@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.},
}

@article {pmid41013258,
year = {2025},
author = {Shelenkov, A and Slavokhotova, A and Yunusova, M and Kulikov, V and Mikhaylova, Y and Akimkin, V},
title = {Genomic typing, antimicrobial resistance gene, virulence factor and plasmid replicon database for the important pathogenic bacteria Staphylococcus aureus.},
journal = {BMC genomic data},
volume = {26},
number = {1},
pages = {65},
pmid = {41013258},
issn = {2730-6844},
mesh = {*Virulence Factors/genetics ; *Plasmids/genetics ; *Staphylococcus aureus/genetics/classification/pathogenicity/drug effects ; *Replicon ; *Drug Resistance, Bacterial/genetics ; Genome, Bacterial ; *Databases, Genetic ; Humans ; Genomics ; Staphylococcal Infections/microbiology ; Anti-Bacterial Agents/pharmacology ; },
abstract = {BACKGROUND: Bacterial infections pose a global health threat across clinical and community settings. Over the past decade, the alarming expansion of antimicrobial resistance (AMR) has progressively narrowed therapeutic options, particularly for healthcare-associated infections. This critical situation has been formally recognized by the World Health Organization as a major public health concern. Epidemiological studies have demonstrated that the dissemination of AMR is frequently mediated by specific high-risk bacterial lineages, often designated as "global clones" or "clonal complexes." Consequently, surveillance of these epidemic clones and elucidation of their pathogenic mechanisms and AMR acquisition pathways have become essential research priorities. The advent of whole genome sequencing has revolutionized these investigations, enabling comprehensive epidemiological tracking and detailed analysis of mobile genetic elements responsible for resistance gene transfer. However, despite the exponential increase in available bacterial genome sequences, significant challenges persist. Current genomic datasets often suffer from uneven representation of clinically relevant strains and inconsistent availability of accompanying metadata. These limitations create substantial obstacles for large-scale comparative studies and hinder effective surveillance efforts.

DESCRIPTION: This database represents a comprehensive genomic analysis of 98,950 Staphylococcus aureus isolates, a high-priority bacterial pathogen of global clinical significance. We provide detailed isolate characterization through several established typing schemes including multilocus sequence typing (MLST), clonal complex (CC) assignments, spa typing results, and core genome MLST (cgMLST) profiles. The dataset also documents the presence of CRISPR-Cas systems in these isolates. Beyond fundamental typing data, our resource incorporates the distribution of antimicrobial resistance determinants, virulence factors, and plasmid replicons. These systematically curated genomic features offer researchers valuable insights into isolate epidemiology, resistance mechanisms, and horizontal gene transfer patterns in this highly concerning pathogen.

CONCLUSION: This database is freely available under CC BY-NC-SA at https://doi.org/10.5281/zenodo.14833440 . The data provided enables researchers to identify optimal reference isolates for various genomic studies, supporting critical investigations into S. aureus epidemiology and antimicrobial resistance evolution. This resource will ultimately inform the development of more effective prevention and control measures against this high-priority pathogen.},
}

*Virulence Factors/genetics
*Plasmids/genetics
*Staphylococcus aureus/genetics/classification/pathogenicity/drug effects
*Replicon
*Drug Resistance, Bacterial/genetics
Genome, Bacterial
*Databases, Genetic
Humans
Genomics
Staphylococcal Infections/microbiology
Anti-Bacterial Agents/pharmacology

@article {pmid41012719,
year = {2025},
author = {Hu, J and Zhou, J and Wang, L and Chen, Z and Tan, Y and Yin, Y and Pei, Z and Li, C and Bai, H and Ma, C and Teng, L and Feng, Y and Li, X and Wei, Y and Peng, H},
title = {Antimicrobial Resistance and Genomic Characterization of an Escherichia coli Strain Harboring p0111 and an IncX1-Type Plasmid, Isolated from the Brain of an Ostrich.},
journal = {Veterinary sciences},
volume = {12},
number = {9},
pages = {},
doi = {10.3390/vetsci12090793},
pmid = {41012719},
issn = {2306-7381},
support = {AB231111//Hechi City Key Research and Development Program/ ; AB24002021//Fangchenggang City Key Research and Development Program/ ; 2024GXZCLK37//Guangxi Self-funded Forestry Science and Technology Project/ ; 4-14, 24-2, 24-10, 24-12//Guangxi Science and Technology Special Projects/ ; 202219; Z202218; Z202214//Guangxi Zhuang Autonomous Region Department of Agriculture and Rural Affairs Self-Funded Projects/ ; 20220136-5//Guilin City Technology Application and Promotion Program/ ; AB241484045, AB23075145//Guangxi Key Research and Development Program/ ; },
abstract = {An outbreak characterized by clinical signs of diarrhea and paralysis, occasionally progressing to fatal outcomes, occurred at an ostrich breeding facility. Conventional antibiotic treatments proved ineffective. To investigate the etiology of the disease, brain and liver specimens were collected for diagnostic analysis. An Escherichia coli (E. coli) isolate, designated strain HZDC01, was obtained from cerebral tissues, and whole-genome sequencing was performed for genomic characterization. Genomic analysis revealed that the chromosomal DNA harbors numerous resistance genes, conferring multidrug resistance through complex mechanisms. Furthermore, a p0111-type plasmid carrying the blaCTX-M-55 gene and an IncX1-type plasmid harboring rmtB, sul1, APH(6)-Id, tet(A), AAC(3)-IIc, aadA2, blaTEM-1B, and floR genes were identified. These plasmids carry numerous mobile genetic elements that can disseminate via horizontal gene transfer, thereby amplifying the risk of resistance-gene spread within bacterial populations. Additionally, the ibeB and ibeC genes, which encode proteins involved in the invasion of brain microvascular endothelial cells, were identified. These genes may facilitate E. coli penetration of the blood-brain barrier, potentially leading to meningitis and posing a life-threatening risk to the host. This is the first report of the isolation and characterization of extended-spectrum beta-lactamase E. coli from the brain of an ostrich with paralysis. The findings provide valuable genomic insights into the antimicrobial resistance profiles and pathogenic mechanisms of ostrich-derived E. coli isolates.},
}

