and negative isolates identified multiple accessory elements associated with erm(B) acquisition, among which the IS607 family transposon-associated tnpB gene exhibited sequence and structural homology to functional progenitors of CRISPR-Cas nucleases. These findings expand our understanding of the epidemiology of erm(B)-mediated macrolide resistance in Campylobacter and underscore the urgent need for enhanced antimicrobial stewardship in poultry production and targeted surveillance programmes to curb the spread of resistance.},
}

*Campylobacter/genetics/drug effects/isolation & purification/classification
*Macrolides/pharmacology
Humans
*Anti-Bacterial Agents/pharmacology
Phylogeny
Animals
*Campylobacter Infections/epidemiology/microbiology
*Drug Resistance, Bacterial/genetics
China/epidemiology
*Methyltransferases/genetics
Genome, Bacterial
Microbial Sensitivity Tests
*Bacterial Proteins/genetics
Gene Transfer, Horizontal
Poultry/microbiology
Evolution, Molecular

@article {pmid41060684,
year = {2025},
author = {Luque-Jiménez, E and Moreno-Rodríguez, A and Garzón, A and Rubio, A and Pérez-Pulido, AJ},
title = {Discovery of a bacteriophage sequence in a mite genome assembly reveals bacterial contamination and opens new possibilities for exploring arthropod symbionts.},
journal = {Microbial genomics},
volume = {11},
number = {10},
pages = {},
doi = {10.1099/mgen.0.001520},
pmid = {41060684},
issn = {2057-5858},
mesh = {Animals ; *Bacteriophages/genetics ; Symbiosis ; *Mites/microbiology/virology/genetics ; *Acinetobacter baumannii/virology/genetics ; *Acinetobacter/genetics/virology ; Genome, Viral ; Gene Transfer, Horizontal ; },
abstract = {While studying the integration site of a bacteriophage associated with the bacterium Acinetobacter baumannii, we found a genome assembly of the mite Oppiella nova that contained a homologous sequence of this locus. We initially thought of horizontal gene transfer, but it actually uncovered the contamination of 41 genome fragments with a total of 2.28 Mb. This has allowed us to assemble a new genome of the species Acinetobacter guillouiae, which could be a symbiont of the mite, based on the identification of genes potentially related to the diet of this arthropod. This contamination has been unknowingly spread, at least in another article in which authors studied a gene associated with antibiotic resistance. These results recommend the re-assembly of the O. nova genome and show how current sequencing databases have information to study microbial symbionts without the need for new experimentation.},
}

Animals
*Bacteriophages/genetics
Symbiosis
*Mites/microbiology/virology/genetics
*Acinetobacter baumannii/virology/genetics
*Acinetobacter/genetics/virology
Genome, Viral
Gene Transfer, Horizontal

@article {pmid41060308,
year = {2025},
author = {Yang, T and Zhang, M and Yi, Y and Wang, Y and Wang, Z and Zhang, R and Xiao, X and Jian, H},
title = {Diversity and Evolution of Prokaryotic Viral Lytic Proteins.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf200},
pmid = {41060308},
issn = {1751-7370},
abstract = {Lytic proteins, essential for viral life cycles, mediate cell lysis, driving nutrient and gene flow in ecosystems. Despite advances in understanding viral lysis mechanisms, the lytic proteins of prokaryotic viruses remain poorly understood at the macroevolutionary scale. Here, we constructed the Prokaryotic DNA Virus Lytic Protein Dataset, revealing the diversity, distribution patterns, and evolutionary drivers of lytic proteins across viral genomes. Our results demonstrate sequence and structural variation, suggesting that the composition of the lysis system is closely linked to viral genome size, host cell wall structure, and lifestyle, reflecting ecological adaptation. We observed that viral lytic proteins exhibit extensive sequence variation but retain structural conservation, suggesting a stronger selective pressure on structure that may be driven by the need to adapt and conform with specific cell envelope architectures. Phylogenetic analyses identified a significant co-evolutionary signal among lytic proteins, alongside extensive horizontal gene transfer of endolysin and holin encoding genes between bacteriophages and bacteria. These analyses also support that viral lytic proteins likely originated from bacterial sources, with different functional types having multiple independent origins. Moreover, comparative analysis of DNA and RNA virus lytic proteins demonstrates their diversity and differences across viral lineages. Revealing vast unexplored lytic proteins diversity, this study highlights their biotechnological potential against multidrug-resistant pathogens.},
}

@article {pmid41060007,
year = {2025},
author = {Gong, L and Yang, H and Wang, X and Wang, K and Yin, B and Yang, X and Ye, H and Lou, Z and Hu, T and Zhu, W and Zheng, B},
title = {Emergence of ST11 Klebsiella pneumoniae co-carrying blaKPC-2 and blaIMP-8 on conjugative plasmids.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0334524},
doi = {10.1128/spectrum.03345-24},
pmid = {41060007},
issn = {2165-0497},
abstract = {UNLABELLED: Klebsiella pneumoniae is a major pathogen with substantial antimicrobial resistance driven by β-lactamase production. The co-existence of carbapenemase genes blaKPC-2 and blaIMP-8 in the prevalent K. pneumoniae clone is rare and poses significant clinical challenges in China. In this study, we report the first identification of a clinical ST11 K. pneumoniae strain Kp4874, isolated from a hospitalized patient in China, co-carrying blaKPC-2 on a ~134 kb IncFII/IncR hybrid plasmid and blaIMP-8 on a ~75 kb untypable plasmid. Whole-genome sequencing revealed key insertion sequences, including TnAs1 and IS26, facilitating horizontal transfer of these resistance genes. Conjugation experiments confirmed the high transferability of both plasmids, particularly the blaKPC-2 plasmid. Despite harboring multiple virulence genes, the strain's clinical threat stems primarily from its multidrug-resistant profile. This study highlights the potential for rapid dissemination of such strains in healthcare settings and underscores the critical need for robust surveillance and infection control measures.

IMPORTANCE: This study is the first to report the co-existence of blaKPC-2 and blaIMP-8 in an ST11 Klebsiella pneumoniae strain, underscoring the clinical threat posed by these carbapenemase genes. The identification of blaKPC-2 on an IncFII/IncR hybrid plasmid, coupled with the successful conjugation of both resistance genes, highlights the significant potential for horizontal gene transfer and multidrug-resistant dissemination. These findings advance our understanding of plasmid-mediated resistance and emphasize the urgent need for enhanced monitoring and infection control strategies to mitigate the spread of such high-risk strains.},
}

@article {pmid41059698,
year = {2025},
author = {Cuevas-Espelid, W and Uzuegbunam, CU and Carag, JH and Hargita, MN and Page, AM and Stallworth, TC and Makkaoui, N and Satola, SW and Rouphael, NG and Sanchez, S and Dretler, AW},
title = {No evidence of multidrug-resistant Enterobacterales transmission between healthy companion animals and pet owners in the greater Atlanta area: a pilot study.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0050325},
doi = {10.1128/spectrum.00503-25},
pmid = {41059698},
issn = {2165-0497},
abstract = {Antimicrobial resistance (AMR) is a global concern affecting both animals and humans. Pets share a close bond with humans and are exposed to human-related conditions that can, in many cases, facilitate the transmission of bacteria and mobile genetic elements. This prospective observational cohort pilot study aimed to determine the prevalence of multidrug-resistant Gram-negative bacteria (MDR-GNB) colonization in healthy individuals and their companion animals (dogs and cats) in the greater Atlanta area, as well as to understand the prevalence of enteric MDR-GNB. Serial fecal samples from paired humans and their pets were collected and analyzed over a 6-month period (at 0, 2, and 6 months). Thirty-four pet owners participated, with 26 providing stool samples at all three time points. A total of 226 fecal samples were collected from owners and their pets. Seven of 26 humans and 12 of 43 animals were found to carry MDR-GNB, specifically species such as Escherichia coli, Enterobacter ludwigii, Enterobacter hormaechei, and Citrobacter pasteurii. Whole-genome sequencing revealed nine different resistance genes in E. coli isolates from pets and eight from humans, six different plasmid replicons, and all were located in four different phylogroups. Phylogenetic analysis indicates species-specific clustering based on host. Our results demonstrate that while MDR Enterobacterales were present in both humans and their pets in this Atlanta population, there was no evidence of bacterial transmission between pets and their owners during the study period. This finding contradicts previous similar studies that have shown transfer of MDR bacteria. However, it aligns with research that suggests bacterial colonization depends on the strain and the host.IMPORTANCEAntimicrobial resistance in animals, particularly pets, may serve as a potential source of antimicrobial resistance. However, a definitive pathway for the transmission of clonal bacteria or horizontal gene transfer between humans and their pets has not yet been identified. This pilot study aimed to assess the risk of multidrug-resistant (MDR) Enterobacterales transmission between healthy humans and their companion animals (dogs and cats) in the greater Atlanta area. Additionally, it sought to explore any association between MDR bacterial colonization and transmission within participating households. Despite the lack of a fully defined method of transmission, our findings demonstrated that while MDR Enterobacterales were present in both humans and their pets in this Atlanta population, there was no evidence of bacterial transmission between pets and their owners during the study period.},
}

@article {pmid41059692,
year = {2025},
author = {Bedi de Silva, A and Polson, SW and Schvarcz, CR and Steward, GF and Edwards, KF},
title = {Genomic diversity and global distribution of four new prasinoviruses from the tropical north Pacific.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0258324},
doi = {10.1128/spectrum.02583-24},
pmid = {41059692},
issn = {2165-0497},
abstract = {Viruses that infect phytoplankton are an integral part of marine ecosystems, but the vast majority of viral diversity remains uncultivated. Here, we introduce four near-complete genomic assemblies of viruses that infect the widespread marine picoeukaryote Micromonas commoda, doubling the number of reported genomes of Micromonas dsDNA viruses. All host and virus isolates were obtained from tropical waters of the North Pacific, a first for viruses infecting green algae in the order Mamiellales. Genome length of the new isolates ranges from 205 to 212 kb, and phylogenetic analysis shows that all four are members of the genus Prasinovirus. Three of the viruses form a clade that is adjacent to previously sequenced Micromonas viruses, while the fourth virus is relatively divergent from previously sequenced prasinoviruses. We identified 61 putative genes not previously found in prasinovirus isolates, including a phosphate transporter and a potential apoptosis inhibitor novel to marine viruses. Forty-eight genes in the new viruses are also found in host genome(s) and may have been acquired through horizontal gene transfer. By analyzing the coding sequences of all published prasinoviruses, we found that ~25% of prasinovirus gene content is significantly correlated with host genus identity (i.e., Micromonas, Ostreococcus, or Bathycoccus), and the functions of these genes suggest that much of the viral life cycle is differentially adapted to the three host genera. Mapping of metagenomic reads from global survey data indicates that one of the new isolates, McV-SA1, is relatively common in multiple ocean basins.IMPORTANCEThe genomes analyzed here represent the first viruses from the tropical North Pacific that infect the abundant phytoplankton order Mamiellales. Comparing isolates from the same location demonstrates high genomic diversity among viruses that co-occur and presumably compete for hosts. Comparing all published prasinovirus genomes highlights gene functions that are likely associated with adaptation to different host genera. Metagenomic data indicate these viruses are globally distributed, and one of the novel isolates may be among the most abundant marine viruses.},
}

@article {pmid41056605,
year = {2025},
author = {Khan, T and Khanem, A and Batool, I and Ullah, I and Younas, F},
title = {Microplastics: Disseminators of antibiotic resistance genes and pathogenic bacteria.},
journal = {Aquatic toxicology (Amsterdam, Netherlands)},
volume = {289},
number = {},
pages = {107591},
doi = {10.1016/j.aquatox.2025.107591},
pmid = {41056605},
issn = {1879-1514},
abstract = {Microplastics (MPs) are emerging pollutants that linger in the air, water, and land. Beyond their physical and chemical risks, there is growing evidence that MPs contribute to the worldwide antimicrobial resistance (AMR) dilemma by acting as carriers of harmful microbes and antibiotic resistance genes (ARGs). Despite an increase in research, the available literature is dispersed, and the part that MPs play in influencing microbial populations and fostering resistance is still not well understood. This review summarizes current research on how MPs contribute to the spread of antibiotic resistance. We concentrated on the ways in which MPs support horizontal gene transfer (HGT) processes such as conjugation, transformation, and transduction, assist biofilm development, and offer surfaces for microbial colonization. Evidence from a variety of settings suggests that MPs serve as vectors for opportunistic pathogens, such as the ESKAPE group, and ARGs, increasing the survival and movement of resistance determinants in ecosystems. Through the consolidation of current developments, this review emphasizes MPs as active resistance vectors instead of passive pollutants. We also point out important limitations, such as the lack of standardized procedures, inadequate risk assessment frameworks, and the absence of real-world exposure research. It is imperative that these issues be approached from a One Health standpoint in order to reduce the risks of both plastic pollution and antibiotic resistance.},
}

@article {pmid41051204,
year = {2025},
author = {Guillén-Navarro, D and Ochoa, SA and De La Rosa-Zamboni, D and Giono-Cerezo, S and Xicohtencatl-Cortes, J and Cruz-Córdova, A},
title = {Comparative genomics of carbapenem-resistant Acinetobacter baumannii isolated from pediatric patients in a tertiary care hospital.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0167625},
doi = {10.1128/spectrum.01676-25},
pmid = {41051204},
issn = {2165-0497},
abstract = {Acinetobacter baumannii is a short gram-negative bacillus, notable for its intrinsic multidrug resistance and genomic plasticity, which facilitates the acquisition of additional resistance genes via mobile genetic elements. Due to its increasing carbapenem resistance, the World Health Organization has classified it as a critical priority pathogen. This study performed a comparative genomic analysis of 20 carbapenem-resistant A. baumannii clinical strains isolated from the Hospital Infantil de México Federico Gómez (CRAB-HIMFG), alongside 11 genomes from other Mexican strains. The pangenome was determined to be open, and core genome single-nucleotide polymorphism-based analysis grouped the CRAB-HIMFG strains within CC758/IC5 and CC92/IC2. A novel sequence type (ST) in the MLST-Pasteur scheme was identified, related to ST[Pas]156, and in the MLST-Oxford scheme, associated with ST[Oxf]758 and ST[Oxf]1054. Virulence and resistance genes comprised 0.61% to 2.23% of the pangenome. Oxacillinase genes and efflux pumps primarily mediated carbapenem resistance, while virulence genes included those encoding biofilm and type IV pili. Capsule typing revealed a correlation with established international clones, IC2 and IC5. Plasmids exhibited high diversity, harboring maintenance modules and toxin-antitoxin systems, with the dissemination of resistance genes linked to insertion sequences. Biofilm formation and twitching motility were not always expressed, as they depend on additional environmental factors. Our study shows that comparative genomics is an essential tool to analyze clinically and epidemiologically significant genomes, providing critical insights into gene distribution, genomic architecture, and horizontal gene transfer mechanisms in microbial populations.IMPORTANCEIn recent years, a reported increase in the mortality rate associated with infections caused by A. baumannii, along with a rise in carbapenem resistance, poses a serious clinical challenge. The WHO considered this microorganism critical for research into alternative therapies and epidemiological surveillance. Despite advances in bioinformatics, genomic studies have yet to fully elucidate the structural rearrangements and secretion systems of A. baumannii. This knowledge gap hinders our understanding of its remarkable genomic plasticity and its ability to acquire and spread resistance and virulence genes through horizontal gene transfer.},
}

@article {pmid40965594,
year = {2025},
author = {Contarin, R and Murri, S and Drapeau, A and Cayssials, T and Madec, J-Y and Dordet-Frisoni, E and Haenni, M},
title = {Comprehensive genomic analysis of antibiotic resistance plasmids in animal-associated Staphylococcus aureus in France.},
journal = {Microbiology spectrum},
volume = {13},
number = {10},
pages = {e0077225},
pmid = {40965594},
issn = {2165-0497},
support = {PhD grant//ANSES/INRAE/ ; },
mesh = {Animals ; *Plasmids/genetics ; *Staphylococcus aureus/genetics/drug effects/isolation & purification ; France ; *Staphylococcal Infections/veterinary/microbiology ; Anti-Bacterial Agents/pharmacology ; Horses ; Livestock/microbiology ; Gene Transfer, Horizontal ; *Drug Resistance, Bacterial/genetics ; Genomics ; Cats ; Drug Resistance, Multiple, Bacterial/genetics ; Microbial Sensitivity Tests ; },
abstract = {UNLABELLED: In Staphylococcus aureus, an animal pathogen and zoonotic agent, plasmids play a pivotal role in the acquisition and spread of antibiotic resistance genes (ARGs). This study investigated the plasmid content of 329 S. aureus isolates from livestock and companion animals collected in France between 2010 and 2021. Plasmids (n = 211) were identified from 139 isolates. The major families identified-rep7a, rep20, and rep10-were associated with specific resistance genes (str, cat, blaZ, erm(C)) and exhibited widespread horizontal transfer across different S. aureus sequence types (STs) and animal hosts. In temporal analysis, the rep7a/str and rep7a/cat plasmids circulating in horses were progressively replaced by a rep7a plasmid carrying both str and cat genes. The study also highlighted the presence of mosaic plasmids, which combined elements from different bacterial species/genera, confirming the broad host range of S. aureus plasmids and their ability to acquire ARGs from diverse sources. Moreover, the occurrence of hybrid plasmids (carrying multiple rep genes) underscores the plasticity of these vectors of ARGs. This study emphasizes the need to investigate the mechanisms driving the spread and persistence of antibiotic-resistant plasmids in S. aureus, with a view to developing strategies aimed at combating antibiotic resistance.

IMPORTANCE: The spread of antibiotic resistance in Staphylococcus aureus is a growing concern, particularly in animals that can serve as reservoirs for resistant strains. This study highlights the crucial role of plasmids in transmitting resistance genes among different animal hosts and S. aureus lineages. The characterization of 329 isolates collected over 10 years revealed how certain plasmid families are associated with specific resistance genes and how they evolve over time. The occurrence of mosaic and hybrid plasmids further underscores the ability of S. aureus to acquire resistance from diverse bacterial sources. These findings provide key insights into the mechanisms shaping antibiotic resistance in this pathogen and emphasize the fact that understanding plasmid-driven resistance is essential for developing effective interventions to limit the spread of multidrug-resistant S. aureus in both veterinary and human medicine.},
}

Animals
*Plasmids/genetics
*Staphylococcus aureus/genetics/drug effects/isolation & purification
France
*Staphylococcal Infections/veterinary/microbiology
Anti-Bacterial Agents/pharmacology
Horses
Livestock/microbiology
Gene Transfer, Horizontal
*Drug Resistance, Bacterial/genetics
Genomics
Cats
Drug Resistance, Multiple, Bacterial/genetics
Microbial Sensitivity Tests

@article {pmid40271811,
year = {2025},
author = {Bravo-Arévalo, JE},
title = {Tracing the evolutionary pathway: on the origin of mitochondria and eukaryogenesis.},
journal = {The FEBS journal},
volume = {292},
number = {19},
pages = {5026-5041},
doi = {10.1111/febs.70109},
pmid = {40271811},
issn = {1742-4658},
support = {CF-2023-I-1545//Consejo Nacional de Humanidades, Ciencias y Tecnologías/ ; PAPIIT: IN218424//Dirección General de Asuntos del Personal Académico, Universidad Nacional Autónoma de México/ ; },
mesh = {*Mitochondria/genetics/metabolism ; Symbiosis/genetics ; Phylogeny ; *Eukaryota/genetics/metabolism ; *Biological Evolution ; *Evolution, Molecular ; *Eukaryotic Cells/metabolism ; Mitochondrial Proteins/genetics/metabolism ; Animals ; Protein Transport ; Humans ; Gene Transfer, Horizontal ; },
abstract = {The mito-early hypothesis posits that mitochondrial integration was a key driver in the evolution of defining eukaryotic characteristics (DECs). Building on previous work that identified endosymbiotic selective pressures as central to eukaryotic cell evolution, this study examines how endosymbiotic gene transfer (EGT) and the resulting genomic and bioenergetic constraints shaped mitochondrial protein import systems. These systems were crucial for maintaining cellular function in early eukaryotes and facilitated their subsequent diversification. A primary focus is the co-evolution of mitochondrial import mechanisms and eukaryotic endomembrane complexity. Specifically, I investigate how the necessity for nuclear-encoded mitochondrial protein import drove the adaptation of bacterial secretion components, alongside eukaryotic innovations, to refine translocation pathways. Beyond enabling bioenergetic expansion, mitochondrial endosymbiosis played a fundamental role in the emergence of compartmentalisation and cellular complexity in LECA, driving the evolution of organellar networks. By integrating genomic, structural and phylogenetic evidence, this study aimed to contribute to the mito-early framework, clarifying the mechanisms that linked mitochondrial acquisition to the origin of eukaryotic cells.},
}

*Mitochondria/genetics/metabolism
Symbiosis/genetics
Phylogeny
*Eukaryota/genetics/metabolism
*Biological Evolution
*Evolution, Molecular
*Eukaryotic Cells/metabolism
Mitochondrial Proteins/genetics/metabolism
Animals
Protein Transport
Humans
Gene Transfer, Horizontal

@article {pmid41049799,
year = {2025},
author = {McLeod, DV and Gandon, S},
title = {Horizontal gene transfer, segregation loss, and the speed of microbial adaptation.},
journal = {Evolution letters},
volume = {9},
number = {5},
pages = {576-588},
pmid = {41049799},
issn = {2056-3744},
abstract = {Microbial adaptation is driven by the circulation of mobile genetic elements (MGEs) among bacteria. On the one hand, MGEs can be viewed as selfish genes that spread like infectious diseases in a host population. On the other hand, the horizontal transfer and the loss of these MGEs are often viewed as a form of sexual reproduction that reshuffles genetic diversity in a way that may sometimes be adaptive for bacteria cells. Here, we show how these 2 perspectives can be reconciled using a single unified framework capturing the dynamics of multiple, interacting MGEs. We apply this framework to study how interactions between MGEs affecting rates of horizontal gene transfer and segregation loss shape the short- and long-term evolutionary dynamics of MGEs and the bacteria population. We show that these interactions produce nonrandom MGE associations that can speed up or slow down microbial adaptation depending on the evolutionary conflicts between MGEs as well as between MGEs and their bacterial hosts. Moreover, we show how these interactions affect the evolutionary potential of the bacteria population. We discuss the implications of these predictions for the community response to environmental stressors such as antibiotic treatment or vaccination campaigns as well as the evolution of accessory genomes.},
}