@article {pmid41011463,
year = {2025},
author = {Tsolakidou, P and Chatzidimitriou, M},
title = {Epidemiological and Microbiological Characterization of Carbapenemase-Producing Klebsiella pneumoniae Isolates in a Regional Greek Hospital: A Retrospective Study.},
journal = {Microorganisms},
volume = {13},
number = {9},
pages = {},
doi = {10.3390/microorganisms13092132},
pmid = {41011463},
issn = {2076-2607},
abstract = {Carbapenemase-producing Klebsiella pneumoniae (CRKP) is a critical public health threat, particularly in Greece, where high prevalence limits therapeutic options. This retrospective study analyzed 26 CRKP isolates recovered at the General Hospital of Volos between July 2024 and January 2025, aiming to correlate carbapenemase phenotypes with clinical and epidemiological parameters. Demographic, clinical, and microbiological data were extracted from patient records, and isolates underwent phenotypic carbapenemase detection, antimicrobial susceptibility testing, and molecular characterization using real-time PCR; four isolates were further analyzed using whole-genome sequencing. CRKP was detected across multiple hospital departments, notably in the Emergency Department (n = 5) and Intensive Care Unit (n = 6). KPC producers predominated (n = 9), followed by NDM (n = 6), VIM (n = 1), and OXA-48 (n = 6). All VIM- or NDM + VIM-positive cases were associated with mortality. High-risk clones, including ST15, ST11, and ST307, were identified, with one ST15 isolate harboring blaNDM-1, blaVIM-1, and chromosomal colistin resistance; this is the first such report in Greece. Colistin and gentamicin were the most active agents in vitro; three isolates were pan-drug-resistant. The findings highlight significant CRKP circulation outside ICUs, the role of horizontal gene transfer in resistance dissemination, and the need to expand screening and rapid diagnostics to non-ICU settings. Enhanced molecular surveillance targeted at infection control and strengthened antimicrobial stewardship programs are essential for limiting the spread of CRKP.},
}

@article {pmid41011454,
year = {2025},
author = {Zhang, P and Mo, Q and Liu, C and Liu, Q and Xu, J and Wang, Y and Wen, X and Wu, Y},
title = {Dose-Dependent Effect of Tilmicosin Residues on ermA Rebound Mediated by IntI1 in Pig Manure Compost.},
journal = {Microorganisms},
volume = {13},
number = {9},
pages = {},
doi = {10.3390/microorganisms13092123},
pmid = {41011454},
issn = {2076-2607},
support = {2023A1515110839//Guangdong Basic and Applied Basic Research Foundation/ ; 32172781//National Natural Science Foundation of China/ ; 2024M760976//China Postdoctoral Science Foundation/ ; 2023B0202060001//Key-Area Research and Development Program of Guangdong Province/ ; GZC20240507//Postdoctoral Fellowship Program of CPSF/ ; 2023B1212060057//Science and Technology Program of Guangdong province, China/ ; },
abstract = {The impact of varying antibiotic residue levels on antibiotic resistance gene (ARG) removal during composting is still unclear. This study investigated the impact of different residue levels of tilmicosin (TIM), a common veterinary macrolide antibiotic, on ARG removal during pig manure composting. Three groups were used: the CK group (no TIM), the L group (246.49 ± 22.83 mg/kg TIM), and the H group (529.99 ± 16.15 mg/kg TIM). Composting removed most targeted macrolide resistance genes (MRGs) like ereA, ermC, and ermF (>90% removal), and reduced ermB, ermX, ermQ, acrA, acrB, and mefA (30-70% removal). However, ermA increased in abundance. TIM altered compost community structure, driving succession through a deterministic process. At low doses, TIM reduced MRG-bacteria co-occurrence, with horizontal gene transfer via intI1 being the main cause of ermA rebound. In conclusion, composting reduces many MRG levels in pig manure, but the persistence and rebound of genes like ermA reveal the complex interactions between composting conditions and microbial gene transfer.},
}

@article {pmid41011444,
year = {2025},
author = {Li, Z and Tang, J and Wang, X and Ma, X and Yuan, H and Gao, C and Guo, Q and Guo, X and Wan, J and Dagot, C},
title = {The Environmental Lifecycle of Antibiotics and Resistance Genes: Transmission Mechanisms, Challenges, and Control Strategies.},
journal = {Microorganisms},
volume = {13},
number = {9},
pages = {},
doi = {10.3390/microorganisms13092113},
pmid = {41011444},
issn = {2076-2607},
support = {241111321400//Henan Provincial Key Research and Development Special Project/ ; },
abstract = {Antibiotics are widely used in modern medicine. However, as global antibiotic consumption rises, environmental contamination with antibiotics and antibiotic resistance genes (ARGs) is becoming a serious concern. The impact of antibiotic use on human health is now under scrutiny, particularly regarding the emergence of antibiotic-resistant bacteria (ARB) in the environment. This has heightened interest in technologies for treating ARGs, highlighting the need for effective solutions. This review traces the life cycle of ARB and ARGs driven by human activity, revealing pathways from antibiotic use to human infection. We address the mechanisms enabling resistance in ARB during this process. Beyond intrinsic resistance, the primary cause of ARB resistance is the horizontal gene transfer (HGT) of ARGs. These genes exploit mobile genetic elements (MGEs) to spread via conjugation, transformation, transduction, and outer membrane vesicles (OMVs). Currently, biological wastewater treatment is the primary pollution control method due to its cost-effectiveness. However, these biological processes can promote ARG propagation, significantly amplifying the environmental threat posed by antibiotics. This review also summarizes key mechanisms in the biological treatment of antibiotics and evaluates risks associated with major ARB/ARG removal processes. Our aim is to enhance understanding of ARB risks, their pathways and mechanisms in biotreatment, and potential biomedical applications for pollution control.},
}