@article {pmid40858018,
year = {2025},
author = {Xu, J and Wen, X and Wang, S and Worrich, A and Ma, B and Zou, Y and Wang, Y and Wu, Y},
title = {Identification of key species and molecular mechanisms driving conjugative transfer of antibiotic resistance genes in swine manure-derived bacterial communities.},
journal = {Journal of hazardous materials},
volume = {497},
number = {},
pages = {139638},
doi = {10.1016/j.jhazmat.2025.139638},
pmid = {40858018},
issn = {1873-3336},
mesh = {*Manure/microbiology ; Animals ; Swine ; *Conjugation, Genetic ; Plasmids/genetics ; *Drug Resistance, Bacterial/genetics ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/drug effects ; Genes, Bacterial ; Gene Transfer, Horizontal ; },
abstract = {The spread of antimicrobial resistance in livestock environments poses a major public health risk. Conjugative transfer plays a key role in antimicrobial resistance transmission, but the diversity of bacterial hosts involved and the molecular mechanisms driving conjugative transfer within complex microbial communities remain poorly understood. To address this, we investigated plasmid-mediated conjugation in both a swine manure-derived bacterial community and isolated strains from manure. Our study identified 53 OTUs as plasmid recipients, with 66 % belonging to Proteobacteria. Exposure to subinhibitory doxycycline levels decreased the diversity of transconjugants, but conjugation-related gene expression was significantly upregulated, which also became apparent in a marked increase in conjugation frequency. Increased conjugation frequency correlated with increased ATP, ROS and eLDH levels both in the complex bacterial community and in pairwise strains, pointing to the physiological shifts occurring in species that engage in conjugation. Among the identified recipients, Bacillus velezensis exhibited the highest conjugation frequency, likely due to the upregulation of its two-component system, quorum sensing pathways, and strong biofilm-forming ability. Our findings provide new insights into conjugative transfer in livestock manure, identifying potential key spreaders and highlighting opportunities for targeted intervention strategies to mitigate antimicrobial resistance transmission, thereby enhancing its sustainability as a fertilizer.},
}

*Manure/microbiology
Animals
Swine
*Conjugation, Genetic
Plasmids/genetics
*Drug Resistance, Bacterial/genetics
*Drug Resistance, Microbial/genetics
Anti-Bacterial Agents/pharmacology
*Bacteria/genetics/drug effects
Genes, Bacterial
Gene Transfer, Horizontal

@article {pmid41048508,
year = {2025},
author = {Olanrewaju, OS and Bezuidenhout, CC},
title = {Harnessing beneficial bacteria to remediate antibiotic-polluted agricultural soils: integrating source diversity, bioavailability modulators, and ecological impacts.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1635233},
pmid = {41048508},
issn = {1664-302X},
abstract = {Antibiotic contamination in agricultural soils, primarily from manure application and wastewater irrigation, has emerged as a critical threat to food security, environmental health, and public safety due to the proliferation and persistence of antibiotic-resistant genes. This review examines the diverse sources and ecological impacts of antibiotics in soil, including their alteration of microbial community structures, promotion of horizontal gene transfer, and subsequent risks to plant and human health. It further evaluates how soil properties, such as pH, organic matter content, and texture, influence the bioavailability of antibiotics and modulate their degradation dynamics. Emphasis is placed on the bioremediation potential of beneficial bacteria, detailing key mechanisms such as enzymatic biodegradation, biosorption, biofilm formation, and the formation of synergistic microbial consortia capable of utilizing antibiotics as nutrient sources. In addition, the manuscript critically discusses the regulatory, technological, and scalability challenges inherent to deploying microbial bioremediation strategies, including integrating gene editing and systems biology approaches under a One Health framework. By synthesizing molecular insights with environmental and policy considerations, this review provides a comprehensive assessment of current bioremediation strategies and outlines future directions to mitigate the ecological and health risks associated with antibiotic pollution in agricultural ecosystems.},
}

@article {pmid41047836,
year = {2025},
author = {Reddy, LB and Saier, MH},
title = {Microbiome: Friend or Friendly Foe.},
journal = {Microbial physiology},
volume = {},
number = {},
pages = {},
doi = {10.1159/000548748},
pmid = {41047836},
issn = {2673-1673},
abstract = {The human microbiome is a dynamic, polymicrobial ecosystem that plays an essential role in nutrition, immune development, barrier integrity, and host physiology, acting as a mutualistic partner under balanced conditions. However, its ecological complexity, genetic adaptability through horizontal gene transfer, and interactions with other prokaryotes as well as protozoan and metazoan parasites can transform commensals into pathobionts, resulting in weakened host's barriers, immunity declines with the progression of age, and community composition shifts toward dysbiosis. Factors such as diet, genetics, aging, immune-senescence, impaired autophagy, and environmental exposure, all influence this delicate balance, determining whether the microbiome remains protective or becomes an opportunistic source of inflammation and disease. This review focuses on the study of the intestinal microbiome in humans. Maintaining microbiome homeostasis is promoted through (a) dietary diversity, (b) limited antimicrobial use, (c) use of probiotics, (d) support for gut barrier function, and (e) healthy lifestyle improvements. These actions and considerations are critical to prevent the emergence of pathogenic states and preserving the microbiome's vital role in host health throughout life.},
}

@article {pmid41045126,
year = {2025},
author = {Sylvester, T and Adams, R and Mitchell, RF and Shen, R and McKenna, DD},
title = {Genomic Architecture of the Pole Borer, Neandra brunnea (Cerambycidae: Parandrinae), Sheds Light on the Evolution of Wood-Feeding in Longhorn Beetles.},
journal = {The Journal of heredity},
volume = {},
number = {},
pages = {},
doi = {10.1093/jhered/esaf080},
pmid = {41045126},
issn = {1465-7333},
abstract = {Neandra brunnea, commonly known as the pole borer, is a species of wood-boring (xylophagous) longhorn beetle (family Cerambycidae) found throughout most of eastern North America. We sequenced, assembled and annotated the genome of N. brunnea and compared it to publicly available genomes of other Cerambycidae. The 1.23 Gb N. brunnea genome assembly was distributed across 78 contigs, with an N50 of 38.88 Mb and largest contig of 74.28 Mb. Most of the genome was comprised of repetitive sequences, with 81.39% comprising interspersed repeats. Most (99.7%) of the expected orthologous genes (BUSCOs) were present and fully assembled, with only 2.5 % duplicated. The genome annotation identified 13,003 genes (15,574 transcripts), including 301 putative horizontally transferred loci from a diversity of both prokaryotic and eukaryotic donors. The assembled mitochondrial genome is relatively large at 17 kb and shows an unusual repeating array of d-loop segments. As the first representative of the longhorn beetle subfamily Parandrinae with a sequenced genome, N. brunnea provides an important new point of reference for the comparative study of beetle genomes and a further resource for studies of the evolution and genomic basis of xylophagy.},
}

@article {pmid41043291,
year = {2025},
author = {Zhang, B and Liu, Q and Wang, L and Tang, J},
title = {Synergistic effects of micro/nanoplastics and Cu(II) on horizontal transfer of antibiotic resistance genes: New insight targeting on cell surface properties.},
journal = {Journal of hazardous materials},
volume = {498},
number = {},
pages = {139975},
doi = {10.1016/j.jhazmat.2025.139975},
pmid = {41043291},
issn = {1873-3336},
abstract = {Microplastics (MPs) and nanoplastics (NPs) facilitate antibiotic resistance genes (ARGs) transfer through horizontal gene transfer (HGT). However, the combined effects of M-NPs and heavy metals on HGT remain poorly understood, and the effects of cell surface properties is neglected. In this study, an antibiotic co-existence heavy metal Cu was used to study its synergetic effect with M-NPs on HGT, with a specific focus on bacterial surface characteristics and physiological responses. Results reveal that NPs amplified Cu(II)'s effect on conjugative transfer of ARGs, while MPs showed mitigation effect. NPs+Cu(II) co-exposure yielded the highest conjugative transfer frequency (4.4-fold) and a 35-fold surge in transformation frequency compared to the control. These disparities stem from bacterial physiological responses, including 4-7-fold elevated reactive oxygen species (ROS), 3-4-fold increased membrane permeability, 1.5-1.8-fold enhanced ATP synthesis, altered drug-resistant efflux and metabolic pathways; Furthermore, cell surface property modulation-Cu(II) stimulated 1.2-fold lipopolysaccharide (LPS) production and M-NPs regulated outer membrane vesicles (OMVs) concentration/sizes, with extracellular polymeric substances (EPS) optimizing interbacterial aggregation for gene transfer. In addition, MPs+Cu(II) induced 49 % viable but non-culturable (VBNC) bacteria and high-dose M-NPs caused excessive bacterial injury/death, reducing gene transfer (VBNC ratio indicating stress severity). These findings highlight co-exposure impacts and offer novel insights into the environmental risks posed by M-NPs and ARGs.},
}

@article {pmid40706873,
year = {2025},
author = {Richer-Fortin, A and Veillette, M and Rossi, F and Longtin, Y and Larrotta, A and Paquet-Bolduc, B and Duchaine, C},
title = {Characterization of the environment of patients colonized with carbapenemase-producing organisms: role of air and surfaces in the dissemination of key resistance genes.},
journal = {The Journal of hospital infection},
volume = {164},
number = {},
pages = {55-63},
doi = {10.1016/j.jhin.2025.07.003},
pmid = {40706873},
issn = {1532-2939},
mesh = {Humans ; *beta-Lactamases/genetics ; *Bacterial Proteins/genetics ; Prospective Studies ; *Environmental Microbiology ; Quebec ; Hospitals ; Cross Infection/microbiology/transmission ; *Air Microbiology ; Real-Time Polymerase Chain Reaction ; *Gene Transfer, Horizontal ; },
abstract = {BACKGROUND: Hospital-associated infections caused by carbapenemase-producing organisms (CPOs) pose a significant health concern. Healthcare settings implement measures to control the spread of CPOs and prevent outbreaks, but the role of air in disseminating carbapenemase genes remains unclear. This study assessed three carbapenemase-associated genes (blaKPC, blaOXA-48 and blaNDM) in the environment of CPO-colonized patients.

METHODS: A prospective observational study was conducted in four hospitals in Quebec, Canada in the rooms of CPO-colonized patients. Air was collected actively inside the rooms of CPO-colonized patients, and floor and no-touch surfaces were sampled using pre-moistened swabs and sponges; the findings were compared with those from control rooms (i.e. rooms hosting non-CPO-colonized patients) located on the same floor. Additional floor samples were collected in adjacent hallways to estimate potential dissemination within the settings. The presence and abundance of carbapenemase-producing genes (blaKPC, blaNDM and blaOXA-48) were evaluated using quantitative polymerase chain reaction.

RESULTS: Carbapenemase-encoding genes were detected frequently in CPO-colonized patient environments, notably on floors (97% of detection frequency), door frames (52%), and no-touch surfaces (42%). Conversely, only one air sample tested positive for blaKPC. These genes were also detected in hallways adjacent to the rooms of CPO-colonized patients (92%), control rooms (100%), and hallways adjacent to the rooms of non-CPO-colonized patients (78%), with abundance decreasing with distance from CPO-colonized rooms.

CONCLUSION: These findings suggest that carbapenem resistance can spread within healthcare settings, and air may play a role in gene dissemination. Additional measures should be considered to limit resistance gene transfer, particularly via floors and air.},
}

Humans
*beta-Lactamases/genetics
*Bacterial Proteins/genetics
Prospective Studies
*Environmental Microbiology
Quebec
Hospitals
Cross Infection/microbiology/transmission
*Air Microbiology
Real-Time Polymerase Chain Reaction
*Gene Transfer, Horizontal

@article {pmid41043234,
year = {2025},
author = {Ukachi, UO and Rajasekar, A and Gao, B and Shen, W},
title = {Dynamics and mitigation of antibiotic resistance genes during manure composting: A comprehensive review.},
journal = {Ecotoxicology and environmental safety},
volume = {304},
number = {},
pages = {119152},
doi = {10.1016/j.ecoenv.2025.119152},
pmid = {41043234},
issn = {1090-2414},
abstract = {The global spread of antibiotic resistance genes (ARGs) poses a significant threat to public health, facilitated by the extensive use of antibiotics in livestock production and the subsequent environmental dissemination of ARGs through animal manure. Manure composting has emerged as a widely adopted strategy for manure management and pathogen reduction; however, its effectiveness in mitigating ARGs remains variable and dependent on specific conditions. This review provides a comprehensive synthesis of the current state of knowledge and understanding of the fate of ARGs during manure composting processes, highlighting the influence of key factors, including temperature, pH, carbon-to-nitrogen ratio, aeration, and moisture content, on ARG dynamics. It further explores the roles of microbial community shifts, horizontal gene transfer, and mobile genetic elements in ARG persistence and attenuation, alongside recent advancements in composting technologies that show promise in ARG mitigation such as hyperthermophilic composting, biochar amendment, electrokinetic and magnetic field-assisted composting, and microbial inoculation, The review also highlights the limitations of current practices, including the potential for ARG resurgence during later composting stages and the lack of standardized evaluation protocols. Finally, it identifies critical research gaps and proposes future directions centered on integrated mitigation strategies, long-term field assessments, and the development of risk assessment frameworks. These insights aim to guide researchers, policymakers, and stakeholders in improving composting practices to curb the dissemination of ARGs and safeguard environmental and public health. This review highlights composting as a promising strategy for reducing ARGs in manure, while identifying knowledge gaps related to long-term ecological impacts and optimal operational conditions.},
}

@article {pmid41042234,
year = {2025},
author = {Sathe, S and Becks, L},
title = {Reciprocal effects of programmed cell death on fitness in unicellular endosymbiotic Chlorella and its ciliate host.},
journal = {Journal of evolutionary biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jeb/voaf119},
pmid = {41042234},
issn = {1420-9101},
abstract = {Programmed cell death (PCD), the genetically controlled active cellular suicide mechanism in multicellular organisms, also exists in unicellular organisms. However, explaining the evolution of PCD by natural selection in these organisms remains a challenge. PCD likely emerged during early endosymbiotic events as an initial antagonistic adaptation, enabling unicellular parasitic proto-endosymbionts to exploit their hosts, for example, by triggering host death in response to nutrient depletion or releasing offspring. Over time, during endosymbiont domestication and, as proposed, through horizontal gene transfer from endosymbionts to the host, PCD evolved in the host, providing benefits to both the host and the endosymbionts. However, the underlying assumption of this hypothesis, that PCD benefits and non-PCD (necrosis) harms the endosymbionts and/or the host, remains untested. Here, we investigated the fitness consequences of heat-shock-induced PCD in the endosymbiotic chlorophyte Chlorella variabilis and its facultative symbiotic ciliate host Paramecium bursaria, the non-symbiotic C. sorokiniana, and the predatory host P. duboscqui. Heat-shock triggered PCD in C. variabilis and the two ciliate species, causing significant fitness consequences. The supernatant from C. variabilis PCD enhanced the growth of its own clones and endosymbiotic host while inhibiting the growth of the predatory host. The supernatants from necrotic C. variabilis reduced growth of both Chlorella and Paramecium. Similarly, PCD in the symbiotic Paramecium host benefited Chlorella, whereas PCD and necrosis in the predatory Paramecium host were detrimental. These results expand the understanding of unicellular PCD, highlighting its dual role in benefiting clonal populations and their specific endosymbiotic partners, thereby affecting endosymbiosis evolution.},
}

@article {pmid41039777,
year = {2025},
author = {Wang, Q and Ye, Y and Wang, L and Guan, Y and Wang, S and Wang, Z and Sun, H and Smith, SM and Huang, J},
title = {Independent horizontal transfer of genes encoding α/β-hydrolases with strigolactone binding and hydrolytic activities from bacteria to fungi and plants.},
journal = {Molecular plant},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.molp.2025.09.021},
pmid = {41039777},
issn = {1752-9867},
abstract = {Strigolactones (SLs) are not only phytohormones that influence multiple aspects of plant growth and development, but also signaling molecules for interactions between plants and certain fungi or bacteria. In plants, the SL receptor is an α/β-hydrolase (ABH) encoded by the D14/KAI2 gene family, which is known to be derived from proteobacterial RsbQ through horizontal gene transfer (HGT). In the phytopathogenic fungus Cryphonectria parasitica, another ABH named CpD14 was found to possess SL binding and hydrolytic activities and mediate SL responses, exhibiting potential SL perception functions. Here, we demonstrate that CpD14 and its homologs in Leotiomyceta fungi were derived from actinobacteria through an independent HGT event, forming a distinct CpD14-like (CDL) family across fungi and bacteria. X-ray crystallography and structural analyses reveal that actinobacterial and fungal CDL proteins share a conserved core 'α/β fold' domain with D14/KAI2/RsbQ but possess a unique lid domain. Biochemical assays show that both actinobacterial CDL and proteobacterial RsbQ can recognize and hydrolyze SLs, suggesting that they are pre-adapted for SL responses and potential perception. Plant D14/KAI2 and fungal CDL proteins retained these functional activities while evolving distinct ligand specificities for SL structural variants. This work reveals that independent HGT events from two bacterial groups apparently provided plants and their interacting fungi with pre-adapted ABH proteins which were deployed for SL perception or responses.},
}

@article {pmid41038999,
year = {2025},
author = {Feng, SY and Arab, Y and Hauck, Y and Poirette, P and Noiray, M and Quevillon-Cheruel, S and Marsin, S and Andreani, J and Mirouze, N},
title = {ComK2 represses competence development for natural transformation in Staphylococcus aureus grown under strong oxygen limitation.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {1416},
pmid = {41038999},
issn = {2399-3642},
support = {ANR-18-CE35-0004, GenTranSa//Agence Nationale de la Recherche (French National Research Agency)/ ; MICROBES//Université Paris-Saclay (University of Paris-Saclay)/ ; MICROBES//Université Paris-Saclay (University of Paris-Saclay)/ ; MICROBES//Université Paris-Saclay (University of Paris-Saclay)/ ; },
mesh = {*Staphylococcus aureus/genetics/metabolism/growth & development ; *Oxygen/metabolism ; *Bacterial Proteins/metabolism/genetics ; Gene Expression Regulation, Bacterial ; Humans ; *Transformation, Bacterial ; },
abstract = {The facultative anaerobe and major human pathogen Staphylococcus aureus is able to sustain growth under a wide range of oxygen concentrations. Importantly, we have already demonstrated that under microaerobic conditions, sensed by the two-component system SrrAB, S. aureus efficiently induces the development of competence for natural transformation, one of the three main horizontal gene transfer mechanisms present in bacteria. Here, we show that when the oxygen concentration decreases even further (reaching almost anaerobic conditions) the development of competence for natural transformation is still allowed but with much less efficiency than under microaerobic conditions. This inhibition is controlled by a central competence regulator, named ComK2, that was not found involved under intermediate oxygen concentrations. This ComK2-dependent inhibitory pathway also involves the SA2107 protein, of unknown function, through a direct protein-protein interaction. Finally, we demonstrate that this inhibition of competence is controlled by this strong oxygen limitation, sensed by another two-component system named NreBC, probably involved in the same pathway as ComK2 and SA2107. All in all, our results show that the oxygen concentration, which varies drastically depending on the site in the human body but also during bacterial infections, is a key environmental factor that tightly modulates S. aureus genomic plasticity.},
}

*Staphylococcus aureus/genetics/metabolism/growth & development
*Oxygen/metabolism
*Bacterial Proteins/metabolism/genetics
Gene Expression Regulation, Bacterial
Humans
*Transformation, Bacterial

@article {pmid41038565,
year = {2025},
author = {Habiba, U and Noor, M and Kayani, MUR and Huang, L},
title = {Horizontal gene transfers differentially shape the functional potential of the infant gut metagenome.},
journal = {Life sciences},
volume = {},
number = {},
pages = {124006},
doi = {10.1016/j.lfs.2025.124006},
pmid = {41038565},
issn = {1879-0631},
abstract = {Horizontal gene transfer (HGT) is a major driver of microbial evolution, influencing the metabolic potential of microbial communities. Despite its significance, the consequences of HGT in shaping the microbial metabolic potential remain poorly understood, particularly in complex environments such as the human gut. This study aimed to assess the impact of HGT in infant gut microbiome from Caesarean section (CSD) and vaginal delivery (VD) groups during the first year of life. At Month 0, CSD infants exhibited a higher number of HGT events than VD infants. However, the numbers converged around Month 2 and remained comparable until Month 9, with no significant differences between groups (p > 0.05). HGT in VD was primarily driven by Coprococcus catus and Ruminococcus sp_5_1_39BFAA, while in CSD, Salmonella enterica and Klebsiella pneumoniae were dominant donors and acceptors. Functional analysis revealed that HGT in VD enriched genes related to carbohydrate metabolism and immune responses, whereas CSD was enriched for metabolic processes and biofilm formation. Additionally, HGT events were associated with Neonatal Intensive Care Unit Admission and diet transitions. These results suggest that HGT events in the VD and CSD groups differently shape the functional potential of the infant gut microbiome, with possible health implications that require further investigation. However, experimental validation is needed to establish a causal link.},
}

@article {pmid41038556,
year = {2025},
author = {Chen, L and Shao, H and Gong, S and Li, C and Jin, L and Huang, Z and Wang, P and Meng, X and Ren, L},
title = {Enhanced Mitigation of Antibiotic Resistance Genes in Anaerobic Digestion of Food Waste Using Biochar-Supported Nanoscale Zero-Valent Iron.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {127191},
doi = {10.1016/j.envpol.2025.127191},
pmid = {41038556},
issn = {1873-6424},
abstract = {Food waste (FW) is a crucial biomass resource and reservoir of antibiotic resistance genes (ARGs). Biochar-supported nanoscale zero-valent iron (BC-nZVI) can enhance methane production in the anaerobic digestion (AD) of FW. However, the mechanisms underlying the effects of BC-nZVI on the fate of ARGs during AD are remain unclear. Here, the impacts of BC-nZVI on the fate of total ARGs were investigated, by analyzing dynamics of representative types of ARGs including intracellular and extracellular ARGs (iARGs and eARGs). We found a significant decrease in the abundance of the most ARGs during AD treated with BC-nZVI. Specially, the relative abundance of iARGs (tet32, ermF, sul1, and tetW) decreased by 30.58%, 11.38%, 16.69%, and 3.65%, respectively, while that of eARGs (tet32, ermF, sul1, and tetW) decreased by 95.09%, 48.18%, 88.55%, and 71.41%, respectively. The relative abundances of intracellular and extracellular intI1 decreased by 17.42% and 41.96%, respectively. BC-nZVI enhanced microbial metabolism, prevented SOS response activation, reduced the expression of type IV secretion systems, and decreased extracellular polymeric substance secretion, which could contribute to the decrease in ARGs. These findings indicate that BC-nZVI can effectively mitigate the risk of ARGs in AD by reducing their abundance and inhibiting their horizontal transfer.},
}