@article {pmid41011422,
year = {2025},
author = {Elbir, H},
title = {Genomic and Phylogenomic Characterization of Three Novel Corynebacterium Species from Camels: Insights into Resistome, Mobilome Virulence, and Biochemical Traits.},
journal = {Microorganisms},
volume = {13},
number = {9},
pages = {},
doi = {10.3390/microorganisms13092090},
pmid = {41011422},
issn = {2076-2607},
abstract = {The genus Corynebacterium is commonly isolated from camel uteri, yet it is rarely identified to the species level. During our routine clinical examination of she-camels brought to the hospital with history of reproductive and systemic health issues, four isolates from the uterus and one isolate from blood could not be assigned to any valid Corynebacterium species. Therefore, we aim to identify these isolates, determine any potential virulence factors, and describe how gene turnover contributed to the evolution of these species. Genome-based and phenotypic identification, along with resistome, mobilome, virulome and phylogenomics analysis, was used to characterize the isolates. The isolates were Gram stain-positive, catalase-positive, and rod-shaped. The isolates were assigned to the genus Corynebacterium based on 16S rRNA gene sequence similarity and phylogenetic analysis. The isolates 3274 and ayman were classified as two new Corynebacterium species based on the average nucleotide identity (ANI) values of 78.46% and 68.88% and digital DNA-DNA hybridization (dDDH) values of 20.9% and 22.4%. The isolates 2581A, 2583C, and 4168A constitute a single Corynebacterium species based on their pairwise ANI value of 99% and dDDH value of more than 90%. In addition, isolates 2581A, 2583C, and 4168A showed ANI values of 75.99%, 75.86%, and 76.04% and dDDH values of 23.1%, 23%, and 22.5% with closely related species, and were designated as single new Corynebacterium species. Genes for mycolic acid and menaquinone biosynthesis were detected in all isolates. The isolates were susceptible to ceftiofur, linezolid, penicillin, erythromycin, and tetracycline. All isolates harbored the antiseptic resistance gene qacA. Moreover, virulence factors involved in cell adhesion and iron acquisition were detected. The evolution of these species is dominated by gene gain rather than gene loss. The majority of these genes are acquired through horizontal gene transfer, mediated by prophages and genomic islands. In summary, we characterized three new Corynebacterium species, expanding the number of new Corynebacterium species from animals. Moreover, we described the mechanism underlying the genome evolution of these new species. The clinical findings and detection of virulence genes highlight the significance of these isolates as possible pathogens, contributing to the development of endometritis in camels.},
}

@article {pmid41011419,
year = {2025},
author = {Ma, J and Xu, L and Shang, K and He, QY and Zhang, G},
title = {RecA Inhibitor Mitigates Bacterial Antibiotic Resistance.},
journal = {Microorganisms},
volume = {13},
number = {9},
pages = {},
doi = {10.3390/microorganisms13092087},
pmid = {41011419},
issn = {2076-2607},
support = {2023YFA0915800//Ministry of Science and Technology of China, National Key Research and Development Program/ ; },
abstract = {Bacterial antibiotic resistance (AR) has become a critical global health threat. AR is mainly driven by adaptive resistance mutations and the horizontal gene transfer of resistance genes, both of which are enhanced by genome recombination. We previously discovered that genome recombination-mediated tRNA upregulation is important for AR, especially in the early stages. RecA is a crucial bacterial factor mediating genome recombination and the DNA damage response. Therefore, RecA inhibitors should be effective in reducing AR. In this study, we found that BRITE-338733 (BR), a RecA inhibitor, can prevent ciprofloxacin (CIP) resistance in subculturing Escherichia coli strain BW25113 in the early stages (up to the 7th generation). In the presence of BR, the tRNA was decreased, so the bacteria cannot evolve resistance via the tRNA upregulation-mediated AR mechanism. The RecA expression level was also not increased when treated with BR. Transcriptome sequencing revealed that BR could inhibit oxidative phosphorylation, the electron transport chain process, and translation, thereby reducing the bacterial energy state and protein synthesis. Also, the effective concentrations of BR do not harm human cell viability, indicating its clinical safety. These findings demonstrate that BR effectively delays the emergence of spontaneous AR by targeting RecA-mediated pathways. Our findings shed light on a new strategy to counteract clinical AR: applying BR with the antibiotics together at the beginning.},
}