@article {pmid41038001,
year = {2025},
author = {Li, H and Liu, Y and Ge, S and Huang, H and Li, W and Li, S and Li, X and Li, C and Du, XD and Xu, C and Yao, H},
title = {Emergence of cfr(C) variant in Campylobacter coli derived food-producing animal origin.},
journal = {Veterinary microbiology},
volume = {310},
number = {},
pages = {110742},
doi = {10.1016/j.vetmic.2025.110742},
pmid = {41038001},
issn = {1873-2542},
abstract = {Campylobacter is the leading cause of foodborne bacterial gastroenteritis globally. The cfr(C) gene encodes a 23S rRNA methyltransferase conferring cross-resistance to multiple classes of antibiotics. Here, we identified three novel cfr(C) variants in C. coli of swine origin. Compared to the original cfr(C), cfr(C)-variant-69 carried substitutions (Glu94Ala, Pro159Leu, Lys178Gln, Ile318Val), and cfr(C)-variant-104 and cfr(C)-variant-1921C17 harbored frame-shift mutations. Functional assay demonstrated that only cfr(C)-variant-69 conferred elevated MIC values 8-fold (florfenicol), 4-fold (chloramphenicol), and 2-fold (linezolid) compared to the parental strain NCTC 11168, respectively. In addition, a total of 67 C. coli isolates were identified to carry cfr(C) (64 from Genbank database and three from this study). WGS analysis revealed the global distribution of cfr(C) across five countries. MLST analysis indicated that 22 distinct sequence types were associated with cfr(C) dissemination, with ST1068 representing the predominant lineage. wg-MLST analysis stratified by collection time, geographic origin, and source, revealed significant clonal relatedness among strains from different years, countries, or origins. Furthermore, 18 distinct genetic environments flanking cfr(C) were identified among the isolates, with type 11 representing the predominant genotype [hph-pcp-hp-aphA3-cfr(C)-hp-hp]. Notably, the cfr(C) gene was flanked by multiple transposable elements (ISAcsp6, ISCco2, ISChh1, ISEncal, and ISSag10) across different genetic contexts, in which ISAcsp6 and ISEncal were firstly reported. In conclusion, we identified a novel functional cfr(C) variant in poultry-derived C. coli and characterized the global dissemination of cfr(C), demonstrating both horizontal gene transfer and regional clonal expansion among C. coli. One Health genomic surveillance for cfr(C)-positive Campylobacter spp. is critical to mitigate this escalating antimicrobial resistance threat.},
}

@article {pmid41034649,
year = {2025},
author = {Szánthó, LL and Merényi, Z and Donoghue, P and Gabaldón, T and Nagy, LG and Szöllősi, GJ and Ocaña-Pallarès, E},
title = {A timetree of Fungi dated with fossils and horizontal gene transfers.},
journal = {Nature ecology & evolution},
volume = {},
number = {},
pages = {},
pmid = {41034649},
issn = {2397-334X},
abstract = {Dating the tree of Fungi has been challenging due to a paucity of fossil calibrations and high taxonomic diversity of the group. Here we reconstructed and dated a comprehensive phylogeny comprising 110 fungal species, utilizing 225 phylogenetic markers and accounting for across-site compositional heterogeneity in amino acid sequences. To address uncertainties in fungal dating, we sampled chronograms from four relaxed molecular clock analyses, each integrating distinct sets of calibrations and relative time-order constraints. The first analysis used a core set of 27 calibrations alongside 17 relative constraints derived from fungi-to-fungi horizontal gene transfer events. Three further analyses extended this core set with additional timing information identified in our reevaluation of the evolution of pectin-specific enzymes in Fungi. Our timetree, integrating analytic uncertainties, suggests older ages for crown Fungi (1,401-896 Ma) than recently reported, providing a minimum age for ancient interactions involving fungi and the algal ancestors of embryophytes in terrestrial ecosystems (1,253-797 Ma). This supports a protracted gap between the onset of these interactions and the rise of modern land plants. Altogether, our study provides a refined timescale for fungal diversification and a temporal framework for future investigations into early interactions involving fungi and the algal ancestors of embryophytes.},
}

@article {pmid41033636,
year = {2025},
author = {Yu, LQ and Chen, Y and Wang, DE and Yao, B and Yuan, F and Yan, YC and Zhang, LB and Liu, JY and Liu, M},
title = {The effect of sulfamethoxazole on methanogenesis and intracellular and extracellular antibiotic resistant genes transmission in anaerobic granular sludge.},
journal = {Environmental research},
volume = {},
number = {},
pages = {122987},
doi = {10.1016/j.envres.2025.122987},
pmid = {41033636},
issn = {1096-0953},
abstract = {Anaerobic granular sludge has been extensively utilized in anaerobic wastewater treatment due to its stable structure and strong resistance to shock loads. However, the mechanisms by which varying concentrations of sulfamethoxazole (SMX) influence methane production, as well as the transmission of intracellular and extracellular antibiotic resistance genes (ARGs), remain unclear. This study investigated the effects of SMX concentration on methane production and intracellular and extracellular ARGs transfer behavior during anaerobic wastewater treatment. Results showed that the final methane yield was 333.2, 470.1, 199.1, and 7.2 mL/gCOD, respectively, under 0, 0.5, 5, and 10 mg/L SMX. 0.5 mg/L SMX enhanced methane yield by 41.1%. This enhancement was attributed to the stimulation of extracellular polymeric substances and catalase secretion, which alleviated oxidative stress caused by reactive oxygen species and increased the abundance of Methanosaeta and Methanobacterium. Simultaneously, the spread of both intracellular and extracellular ARGs was suppressed through the regulation of host microbial communities, specifically reflected in the reduced abundance of ARGs, decreased abundance of cell membrane permeability genes and the type IV secretion system. In contrast, 5 and 10 mg/L SMX inhibit methane production while facilitating ARGs dissemination. This study demonstrates that SMX concentration significantly affects methane production and the prevalence of ARGs during anaerobic wastewater treatment.},
}

@article {pmid41033070,
year = {2025},
author = {Han, M and Chen, Q and Li, Z and Hu, X and Ma, J and Qin, C and Gao, Y},
title = {Cellular mechanism of perfluoroalkyl substances with different chain lengths influence conjugative transfer of antibiotic resistance genes.},
journal = {Environment international},
volume = {204},
number = {},
pages = {109810},
doi = {10.1016/j.envint.2025.109810},
pmid = {41033070},
issn = {1873-6750},
abstract = {Per- and polyfluoroalkyl substances (PFAS) are emerging persistent environmental pollutants with potential risks to microbial ecosystems. However, the influence of PFAS with different chain lengths on horizontal gene transfer, particularly plasmid-mediated antibiotic resistance genes (ARGs) conjugation, remains poorly understood. This study investigated the impacts of short-chain (PFBA, PFHxA) and long-chain (PFNA) PFAS exhibited dual effects on the conjugative transfer of ARGs: PFAS with lower concentration (<0.05 mg/L) enhanced ARGs transfer by increasing the permeability of the cell membrane and ROS content, while higher concentration (>0.05 mg/L) of PFAS led to stronger inhibition through suppressing adenosine triphosphate (ATP) production. The scarcity of ATP caused cells to rebuild their energy allocation strategies, diverting more energy towards maintaining vital life activities rather than for gene transmission. Notably, short-chain PFAS (e.g. PFBA) of smaller molecular possessed greater facility for entering cells and caused stronger dual effects on cells. However, long-chain PFAS with high hydrophobicity prefers to embed in the phospholipid bilayer, causing weaker dual effects on cells and less frequency of conjugative transfer. These findings revealed the distinct effects of PFAS with different chain lengths on the conjugative transfer of ARGs, and highlighted the critical role of the cell membrane in this phenomenon. This research provides critical insights into the ecological risks posed by PFAS.},
}

@article {pmid41031813,
year = {2025},
author = {Mavrodi, DV and Blankenfeldt, W and Mavrodi, OV and Weller, DM and Thomashow, LS},
title = {Microbial phenazines: biosynthesis, structural diversity, evolution, regulation, and biological significance.},
journal = {Microbiology and molecular biology reviews : MMBR},
volume = {},
number = {},
pages = {e0014723},
doi = {10.1128/mmbr.00147-23},
pmid = {41031813},
issn = {1098-5557},
abstract = {SUMMARYPhenazines are small, redox-active secondary metabolites produced by various bacterial species. These compounds participate in electron-transfer reactions, aiding microbes in surviving stressful or oxygen-limited environments. In this review, we examine the extensive structural diversity of phenazines and trace the evolutionary history of their biosynthetic pathways, which often move between distantly related species through horizontal gene transfer. We also explore how environmental factors such as nutrient levels and cell-to-cell signaling regulate phenazine production. Beyond their roles in microbial physiology, phenazines influence interactions among organisms, acting as antimicrobial agents, signaling molecules, and factors that shape microbiome dynamics in soils, plant roots, and other habitats. A better understanding of phenazine biology reveals how microbes adapt and thrive in diverse environments and emphasizes the potential applications of these compounds in agriculture and human health.},
}

@article {pmid41030841,
year = {2025},
author = {Anueyiagu, KN and Agusi, ER and Kabantiyok, D and Ayanbimpe, GM and Ikeh, EI},
title = {Zoonotic potential of ESBL-producing coliforms in pastorally managed ruminants with subclinical mastitis in Plateau State, Nigeria.},
journal = {Frontiers in antibiotics},
volume = {4},
number = {},
pages = {1632264},
pmid = {41030841},
issn = {2813-2467},
abstract = {BACKGROUND: Environmental coliform bacteria are frequently the cause of subclinical mastitis (SCM), a serious health issue in the dairy industry. Extended-spectrum β-lactamase (ESBL)-producing coliforms in livestock are a serious public health concern, particularly in environments where people and animals coexist. With an emphasis on their zoonotic and One Health implications, this study sought to evaluate the incidence of SCM and the occurrence of ESBL-producing coliforms in ruminants in Plateau State, Nigeria.

METHODS: The California Mastitis Test (CMT) was used to screen 287 milk samples that were taken from cows, ewes, and does. Standard microbiological methods were used to identify the bacterial isolates from CMT-positive samples. The presence of resistance genes (bla TEM and bla CTX-M) was ascertained by PCR, and ESBL production was confirmed phenotypically. Phylogenetic analysis showed genetic diversity and possible horizontal gene transfer among isolates.

RESULTS: Out of 287 milk samples, 79 (27.5%) had subclinical mastitis through the CMT, with a higher prevalence recorded in does 18(22.8%) while ewes and cows recorded 23(29.1%), and 38(48.1%) respectively. Of the 79 CMT-positive samples, the following isolates were identified: Citrobacter freundii (6.3%), Klebsiella pneumoniae (21.6%), K. oxytoca (2.5%), K. aerogenes (6.3%), and E. coli, being the most prevalent in cows (71%). Through PCR, 46 isolates expressed two important ESBL genes, bla TEM and bla CTX-M.