@article {pmid41011399,
year = {2025},
author = {Kim, S and Jeong, H and Lee, NK and Kang, DK and Paik, HD and Park, YS and Lee, JH},
title = {Comprehensive Safety Assessment of Lentilactobacillus buchneri KU200793 as a Potential Probiotic.},
journal = {Microorganisms},
volume = {13},
number = {9},
pages = {},
doi = {10.3390/microorganisms13092067},
pmid = {41011399},
issn = {2076-2607},
support = {GCU-202406430001//Gachon University/ ; 321035052HD020//Korea Institute of Planning and Evaluation for Technology in Food, Agriculture, and Forestry/ ; },
abstract = {The safety profile of Lentilactobacillus buchneri KU200793, which has neuroprotective effects, was comprehensively evaluated through both phenotypic and genotypic analyses. Phenotypically, the strain exhibited no β-hemolysis, mucin degradation, indole production, gelatin liquefaction, urease activity, or β-glucuronidase activity. Additionally, it did not produce D-lactate, and only trace amounts of spermidine were detected among the biogenic amines. Furthermore, L. buchneri KU200793 did not exhibit bile salt deconjugation, further supporting its safety profile. However, its tetracycline resistance exceeded the threshold set by the European Food Safety Authority. Genotypic analysis using the HGTree program identified tetA(58) and nalD genes with sequence similarities of 33.64% and 30.17%, respectively, indicating a low level of homology. These findings suggest that tetracycline resistance in L. buchneri KU200793 is unlikely to have been acquired through horizontal gene transfer, thereby minimizing the risk of resistance gene dissemination. This study underscores the importance of comprehensive safety assessments to evaluate the suitability of L. buchneri KU200793 for probiotic applications.},
}

@article {pmid41009907,
year = {2025},
author = {Iorgoni, V and Stanga, L and Iancu, I and Degi, J and Popa, I and Gligor, A and Orghici, G and Sicoe, B and Dreghiciu, IC and Purec, D and Nistor, P and Florea, B and Kracunović, C and Herman, V},
title = {Multidrug-Resistant Escherichia coli Associated with Respiratory and Systemic Infection in a Domestic Rabbit in Romania: First Confirmed Case.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/antibiotics14090929},
pmid = {41009907},
issn = {2079-6382},
abstract = {BACKGROUND/OBJECTIVES: This report documents the first confirmed case in Romania of fatal pneumonia and septicemia in a domestic rabbit caused by multidrug-resistant Escherichia coli, highlighting both its pathogenic potential and One Health implications.

CASE STUDY: An 8-month-old male German Giant Spotted rabbit raised on a rural farm under poor husbandry conditions developed acute respiratory distress and died within 48 h. Post-mortem examination revealed severe pulmonary congestion, tracheal inflammation, serofibrinous pericarditis, and systemic vascular lesions. Bacteriological analysis confirmed E. coli from lung, trachea, and bone marrow samples. The isolate demonstrated strong Congo red binding, was confirmed by MALDI-TOF mass spectrometry, and showed resistance to beta-lactams, fluoroquinolones, tetracyclines, sulfonamides, macrolides, and phenicols, remaining susceptible only to aminoglycosides. PCR screening identified virulence genes (fimH, papC, iutA, ompA) linked to adhesion, immune evasion, and iron acquisition, with potential for horizontal gene transfer.

CONCLUSIONS: This first documented case in Romania emphasizes the clinical threat posed by multidrug-resistant E. coli in rabbits and the importance of early diagnosis, improved biosecurity, and responsible antimicrobial use. The zoonotic and environmental risks in backyard farming underscore the urgent need for integrated surveillance. Alternative control strategies, including phage therapy and probiotics, should be explored to reduce reliance on conventional antibiotics.},
}

@article {pmid41009900,
year = {2025},
author = {Ngan, WY and Rao, S and Fung, AHY and Habimana, O},
title = {Genomic Profiling Reveals Clinically Relevant Antimicrobial Resistance and Virulence Genes in Klebsiella pneumoniae from Hong Kong Wet Markets.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/antibiotics14090922},
pmid = {41009900},
issn = {2079-6382},
support = {104006142.095798.26000.301.01//The University of Hong Kong's University Research Committee Seed Fund for Basic Research/ ; GCII-Seed-202409//GTIIT-Changzhou Innovation Institute/ ; },
abstract = {Background:Klebsiella pneumoniae is a highly dangerous microorganism that presents significant challenges to effectively eliminate in food production facilities, making it a serious and urgent public health concern. The wet markets of Hong Kong represent a considerable yet insufficiently explored source for the spread of microorganisms. Methods: This investigation employed whole-genome sequencing and comparative genomics to assess the genomic variation and adaptive traits of K. pneumoniae extracted from wooden cutting boards in these marketplaces. We examined four wet market isolates in conjunction with 39 publicly accessible genomes from diverse origins. Results: Pan-genome analysis revealed a diverse and open genetic structure significantly shaped by horizontal gene transfer. Phylogenetic reconstruction did not categorize the wet market isolates into a singular clade, indicating varied contamination sources; nonetheless, certain market isolates exhibited close phylogenetic affiliations with high-risk clinical clones, implying possible spillover events. These isolates exhibited a concerning variety of antimicrobial resistance genes (ARGs), chiefly encoding efflux pumps (acrAB, oqxAB), which confer resistance to numerous drug categories. Moreover, the evaluation for pathogenicity attributes uncovered genes associated with robust biofilm development (fim and mrk operons) and efficient iron procurement strategies. Conclusions: The existence of these genetically adaptable isolates, possessing multidrug resistance and virulence factors, renders wet markets potential amplifiers and reservoirs for the spread of resistant pathogens. These findings present the initial genomic evidence of such risks in Hong Kong's wet markets and emphasize the immediate necessity for improved hygiene protocols and comprehensive One Health surveillance to reduce transmission at the human-animal-environment interface.},
}

@article {pmid41009471,
year = {2025},
author = {Miftode, IL and Vâţă, A and Miftode, RŞ and Oancea, AF and Pasăre, MA and Parângă, TG and Miftode, EG and Mititiuc, IL and Radu, VD},
title = {The Gut Microbiome and Colistin Resistance: A Hidden Driver of Antimicrobial Failure.},
journal = {International journal of molecular sciences},
volume = {26},
number = {18},
pages = {},
doi = {10.3390/ijms26188899},
pmid = {41009471},
issn = {1422-0067},
mesh = {*Gastrointestinal Microbiome/drug effects ; Humans ; *Colistin/pharmacology/therapeutic use ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Animals ; *Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; },
abstract = {Colistin, a polymyxin antibiotic reintroduced as a last-resort therapy against multidrug-resistant Gram-negative bacteria, is increasingly being compromised by the emergence of plasmid-mediated colistin resistance genes (mcr-1 to mcr-10). The human gut microbiota serves as a major reservoir and transmission hub for these resistance determinants, even among individuals without prior colistin exposure. This review explores the mechanisms, dissemination, and clinical implications of mcr-mediated colistin resistance within the gut microbiota, highlighting its role in horizontal gene transfer, colonization, and environmental persistence. A comprehensive synthesis of the recent literature was conducted, focusing on epidemiological studies, molecular mechanisms, neonatal implications and decolonization strategies. The intestinal tract supports the enrichment and exchange of mcr genes among commensal and pathogenic bacteria, especially under antibiotic pressure. Colistin use in agriculture has amplified gut colonization with resistant strains in both animals and humans. Surveillance gaps remain, particularly in neonatal populations, where colonization may occur early and persist silently. Promising interventions, such as fecal microbiota transplantation and phage therapies, are under investigation but lack large-scale clinical validation. The gut microbiome plays a central role in the global spread of colistin resistance. Mitigating this threat requires integrated One Health responses, improved diagnostics for gut colonization, and investment in microbiome-based therapies. A proactive, multisectoral approach is essential to safeguard colistin efficacy and address the expanding threat of mcr-mediated resistance.},
}

*Gastrointestinal Microbiome/drug effects
Humans
*Colistin/pharmacology/therapeutic use
*Anti-Bacterial Agents/pharmacology/therapeutic use
Animals
*Drug Resistance, Bacterial/genetics
Gene Transfer, Horizontal

@article {pmid41004892,
year = {2025},
author = {Okada, K and Wongboot, W and Roobthaisong, A and Hanchanachai, N and Doung-Ngern, P and Okada, PA and Wongchai, T and Swaddiwudhipong, W and Iida, T and Hamada, S},
title = {Genomic analyses of enteroinvasive Escherichia coli revealed the circulation of conjugative virulence plasmids and emergence of novel clones.},
journal = {International journal of medical microbiology : IJMM},
volume = {321},
number = {},
pages = {151677},
doi = {10.1016/j.ijmm.2025.151677},
pmid = {41004892},
issn = {1618-0607},
abstract = {Enteroinvasive Escherichia coli (EIEC) is a diarrhoeagenic E. coli pathotype that shares key virulence traits with Shigella, including the invasion plasmid (pINV). In Thailand, an outbreak caused by the EIEC serotype O8:H19-the first reported in the country-occurred in 2023, affecting over 150 patients. To elucidate the emergence, clinical relevance, and epidemiological distribution of EIEC in Thailand, we conducted a comprehensive investigation. We isolated and genomically characterised 63 isolates, comprising 28 EIEC (eight serotypes, including O96:H19 from a 2024 outbreak) and 35 Shigella (25 S. sonnei and 10 S. flexneri), along with 85 global reference strains. Comparative genomics revealed that the 2023 and 2024 EIEC outbreak isolates, along with a novel OX18:H25 EIEC lineage, harboured highly similar pINV plasmids with conserved invasion genes and complete conjugation elements. These isolates retained several biochemical traits that were more typical of commensal E. coli than classical EIEC. Limited chromosomal genome reduction-a hallmark of Shigella- was observed, which suggests that these lineages are in an early stage of adaptation toward a pathogenic lifestyle. Phylogenomic analysis showed that OX18:H25 is closely related to livestock-associated E. coli, supporting the hypothesis that pINV was recently acquired via horizontal gene transfer. These findings highlight the active circulation of putatively conjugative virulence plasmids among E. coli populations and the ongoing emergence of novel EIEC clones with epidemic-inducing potential.},
}

@article {pmid41003748,
year = {2025},
author = {Sundar Rajan, M and Jayavelu, T and Pennathur, G},
title = {Phylogenetic Studies on Taurine Dioxygenase (TauD).},
journal = {Current microbiology},
volume = {82},
number = {11},
pages = {526},
pmid = {41003748},
issn = {1432-0991},
support = {DBT/2017/Anna Univ/966//Department of Biotechnology, Ministry of Science and Technology, India/ ; },
mesh = {*Phylogeny ; Promoter Regions, Genetic ; Gene Transfer, Horizontal ; *Bacteria/enzymology/genetics/classification ; Taurine/metabolism ; Operon ; *Mixed Function Oxygenases/genetics/metabolism ; Fungi/genetics/enzymology ; Bacterial Proteins/genetics/metabolism ; },
abstract = {Taurine dioxygenase (TauD) catalyses α-ketoglutarate-dependent oxidative decomposition of taurine and is grouped into an eponymous protein family (Pfam 02668-Taurine Catabolism Dioxygenase TauD, TfdA) with other enzymes that share this domain, but differ in substrates. In this study, we have detected Low Complexity Regions (LCRs) that set TauD apart from other members of its family. Using these regions, we designed patterns that reliably give true hits when queried against UniProt. We further demonstrate the use of these LCRs in detecting horizontal gene transfer (HGT) that led to TauD incorporation in at least one fungus genome. Additionally, we studied the genomic context of tauD across bacterial species and also performed promoter analysis to gain insights into its regulation. The tauABCD operon is restricted to certain genera of class Gammaproteobacteria with few exceptions, suggesting inheritance from a common ancestor. In other classes, TauD was found to have diverse genomic neighbours. Promoter analysis reveals several global and local regulators for tauABCD operon and other operons containing tauD.},
}