CONCLUSION: A possible zoonotic reservoir for antibiotic resistance in Nigeria is highlighted by the increased frequency of ESBL-producing coliforms in ruminants with SCM. These results highlight the necessity of implementing integrated One Health initiatives, such as public education, surveillance, and antimicrobial stewardship, in order to reduce the risk of resistant pathogen transmission from animals to people.},
}

@article {pmid41030195,
year = {2025},
author = {Vancaester, E and Oldrieve, GR and Reid, A and Koutsovoulos, G and Laetsch, DR and Makepeace, BL and Tanya, V and Poppert, S and Krücken, J and Wolstenholme, A and Blaxter, M},
title = {Ghosts of symbionts past: The hidden history of the dynamic association between filarial nematodes and their Wolbachia endosymbionts.},
journal = {G3 (Bethesda, Md.)},
volume = {},
number = {},
pages = {},
doi = {10.1093/g3journal/jkaf226},
pmid = {41030195},
issn = {2160-1836},
abstract = {Many, but not all, parasitic filarial nematodes (Onchocercidae) carry intracellular, maternally-transmitted, alphaproteobacterial Wolbachia symbionts. The association between filarial nematodes and Wolbachia is often portrayed as mutualist, where the nematode is reliant on Wolbachia for an essential but unknown service. Wolbachia are targets for anti-filarial chemotherapeutic interventions for human disease. Wolbachia of Onchocercidae derive from four of the major supergroups (C, D, F and J) defined within the genus. We explored the evolutionary history of the filarial nematode-Wolbachia symbiosis in twenty-two nematode species, sixteen of which have current Wolbachia infections, by screening the nematode nuclear genome sequences for nuclear Wolbachia transfers, fragments of the Wolbachia genome that have been inserted into the nuclear genome. We identified Wolbachia insertions in five of the six species that have no current Wolbachia infection, showing they have previously had and have now lost Wolbachia infections. In currently-infected species we found a diversity of origins of the insertions, including many cases where they derived from a different supergroup to the current live infection. Mapping the origins of the insertions onto the filarial nematode phylogeny we derive a complex model of evolution of Wolbachia symbiosis. The history of association between Wolbachia and onchocercid nematodes includes not only cospeciation, as would be expected from a mutualist symbiosis, but also loss (in the five Wolbachia-free species), frequent symbiont replacement, and dual infection. This dynamic pattern is challenging to models that assume host-symbiont mutualism.},
}

@article {pmid41026744,
year = {2025},
author = {Disastra, Y and Wongsurawat, T and Jenjaroenpun, P and Hampson, DJ and Kamwa, R and Prapasarakul, N},
title = {Integrative genomic characterization of five Pediococcus acidilactici strains reveals differing probiotic safety profiles.},
journal = {PloS one},
volume = {20},
number = {9},
pages = {e0332506},
pmid = {41026744},
issn = {1932-6203},
mesh = {*Probiotics/adverse effects ; *Pediococcus acidilactici/genetics/drug effects/pathogenicity ; *Genome, Bacterial ; Gene Transfer, Horizontal ; Plasmids/genetics ; Genomics ; Virulence Factors/genetics ; Whole Genome Sequencing ; Animals ; Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; },
abstract = {The increasing use of probiotics in livestock necessitates rigorous safety assessments to mitigate risks such as their inadvertent contribution to antimicrobial resistance (AMR) and horizontal gene transfer (HGT). This study employs whole-genome sequencing using both long-read (GridION, Oxford Nanopore Technologies) and short-read (Illumina, San Diego, CA, USA) platforms to assess the genomic and plasmidome profiles of five Thai strains of Pediococcus acidilactici, that previously have been evaluated for probiotic potential in livestock. Our comprehensive analysis identified genes encoding AMR, virulence factors, and probiotic-related genes. Notably, strains AF2519 and AF2019 harbored plasmid-borne tet(M) and erm(B) genes, with tet(M) embedded in a novel composite genetic arrangement flanked by mobile elements, suggesting historical recombination and altered mobility potential. Strains IAF6519, IAF5919, and P72N, free from plasmid-borne AMR genes, emerged as safer candidates, lacking virulence genes. Phenotypic tests revealed discrepancies with genomic data; for instance, AF2019 was resistant to clindamycin without detectable genes, and showed susceptibility to tetracycline despite the presence of tet(M). The absence of complete transfer machinery in AF2519 and AF2019 suggests a reduced HGT risk. These findings underscore the importance of integrating genomic and phenotypic approaches in probiotic safety evaluations. The presence of plasmid-borne AMR genes in certain strains advises caution in their use, impacting probiotic selection and regulatory compliance in agriculture. This research informs policies and best practices for safe probiotic deployment, ensuring both efficacy and safety.},
}

*Probiotics/adverse effects
*Pediococcus acidilactici/genetics/drug effects/pathogenicity
*Genome, Bacterial
Gene Transfer, Horizontal
Plasmids/genetics
Genomics
Virulence Factors/genetics
Whole Genome Sequencing
Animals
Drug Resistance, Bacterial/genetics
Anti-Bacterial Agents/pharmacology

@article {pmid41025674,
year = {2025},
author = {Ste-Croix, DT and Gagnon, AÈ and Mimee, B},
title = {The genome and stage-specific transcriptomes of the carrot weevil, Listronotus oregonensis, reveal adaptive mechanisms for host specialisation and symbiotic interactions.},
journal = {Insect molecular biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/imb.70012},
pmid = {41025674},
issn = {1365-2583},
support = {J-002846//Alternative Pest Management Solutions initiative/ ; //Agriculture and Agri-Food Canada/ ; },
abstract = {Throughout their evolution, insects have become specialised to occupy diverse ecological niches. The carrot weevil, Listronotus oregonensis, is an important agricultural pest that exhibits a very specific host range. In this study, we characterised the genome and transcriptomes of each developmental stage of L. oregonensis and its Wolbachia endosymbiont to gain deeper knowledge of the genetic determinants controlling its biology. We annotated 14,637 genes and showed expression profiles across the developmental stages. We also compared orthologous genes between L. oregonensis and nine other species, with particular focus on chemoreceptors and detoxification genes. We identified 24 distinct odorant-binding protein genes and 41 genes for receptors involved in stimulus perception, relatively low numbers compared with other species, which would be consistent with a narrow host range. In contrast, we found a high number of detoxification genes, with significant expansion of certain gene families. Among the annotated genes, 46 were putatively acquired through horizontal gene transfer, with 17 showing strong evidence for this, including several cell-wall degrading enzymes. The phylogeny of a cytolethal distending toxin gene also suggests an initial transfer from a prokaryotic source and vertical dissemination in members of Curculionidae through recent evolution. The presence of the endosymbiotic bacterium Wolbachia (supergroup A) was confirmed in all tested L. oregonensis individuals from several regions in northeastern North America and showed very little diversity. This study enhances our understanding of the genomic, functional, and evolutionary aspects of a significant agricultural pest and makes important and useful databases available to the scientific community.},
}

@article {pmid41025482,
year = {2025},
author = {Karan, R and Pyne, A and Panda, SK and Sen Gupta, PS and Hazra, S},
title = {Mechanistic insights into ESBL activity of subclass A2 in Class A beta-lactamase revealing a distinct strategy towards conferring drug resistance.},
journal = {Journal of biomolecular structure & dynamics},
volume = {},
number = {},
pages = {1-22},
doi = {10.1080/07391102.2025.2563080},
pmid = {41025482},
issn = {1538-0254},
abstract = {The twenty first century has witnessed challenges with antimicrobial resistance (AMR) emerging as a critical global threat. Among its most concerning is antibiotic resistance (ABR), highly linked to beta-lactamases. Among others, Class A beta-lactamases, present significantly with functional diversity, although ESBLs are one of the major concerns. A key defence mechanism in Gram-negative bacteria is the overexpression of ESBLs (Extended spectrum beta-lactamases) which spread across the bacterial population through horizontal gene transfer causes serious nosocomial infections. Since ESBLs have developed to increase their substrate specificity and hydrolyse most cephalosporins, penicillins, and monobactams, research into them is urgently needed.However, despite attempts functional classification, based on sequence identity, fold similarity, the presence or absence of insertions, particularly in loop regions and mode of action, a universally accepted framework remains elusive. Previous studies have broadly categorized Class A beta-lactamases into subclasses A1 and A2, yet the mechanistic intricacies of subclass A2 only as ESBL demand a more nuanced, multilevel analysis, underlying their role in antibiotic resistance. To bridge this knowledge gap, we employed on a comprehensive investigation encompassing sequence, structure, molecular docking, and dynamic analyses to elucidate the mechanistic approach of antibiotic resistance profiles for these two subclasses. Our sequence and structural studies revealed differences, particularly in insertions, structural alignments, and loop regions, including the omega loop and loops near the active site. Molecular docking study demonstrated better binding of the bigger substrate in the active site cavity of A2 subclass representatives. Dynamic analyses further confirmed our findings, employing root mean square deviation (RMSD), root mean square fluctuation (RMSF), flexibility of the extended and omega loops, radius of gyration (Rg), solvent-accessible surface area (SASA), clustering, hydrogen bonding patterns, principal component analysis (PCA), and free energy landscape (FEL). This study provides insights into the molecular distinctions and resistance mechanisms of these subclasses, paving the way for advanced research in antibiotic resistance and strengthening novel therapeutic strategies.},
}

@article {pmid41024490,
year = {2025},
author = {Speijer, D},
title = {Eukaryogenesis From FECA to LECA: Radical Steps Along the Way.},
journal = {BioEssays : news and reviews in molecular, cellular and developmental biology},
volume = {},
number = {},
pages = {e70063},
doi = {10.1002/bies.70063},
pmid = {41024490},
issn = {1521-1878},
abstract = {The characteristics of the last eukaryotic common ancestor (LECA) population and the root of the eukaryotic tree have been coming into focus lately. However, the trajectory taking the host, related to present-day Asgard archaea and the endosymbiont, related to present-day alphaproteobacteria, toward such fully integrated and complex organisms is still unclear. Here I marshal recent evidence supporting the early arrival of the "mitochondrion-to-be", setting up the evolutionary dynamic for a series of mutual adaptations leading to eukaryotes. Upon critical analysis of some presuppositions in phylogenomic reconstructions of eukaryogenesis, I again propose that pre-symbiosis, efficient ATP generation, internal reactive oxygen species (ROS) formation and enhanced retention of genes supplied by horizontal gene transfer (HGT) interdependently allowed this unique transformation to occur.},
}

@article {pmid41023737,
year = {2025},
author = {Dandare, SU and Allenby, A and Silvano, E and Nockemann, P and Chen, Y and Smith, TJ and Kumaresan, D},
title = {Diversity and distribution of the lanthanome in aerobic methane-oxidising bacteria.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {120},
pmid = {41023737},
issn = {2524-6372},
support = {NE/X005119//UK Research and Innovation/ ; NE/X005062//UK Research and Innovation/ ; },
abstract = {BACKGROUND: Lanthanides (Ln) play important and often regulatory roles in the metabolism of methylotrophs, including methanotrophs, particularly through their involvement in methanol oxidation. However, the diversity, distribution, and ecological relevance of Ln-associated proteins (the lanthanome) in aerobic methane-oxidising bacteria (MOB) remain underexplored. This study investigates the lanthanome using genome, plasmid, and proteome data, alongside metatranscriptome data from methane-rich lake sediments.

RESULTS: We surveyed 179 genomes spanning Proteobacterial, Verrucomicrobial, and Actinobacterial MOBs to examine the distribution of Ln-dependent methanol dehydrogenases (MDHs) and Ln transport proteins. Distinct lineage-specific patterns were observed: XoxF5 was the most widespread MDH variant in Proteobacteria, while XoxF2 was restricted to Verrucomicrobia. Transporter systems also showed distinct patterns, with LanM restricted to Alphaproteobacteria, LanPepSY and LanA confined to Gammaproteobacteria, and LutH-like receptors broadly distributed across all lineages. Homologues of these genes were also detected on plasmids, indicating potential for horizontal gene transfer. In Lake Washington sediment metatranscriptomes, lanthanome transcripts were detected, with Proteobacteria as dominant contributors. Notably, a large fraction of xoxF transcripts were affiliated with non-MOB Methylophilaceae, consistent with known cooperative interactions with MOB. Using Methylosinus trichosporium OB3b as a model, we assessed methane oxidation and proteomic responses to soluble CeCl3 and a mixed-lanthanide ore. Lag phases were prolonged in the presence of lanthanides, particularly with ore, but methane oxidation rates converged across treatments after acclimation. Proteomic analysis revealed extensive condition-specific responses, with 724 proteins differentially expressed in Ore treatment compared to 60 under CeCl3. XoxF3 and XoxF5 were upregulated while MxaF and its accessory proteins were downregulated, consistent with the "lanthanide switch". Notably, LanM was not expressed despite being encoded, whereas LutH-like receptor was downregulated under both treatments, likely reflecting regulatory control to prevent excess metal uptake. Additional upregulation of a TonB-dependent receptor and ABC transporter suggests a potential lanthanophore-mediated uptake strategy.