*Phylogeny
Promoter Regions, Genetic
Gene Transfer, Horizontal
*Bacteria/enzymology/genetics/classification
Taurine/metabolism
Operon
*Mixed Function Oxygenases/genetics/metabolism
Fungi/genetics/enzymology
Bacterial Proteins/genetics/metabolism

@article {pmid41003510,
year = {2025},
author = {Ding, Q and Liu, T and Li, Z and Sun, R and Zhang, J and Yin, L and Pu, Y},
title = {Comprehensive Insight into Microcystin-Degrading Mechanism of Sphingopyxis sp. m6 Based on Mlr Enzymes.},
journal = {Toxins},
volume = {17},
number = {9},
pages = {},
doi = {10.3390/toxins17090446},
pmid = {41003510},
issn = {2072-6651},
support = {2024M760442//China Postdoctoral Science Foundation funded project/ ; GZC20240246//Postdoctoral Fellowship Program of CPSF/ ; 82404225, 81972997//the National Nature Science Foundation of China/ ; },
mesh = {*Microcystins/metabolism ; *Sphingomonadaceae/genetics/enzymology/metabolism ; *Bacterial Proteins/metabolism/genetics ; Biodegradation, Environmental ; },
abstract = {Bacterial degradation is one important Microcystin (MC) removal method in the natural environment. The traditional MC-degrading pathway was proposed based on the functions of individual recombinant Mlr enzymes and the structures of the main MC-degrading products. However, the actual MC-degrading mechanism by Mlr enzymes in wild-type bacteria remains unclear. In this study, bioinformatic analysis, heterologous expression, and knockout mutation were performed to elaborate the MC-degrading mechanism by Mlr enzymes in Sphingopyxis sp. m6. The results showed that mlr gene cluster was initially acquired by horizontal gene transfer, followed by vertical inheritance within Alphaproteobacteria. Mlr enzymes exhibit distinct subcellular localizations and possess diverse conserved catalytic domains. The enzymatic cascade MlrA/MlrB/MlrC sequentially cleaves Microcystin-LR (MC-LR) via Adda-Arg, Ala-Leu, and Adda-Glu bonds, generating characteristic intermediates (linearized MC-LR, tetrapeptide, and Adda). Notably, recombinant MlrC demonstrated dual-targeting degrading capability (linearized MC-LR and tetrapeptide), while tetrapeptide specificity in endogenous processing of Sphingopyxis sp. m6. Marker-free knockout mutants of mlr genes were first constructed in MC-degrading bacteria, unveiling that mlrA was indispensable in initial MC cleavage, whereas mlrB/mlrC/mlrD displayed functional compensation through other enzymes with similar functions. This study promotes the mechanistic understanding of MC bacterial degradation and offers a theoretical basis for a bioremediation strategy targeting cyanotoxin pollution.},
}

*Microcystins/metabolism
*Sphingomonadaceae/genetics/enzymology/metabolism
*Bacterial Proteins/metabolism/genetics
Biodegradation, Environmental

@article {pmid41003187,
year = {2025},
author = {Chattopadhyay, P and Banerjee, G},
title = {Diversity and Distribution of Non-Reducing Polyketide Synthases (NR-PKSs) in Ascomycota (Fungi).},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {11},
number = {9},
pages = {},
doi = {10.3390/jof11090641},
pmid = {41003187},
issn = {2309-608X},
abstract = {(1) Background: This study highlights the diversity and distribution of non-reducing polyketide synthases (NR-PKSs) in Ascomycota and their role in producing bioactive aromatic polyketides. (2) Methods: A reference dataset of non-NR-PKSs was compiled from published literature and cross-examined using NaPDoS2 and Kyoto Encyclopedia of Genes and Genomes Ortholog (KEGG KO) databases. Signature domains were validated through Pfam and CDD, while phylogenetic classification was conducted by comparing the dataset with the NaPDoS2 reference tree. Cluster support was derived from KEGG KO and homology-based modeling. Additionally, NR-PKS clade distribution across KEGG genomes was analyzed, and co-expression patterns were examined using STRING. (3) Results: This study identified nine distinct clades of NR-PKSs, six of which are supported by unique KEGG Orthology (KO) numbers. These clades are as follows: clade 1: polyketide synthase A (PksA, K15316); clade 2: fusarubinsynthase 1 (Fsr1); clade 3: white A (WA, K15321); clade 4: polyketide synthase citrinin (PksCT); clade 5: zearalenone synthase 1 (Zea1, K15417); clade 6: orsellinic acid synthase A (OrsA, K15416); clade 7: aurofusarin polyketide synthase A (AptA, K15317); clade 8: monodictyphenone polyketide synthase G (MdpG, K15415); and clade 9: bikaverin polyketide synthase (Bik1). The present investigation also reports incongruency in the distribution of different NR-PKSs and fungi phylogeny within the phylum Ascomycota. (4) Conclusions: The distribution of NR-PKSs in Ascomycota defies phylogenetic boundaries, reflecting the impact of horizontal gene transfer, gene loss, and ecological adaptation.},
}

@article {pmid41002241,
year = {2025},
author = {Kurushima, J and Nomura, T and Ota, N and Tomita, H},
title = {Complete genomes of clade A1 and B Enterococcus faecium isolates harboring pHTβ, a vanA-type vancomycin-resistant pMG1-like plasmid.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0068425},
doi = {10.1128/mra.00684-25},
pmid = {41002241},
issn = {2576-098X},
abstract = {Enterococcal conjugative plasmids play a key role in the widespread expansion of antimicrobial resistance genes among Enterococcus faecium via horizontal gene transfer. Herein, we report the complete genomes of clinical E. faecium isolates harboring pHTβ, a pMG1-like plasmid containing an inserted vancomycin resistance operon.},
}

@article {pmid41001059,
year = {2025},
author = {Thoenen, L and Hummerjohann, J and Schwendimann, L and Marti, E},
title = {Phenotypic and genotypic characterization of antibiotic-resistant bacteria from Swiss ready-to-eat meat products.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1649307},
pmid = {41001059},
issn = {1664-302X},
abstract = {Antimicrobial resistance is a global health concern, which is partly driven by rising meat consumption, which has led to the intensive farming of livestock that relies on antibiotics. ready-to-eat animal products can carry antibiotic-resistant bacteria, posing risks to humans since they are often consumed without further cooking. While countries such as Switzerland limit antibiotic use in agriculture, contamination of meat with antibiotic-resistant bacteria can still occur during meat processing, and non-antibiotic agents such as heavy metals may contribute to the co-selection of resistance. This study aimed to characterize antibiotic-resistant bacteria in ready-to-eat meat products from various Swiss butcheries. Presumptive resistant bacteria were isolated using selective plating and analyzed phenotypically and genotypically. A total of 53 bacteria-antibiotic resistance combinations were identified, including Enterobacterales resistant to third-generation cephalosporins, vancomycin-resistant Enterococci, and one strain of methicillin-resistant Staphylococcus aureus. Of the 804 products sampled, 177 antibiotic-resistant bacteria were isolated, 148 of which showed multidrug resistance. Notably, these strains remained susceptible to last-resort antibiotics such as carbapenems and colistin. Whole-genome sequencing of 31 selected isolates revealed 164 antibiotic resistance genes spanning 25 classes, confirming resistance to beta-lactams, cephalosporins, and tetracyclines. We also detected genes conferring resistance to metals, suggesting co-selection pressures. Long-read sequencing revealed that the majority of the antibiotic resistance genes were chromosomal, while others were plasmid-encoded, indicating the potential for horizontal gene transfer. This study demonstrates that ready-to-eat meat products are reservoirs of antibiotic and metal resistance genes, as well as antibiotic-resistant bacteria, even at low levels. From a One Health perspective, our results highlight the importance of extending AMR surveillance across the food chain and underscore the need to include non-traditional bacterial indicators.},
}

@article {pmid41000824,
year = {2025},
author = {Ejikeugwu, CP and Edeh, C and Nwakaeze, EA and Adikwu, MU and Torres, C and Creevey, CJ and Eze, PM},
title = {Whole-Genome Sequencing Uncovers Chromosomal and Plasmid-Borne Multidrug Resistance and Virulence Genes in Poultry-Associated Escherichia coli from Nigeria.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.09.18.677015},
pmid = {41000824},
issn = {2692-8205},
abstract = {BACKGROUND: Broad and unregulated antibiotic use in livestock production, particularly poultry farming, has increased the development and persistence of multidrug-resistant (MDR) bacterial strains in animals. These resistant pathogens and their antibiotic resistance genes (ARGs) can spread to humans through environmental exposure and the food chain, posing serious public health risks. Whole-genome sequencing (WGS), alongside phenotypic antimicrobial susceptibility testing (AST), enables a comprehensive understanding of resistance mechanisms and informs antimicrobial stewardship strategies, particularly in resource-limited settings.

AIM: This study aimed to characterize the phenotypic and genotypic antimicrobial resistance profiles, plasmid content, and virulence factors of an MDR E. coli strain (S3) isolated from a poultry farm in Enugu State, Nigeria, to elucidate potential risks to public health and the role of poultry as a reservoir for resistance determinants.

METHODS: E. coli strain S3 was isolated from chicken droppings using standard microbiological methods and confirmed by MALDI-TOF mass spectrometry. AST was assessed using disc diffusion and broth microdilution to determine minimum inhibitory concentrations (MICs) for ten antibiotics across multiple classes. WGS was performed with a hybrid approach combining Illumina and Nanopore platforms, followed by genome assembly and annotation. ARGs, plasmid replicons, and virulence factors were identified in silico using AMRFinderPlus, starAMR, RGI/CARD, PlasmidFinder, MOB-suite, and the Virulence Factor Database (VFDB).

RESULTS: Phenotypic testing revealed extensive resistance, with complete resistance to six of seven tested antibiotics (cefotaxime, ampicillin, erythromycin, gentamicin, ciprofloxacin, and doxycycline). MICs exceeded clinical breakpoints for multiple classes, confirming an MDR phenotype. Genome analysis indicated a 5.33 Mb genome distributed across five contigs, including one chromosome and four plasmid-associated contigs. The strain harboured numerous ARGs, including [bla] CTX-M-15 , [bla] OXA-1 , [bla] TEM-1, aac(6')-Ib-cr, aadA5, aph(3'')-Ib, sul1/sul2, tet(A), dfrA17 , and mph(A) , co-localized on plasmids indicative of horizontal gene transfer (HGT) potential. Plasmid types included Col156, IncF, and two rep clusters. Virulence profiling revealed genes associated with adhesion (pap cluster, ECP), iron acquisition (enterobactin, yersiniabactin, aerobactin, heme uptake), and toxins (sat, senB), highlighting the isolate's potential for urinary tract and intestinal infections.