CONCLUSION: This study highlights the diversity and ecological activity of Ln-binding and transport systems in MOBs, their plasmid localisation and potential mobility, and their distinct regulation under different Ln sources. The strong proteomic response to complex ore underscores the physiological flexibility of MOBs in coping with natural lanthanide forms. These findings provide a framework for ecological studies and candidate targets for biotechnological applications in methane bioconversion and sustainable lanthanide recovery from complex materials.},
}

@article {pmid41022706,
year = {2025},
author = {Füssy, Z and Lampe, RH and Arrigo, KR and Barry, K and Brisbin, MM and Brussaard, CPD and Decelle, J and de Vargas, C and DiTullio, GR and Elbourne, LDH and Frischer, ME and Goodstein, DM and Grigoriev, IV and Hayes, RD and Healey, AL and James, CC and Jenkins, JW and Juery, C and Kumar, M and Kustka, AB and Maumus, F and Novák Vanclová, AMG and Oborník, M and Paulsen, IT and Probert, I and Saito, MA and Schmutz, J and Skalický, T and Tec-Campos, D and Tomelka, H and Věchtová, P and Venepally, P and Wilson-Mortier, B and Zengler, K and Zheng, H and Allen, AE},
title = {Genome-resolved biogeography of Phaeocystales, cosmopolitan bloom-forming algae.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {8559},
pmid = {41022706},
issn = {2041-1723},
support = {NA15OAR4320071//United States Department of Commerce | National Oceanic and Atmospheric Administration (NOAA)/ ; NA19NOS4780181//United States Department of Commerce | National Oceanic and Atmospheric Administration (NOAA)/ ; NSF OCE-1756884//National Science Foundation (NSF)/ ; 970820//Simons Foundation/ ; },
mesh = {Phylogeny ; *Haptophyta/genetics/classification/metabolism ; Phylogeography ; Gene Transfer, Horizontal ; Metagenome ; Oceans and Seas ; Genome ; Genomics ; },
abstract = {Phaeocystales, comprising the genus Phaeocystis and an uncharacterized sister lineage, are nanoplanktonic haptophytes widespread in the global ocean. Several species form mucilaginous colonies and influence key biogeochemical cycles, yet their underlying diversity and ecological strategies remain underexplored. Here, we present new genomic data from 13 strains, including three high-quality reference genomes (N50 > 30 kbp), and integrate previous metagenome-assembled genomes to resolve a robust phylogeny. Divergence timing of P. antarctica aligns with Miocene cooling and Southern Ocean isolation. Genomic traits reveal metabolic flexibility, including mixotrophic nitrogen acquisition in temperate waters and gene expansions linked to polar nutrient adaptation. Concordantly, transcriptomic comparisons between temperate and polar Phaeocystis suggest Southern Ocean populations experience iron and B12 limitation. We also identify signatures of horizontal gene transfer and endogenous giant virus/virophage insertions. Together, these findings highlight Phaeocystales as an ecologically versatile and geographically widespread lineage shaped by evolutionary innovation and adaptation to contrasting environmental stressors.},
}

Phylogeny
*Haptophyta/genetics/classification/metabolism
Phylogeography
Gene Transfer, Horizontal
Metagenome
Oceans and Seas
Genome
Genomics

@article {pmid41022263,
year = {2025},
author = {Zhang, J and Liu, Y and Fang, L and Wang, X and Xu, H and Lou, D},
title = {Molecular Characterization of blaVIM-2-carrying Pseudomonas asiatica L2126: Identification of a ∼44 kb Untypable Plasmid with Intra-Genus Dissemination Potential.},
journal = {Journal of global antimicrobial resistance},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jgar.2025.09.012},
pmid = {41022263},
issn = {2213-7173},
abstract = {OBJECTIVES: This study aims to elucidate the molecular characteristics of a blaVIM-2-carrying Pseudomonas asiatica isolate (L2126) from China and to characterize a ∼44 kb untypable plasmid harboring blaVIM-2. We investigated the genetic context of blaVIM-2, assessed the associated antimicrobial resistance determinants, and explored the role of this plasmid in mediating gene dissemination.

METHODS: The isolate L2126 was recovered from an intestinal colonization sample in a patient from Hangzhou, China. Species identification was confirmed by average nucleotide identity (ANI) analysis. Hybrid whole-genome sequencing was performed using Illumina short-read and Oxford Nanopore long-read platforms. Genome assembly was conducted using Unicycler and annotated with Prokka. Antimicrobial resistance genes were identified via ResFinder and CARD. The genetic context of blaVIM-2 was delineated using IntegronFinder. Plasmid profiles were determined by S1-nuclease pulsed-field gel electrophoresis (S1-PFGE) and in silico replicon analysis.

RESULTS: L2126 exhibited a multidrug-resistant profile with high-level resistance to carbapenems, cephalosporins, and fluoroquinolones. Genome analysis revealed 7 resistance genes, including blaVIM-2 and sul1. Notably, blaVIM-2 resides within a class 1 integron (intI1-attI1- blaVIM-2-qacEΔ1-sul1) embedded in a Tn402-like platform on a ∼44 kb untypable plasmid. The adjacent tni module (tniR-tniQ-tniB-tniA) is encoded on the opposite strand, indicating that it is part of the transposition platform rather than the integron cassette array. S1-PFGE confirmed the presence of the ∼44 kb plasmid, and in silico analysis provided a schematic representation of its genetic organization. BLAST analysis demonstrated that this plasmid shares high sequence homology with a plasmid previously identified in Pseudomonas monteilii, despite the two isolates belonging to different species.

CONCLUSIONS: Our findings demonstrate that the carriage of blaVIM-2 on a novel ∼44 kb untypable plasmid in P. asiatica L2126 could facilitate horizontal gene transfer of carbapenem resistance. The plasmid's high homology to one previously identified in P. monteilii suggests that it has the potential for intra-genus dissemination, posing a significant threat to the spread of carbapenem resistance.},
}

@article {pmid41021386,
year = {2025},
author = {Dechêne-Tempier, M and Bougeard, S and Loux, V and Chiapello, H and Libante, V and Marois-Créhan, C and Leblond-Bourget, N and Payot, S},
title = {Pan-immune system, mobilome and resistome in Streptococcus suis.},
journal = {Microbial genomics},
volume = {11},
number = {9},
pages = {},
doi = {10.1099/mgen.0.001521},
pmid = {41021386},
issn = {2057-5858},
mesh = {*Streptococcus suis/genetics/immunology/drug effects ; *Interspersed Repetitive Sequences ; Phylogeny ; Genome, Bacterial ; Swine ; Animals ; Gene Transfer, Horizontal ; Streptococcal Infections/microbiology ; *Drug Resistance, Bacterial/genetics ; Swine Diseases/microbiology ; },
abstract = {Streptococcus suis is a bacterial pathogen responsible for infections in pigs and in wild fauna that can also lead to severe infections in humans. Increasing antimicrobial resistance (AMR) has been described for this zoonotic pathogen worldwide. Since most of these AMR genes are carried by mobile genetic elements (MGEs), they can largely disseminate by horizontal gene transfer. Taking advantage of the large set of genomes available for this species, an exhaustive search of integrative and conjugative elements (ICEs) and integrative and mobilizable elements (IMEs) was undertaken in a representative set of 400 selected high-quality genomes of S. suis. We examined how these elements vary across phylogenetic clades and ecotypes and their association with AMR genes and defence systems (DSs), including restriction-modification (RM), CRISPR and also less studied DSs. This investigation identified 569 ICEs, belonging to the 7 families previously described in streptococci, inserted in 12 distinct specific integration sites. Additionally, 1,035 IMEs characterized by 11 distinct relaxase families and integrated in 10 specific chromosomal sites were detected in the 400 genomes of S. suis. New associations between ICE/IME and AMR genes were discovered. A huge diversity of putative DSs was observed including 2,035 RM systems, 124 CRISPR systems and systems belonging to 20 other categories, most of them described as efficient against phages and plasmids. Furthermore, most of the spacers associated with CRISPR systems target these MGEs rather than integrative elements. In addition, many integrative elements appear to carry an orphan methylase that could help them escape RM systems. Altogether, this points out that ICEs and IMEs are spared by DSs and play a major role in AMR dissemination in S. suis. In addition, most of the strains have the full set of genes required for competence, i.e. for the acquisition of extracellular DNA by natural transformation. This suggests a high risk of AMR dissemination in S. suis.},
}

*Streptococcus suis/genetics/immunology/drug effects
*Interspersed Repetitive Sequences
Phylogeny
Genome, Bacterial
Swine
Animals
Gene Transfer, Horizontal
Streptococcal Infections/microbiology
*Drug Resistance, Bacterial/genetics
Swine Diseases/microbiology

@article {pmid41020918,
year = {2025},
author = {Kunarisasi, S and Yuliandari, P and Pramono, AK and Furqoni, AH and Aliyah, SH and Nurjannah, I and Thaiyibah, N and Pratama, R and Permata Sari, NI},
title = {Genomic characterization of multidrug-resistant Escherichia coli isolates from hospital wastewater in Jakarta, Indonesia.},
journal = {Molecular biology reports},
volume = {52},
number = {1},
pages = {960},
pmid = {41020918},
issn = {1573-4978},
support = {UN.01/KPA/1068/2024//Faculty of Medicine, Universitas Islam Negeri Syarif Hidayatullah, Jakarta, Indonesia/ ; UN.01/KPA/1068/2024//Faculty of Medicine, Universitas Islam Negeri Syarif Hidayatullah, Jakarta, Indonesia/ ; UN.01/KPA/1068/2024//Faculty of Medicine, Universitas Islam Negeri Syarif Hidayatullah, Jakarta, Indonesia/ ; },
mesh = {*Wastewater/microbiology ; Indonesia ; *Escherichia coli/genetics/isolation & purification/drug effects/pathogenicity ; *Drug Resistance, Multiple, Bacterial/genetics ; Multilocus Sequence Typing/methods ; Hospitals ; Phylogeny ; Virulence Factors/genetics ; Plasmids/genetics ; Genome, Bacterial/genetics ; Genomics/methods ; Humans ; Anti-Bacterial Agents/pharmacology ; High-Throughput Nucleotide Sequencing/methods ; Microbial Sensitivity Tests ; Virulence/genetics ; },
abstract = {BACKGROUND: Hospital wastewater is a reservoir of antimicrobial resistance (AMR), yet the genetic diversity and resistance mechanisms of environmental Escherichia coli in such settings remain underexplored. This study aimed to investigate the genomic characteristics, resistance profiles, and virulence potential of E. coli isolates recovered from a hospital wastewater in Jakarta, Indonesia.

METHODS AND RESULTS: Six Escherichia coli isolates from hospital wastewater were sequenced using short-read next-generation sequencing (NGS). Raw reads were quality-checked and assembled with SPAdes, with five genomes retained for downstream analysis. Antimicrobial resistance (AMR) genes were identified using Staramr and the CARD database, while virulence factors were predicted using Abricate against the Virulence Factors Database (VFDB). Plasmid replicons were detected with PlasmidFinder. Phylogroup assignment followed the Clermont typing method, and phylogenetic analysis was conducted using a neighbor-joining tree based on core genome MLST (cgMLST) generated with chewBBACA v3.3.10. Multilocus sequence typing (MLST) revealed five distinct sequence types (ST744, ST156, ST1196, ST38, and ST10) across three phylogroups (A, B1, and D). A total of 57 AMR genes were detected, including blaCTX-M-15, blaCMY-2, and blaOXA-1 along with plasmid-mediated and chromosomal mutations conferring resistance to fluoroquinolones, aminoglycosides, and tetracyclines.

CONCLUSIONS: E. coli from hospital wastewater in Jakarta exhibited high genomic diversity, multidrug resistance, and variable virulence profiles. The findings support the role of untreated hospital effluents as a hotspot for AMR emergence and horizontal gene transfer. This showed the need for routine environmental surveillance to mitigate the public health risks associated with environmental reservoirs of resistant pathogens.},
}

*Wastewater/microbiology
Indonesia
*Escherichia coli/genetics/isolation & purification/drug effects/pathogenicity
*Drug Resistance, Multiple, Bacterial/genetics
Multilocus Sequence Typing/methods
Hospitals
Phylogeny
Virulence Factors/genetics
Plasmids/genetics
Genome, Bacterial/genetics
Genomics/methods
Humans
Anti-Bacterial Agents/pharmacology
High-Throughput Nucleotide Sequencing/methods
Microbial Sensitivity Tests
Virulence/genetics

@article {pmid41020186,
year = {2025},
author = {Kleyn, MS and Akinyemi, MO and Bezuidenhout, C and Adeleke, R},
title = {Draft genome sequence of Lysinibacillus capsici NAVL5D with potential for plant growth promotion.},
journal = {3 Biotech},
volume = {15},
number = {10},
pages = {359},
pmid = {41020186},
issn = {2190-572X},
abstract = {UNLABELLED: The use of plant growth-promoting (PGP) bacteria is an emerging strategy for sustainable agriculture, offering alternatives to chemical fertilisers and pesticides. Here, we report the draft genome sequence and functional characterization of Lysinibacillus capsici NAVL5D isolated from the leaf of ready-to-eat lettuce plant grown in South Africa. The genome generated using the Illumina NovaSeq 6000 had a size of 4,631,824 bp, with 22 contigs and a G + C content of 37.3%. In vitro tests demonstrated the strain's potential for plant growth promotion through nitrogen fixation, phosphate solubilization, indole-3-acetic acid (IAA) production, hydrogen cyanide (HCN) synthesis, and siderophore production. Genome analysis revealed key subsystems underpinning these traits such as auxin biosynthesis, nitrogen, phosphorus, and potassium metabolism, as well as putative PGP genes supporting these growth-promoting traits. In addition, five biocontrol secondary metabolites were predicted in the genome including terpenes and cyclic-lactone-autoinducers. However, eight minimal pathogenicity-related genes and six antibiotic resistance genes were also identified, including vanW, vanT, vanY, qacJ, msr(G), and FosBx1. Antibiotic susceptibility testing confirmed resistance to beta-lactams. Evidence of phage with could mediate horizontal gene transfer was observed in the genome. In vivo seed germination assays further demonstrated the strain's ability to promote plant growth, confirming its functional potential beyond in vitro observations. While L. capsici NAVL5D shows promise for sustainable agriculture applications, its potential warrant further investigation to ensure its safe use as a plant growth-promoting agent.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-025-04488-y.},
}

@article {pmid41019531,
year = {2025},
author = {Bhat, BA and Mir, RA and Qadri, H and Dhiman, R and Almilaibary, A and Alkhanani, M and Mir, MA},
title = {Correction: Integrons in the development of antimicrobial resistance: critical review and perspectives.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1681413},
doi = {10.3389/fmicb.2025.1681413},
pmid = {41019531},
issn = {1664-302X},
abstract = {[This corrects the article DOI: 10.3389/fmicb.2023.1231938.].},
}

@article {pmid41016251,
year = {2025},
author = {Schubert, K and Shosanya, T and García-Bayona, L},
title = {The role of mobile genetic elements in adaptation of the microbiota to the dynamic human gut ecosystem.},
journal = {Current opinion in microbiology},
volume = {88},
number = {},
pages = {102675},
doi = {10.1016/j.mib.2025.102675},
pmid = {41016251},
issn = {1879-0364},
abstract = {The human intestinal microbiota is a dynamic ecosystem shaped by extensive horizontal gene transfer, particularly in individuals from industrialized populations. In this review, we discuss recent advances in our understanding of how mobile genetic elements (MGEs) contribute to microbial ecology and evolution in this diverse community, focusing on MGEs carrying fitness-conferring genes. Bacteroidales species can colonize individuals for decades and serve as major hubs for MGE exchange. Most MGEs are highly variable across individuals and geographies. Occasionally, conserved MGEs can spread across geography and lifestyles. Functional characterizations of MGEs reveal their roles in antibiotic resistance, interbacterial antagonism, biofilm formation, immune evasion, and nutrient acquisition, among others. Substantive progress in our understanding of MGEs in the gut microbiome offers promising avenues for therapeutic microbiome interventions. However, major challenges remain in functional prediction, host-MGE linkage, and experimental characterization.},
}

@article {pmid41016209,
year = {2025},
author = {Zhao, Q and Yu, C and Liu, X and Hu, X and Yang, Q},
title = {Multi-omics reveals the systematical influence of composite heavy metal(loid)s on soil microbial function: Elemental cycling and microbial adaptation mechanisms.},
journal = {Journal of hazardous materials},
volume = {498},
number = {},
pages = {139973},
doi = {10.1016/j.jhazmat.2025.139973},
pmid = {41016209},
issn = {1873-3336},
abstract = {As the core of soil material cycling, soil microecosystems contaminated by combined heavy metal(loid)s have attracted widespread concern. Previous studies mostly focused on community-level ecological functions, neglecting genomic-level investigations and comprehensive microbial adaptation mechanisms. Here, we integrated multi-omics (metagenomics, genome assemblies, comparative genomics) with field and lab studies to explore responses from community to genomic scales. We found that metal(loid)s altered the assembly of microbial functional genes and weakened functional networks linking carbon, nitrogen, phosphorus, and sulfur cycling. They reduced the potential of carbohydrate metabolism, carbon fixation, and sulfur metabolism involved in protein synthesis and disrupted normal organic matter decomposition (via certain CAZymes). Conversely, they increased the potential of methanogenesis, denitrification, and organic phosphorus mineralization, as well as stimulating dissimilatory sulfate reduction and sulfur disproportionation. Microbes employed multi-level strategies to combat persistent heavy metal(loid)s stress, including reducing metal ion uptake, facilitating intracellular detoxification, and activating efflux pathways. They underwent adaptive evolution through mechanisms such as enhancing the synthesis and transportation of siderophores, strengthening DNA damage repair, and promoting genome streamlining. Notably, our analysis revealed that horizontal gene transfer, mediated by mobile genetic elements, drives the acquisition of resistance genes. This study provides systematic genomic evidence for such adaptive mechanisms in functional microbes, greatly advancing our understanding of their bioremediation potential.},
}

@article {pmid41015591,
year = {2025},
author = {Raziq, K and Saleem, R and Zafar, S and Sanaullah, T and Nazir, MM and Ummara, UE and Abbasi, A},
title = {Environmental resistomes and antimicrobial resistance: integrating the One Health framework.},
journal = {Naunyn-Schmiedeberg's archives of pharmacology},
volume = {},
number = {},
pages = {},
pmid = {41015591},
issn = {1432-1912},
abstract = {Antimicrobial resistance (AMR) has emerged as a critical global health challenge, exacerbated by the interconnected dynamics of human, animal, and environmental health systems. The "One Health" approach, which integrates these domains, offers a comprehensive framework for addressing AMR at its roots. This review explores the environmental dimension of AMR by examining the role of environmental microbiomes as reservoirs and transmission vectors of antimicrobial resistance genes (ARGs). It highlights emerging evidence, transmission pathways, detection methodologies, and policy gaps, with an emphasis on low- and middle-income countries (LMICs). An in-depth literature synthesis was conducted across environmental, clinical, and molecular microbiology studies to understand the eco-evolutionary dynamics of resistance, routes of ARG transmission, and effectiveness of current surveillance models. Emphasis was placed on novel detection technologies and integrated policy frameworks. Environmental resistomes present in soil, water, air, and waste play a pivotal yet underappreciated role in ARG dissemination via horizontal gene transfer, mobile genetic elements, and co-selectors like heavy metals and biocides. The complexity of microbial communities in diverse ecological matrices fosters the persistence and evolution of resistance. Current surveillance systems often neglect environmental inputs, particularly in LMICs, limiting the effectiveness of AMR mitigation efforts. A paradigm shift is required to recognize the environmental microbiome as a central component of AMR. Integrated "One Health" strategies, improved environmental surveillance, policy reforms, and novel technological interventions are critical for global AMR control. Bridging the research-policy gap and empowering local surveillance infrastructure can significantly enhance resistance management and public health outcomes.},
}

@article {pmid41014670,
year = {2025},
author = {Liu, W and Gong, F and Huang, Y and Shao, Y and Wang, Z and Xiao, X},
title = {Acetylshikonin regulates the gut microbiota and inhibits the horizontal transmission of colistin-resistant plasmids.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {148},
number = {},
pages = {157287},
doi = {10.1016/j.phymed.2025.157287},
pmid = {41014670},
issn = {1618-095X},
abstract = {BACKGROUND: The gut microbiota serves as a major reservoir for antibiotic resistance genes (ARGs), driving the spread of antimicrobial resistance (AMR) via horizontal gene transfer (HGT). Acetylshikonin (ASK), a naphthoquinone derived from the medicinal plant Lithospermum erythrorhizon, was proved to inhibit plasmid conjugation in vitro and in vivo. However, its impact on gut microbiota composition and precise HGT inhibition process within complex gut microbiota community remains unexplored.

PURPOSE: This study aims to clarify the precise inhibition effect of ASK on the transfer process of colistin-resistant plasmid in gut microbiota and its mechanisms.

METHODS: High-throughput cell sorting and 16S rRNA gene amplicon sequencing were employed to assess the precise gut microbiota species that ASK inhibited the resistant plasmid transfer to. The plasmid stability and re-transferability of transconjugants was evaluated by passaging culture and in vitro conjugative assay. The biochemical impact of ASK on donor cell and gut microbiota were tested by fluorescence assay and ELISA.

RESULTS: ASK changed the gut microbiota composition by enriching probiotics and reducing Gram-positive bacteria. In addition, ASK effectively inhibited the conjugative transfer of colistin-resistant plasmids to Proteobacteria (Escherichia and Ligilactobacillus) within the gut community. Furthermore, ASK weakened the stability and re-transferability of transconjugants, thereby limiting ARG further dissemination in gut. Moreover, ASK inhibited the electronic transport chain (ETC) and suppressed the ATP supply for both donor cells and the gut microbiota. Thus the plasmid conjugation processing in gut microbiota was inhibited by ASK.

CONCLUSION: This study demonstrated that ASK restructured gut microbiota and disarmed plasmid-mediated resistance spreading, offering a dual-targeted strategy against antimicrobial resistance.},
}