CONCLUSION: This study highlights the significant role of poultry-associated bacteria as reservoirs of AMR genes, particularly those harboured on mobile plasmids with potential for HGT. E. coli strain S3 exhibits extensive multidrug resistance and carries a complex plasmid repertoire facilitating horizontal transfer of ARGs. Coupled with a rich virulence gene profile, this strain underscores the public health risk posed by poultry-associated E. coli in Nigeria. These findings demonstrate the urgent need for stringent antimicrobial stewardship, regulatory oversight, and genomic surveillance in poultry production milieus to mitigate the dissemination of MDR pathogens.},
}

@article {pmid41000675,
year = {2025},
author = {Komine, T and Sathianpitayakul, P and Sakagami, N and Yoshida, M and Suzuki, M and Hoshino, Y and Ratthawongjirakul, P and Ato, M and Fukano, H},
title = {Plasmid-mediated macrolide resistance among rapidly growing mycobacteria in Japan.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.09.17.676775},
pmid = {41000675},
issn = {2692-8205},
abstract = {OBJECTIVES: The spread of a transmissible plasmid carrying the 23S rRNA methylase gene erm (55), which confers inducible macrolide resistance in rapidly growing mycobacteria (RGM), has raised significant clinical concerns. The aim of this study was to investigate the prevalence of erm (55)-carrying plasmids in clinically isolated RGM strains in Japan.

METHODS: In total, 607 RGM clinical isolates, representing 32 species or complexes, collected between 2019 and 2023 in Japan were examined. To detect the presence of erm (55)-carrying plasmids, we conducted PCR screening, minimum inhibitory concentration testing for clarithromycin, and whole-plasmid genome sequencing. Comparative genomic analyses were performed to characterise the plasmids.

RESULTS: Among the 607 RGM isolates, 0.8% (5/607) possessed the plasmid with the erm (55) gene and exhibited inducible macrolide resistance, with ratios of 100% (1/1) in Mycobacterium murale , 50% (3/6) in M. obuense , and 0.8% (1/125) in M. chelonae . The erm (55)-carrying plasmids ranged from 126,187 to 170,220 bp in size. Pairwise BLASTn comparisons of the erm (55)-carrying plasmids showed weighted percent identity values ranging from 99.5% to 99.9%, with query and subject coverage values ranging from 74.2% to 100%. All erm (55) sequences (813 bp) were identical and located within a horizontal gene transfer region.

CONCLUSIONS: This study confirmed the presence of macrolide-resistant RGMs related to the erm (55)-carrying plasmid in Japan, although the overall prevalence remains low. These findings emphasise the need to consider plasmid-mediated resistance when treating infections caused by the RGM species.},
}

@article {pmid40999775,
year = {2025},
author = {Sabio, L and Day, GJ and Salmeron-Sanchez, M},
title = {Probiotic-Based Materials as Living Therapeutics.},
journal = {Advanced materials (Deerfield Beach, Fla.)},
volume = {},
number = {},
pages = {e08500},
doi = {10.1002/adma.202508500},
pmid = {40999775},
issn = {1521-4095},
support = {Devise 101054728/ERC_/European Research Council/International ; EP/X033554/1//EPSRC HT2050/ ; EP/Y03029X/1//UK Research and Innovation (UKRI)/ ; 10052844//UK government's Horizon Europe/ ; 101070913//European Union under Horizon Europe project PRISM-LT/ ; },
abstract = {The growing demand for safer, more targeted therapeutics requires the development of advanced biomaterials. Among these, Engineered Living Materials (ELMs)-which integrate synthetic biology with material science-are emerging as promising platforms for biomedical applications. This review focuses on a subclass of ELMs based on genetically engineered probiotics combined with matrices, that are termed Probiotic Living Materials (PLMs) to differentiate them from Living Biotherapeutic Products (LBPs). Recent studies highlight PLM's potential in addressing different health conditions, offering targeted and dynamic therapies. However, PLMs face multiple challenges to be implemented in clinics, including a lack of robust genetic toolkits for probiotic engineering, concerns about biosafety (e.g., horizontal gene transfer or non-desirable biological activity), difficulties in translating preclinical results to humans, and the absence of clear regulatory guidance for clinical use. This review first explores the fundamental features of ELMs, then provides an overview of probiotics, followed by recent advances in the design of engineered PLMs for biomedical applications, particularly in biosensing development, infection treatment, bone repair, wound healing, vaginal imbalances, gut-related conditions, and cancer therapy. Finally, biosafety issues and current gaps in regulatory frameworks to ensure safe and effective use of PLMs, with a particular focus on vulnerable populations, are discussed.},
}

@article {pmid40997705,
year = {2025},
author = {Sheng, B and Liu, S and Xiong, K and Liu, J and Zhu, S and Zhang, H and Zhang, R},
title = {Response of bacterial pathogens to process upgrades and floc sizes in a full-scale landfill leachate treatment plant.},
journal = {Journal of environmental management},
volume = {394},
number = {},
pages = {127377},
doi = {10.1016/j.jenvman.2025.127377},
pmid = {40997705},
issn = {1095-8630},
abstract = {Bacterial pathogens in wastewater environments pose serious public health risks, serving as reservoirs for antibiotic resistance genes (ARGs) and contributing to the global antimicrobial resistance (AMR) crisis. This study investigated how process upgrades and sludge aggregate sizes influence the distribution of bacterial pathogens and ARGs in a full-scale landfill leachate treatment plant (LLTP). Using 16S rRNA and metagenomic sequencing, we analyzed potential pathogens and ARG profiles during the progression from conventional nitrification-denitrification (CND) to partial nitrification-denitrification (PND). Results showed a notable increase in the relative abundance of potential pathogenic genera in large aggregates following the process upgrade, indicating structural and functional shifts in microbial communities. The average abundance of WHO-priority ARGs, including baeR, smeR, and adeL, was significantly higher at the PND phase, likely linked to the process upgrade. Additionally, the activity of mobile genetic elements (MGEs), particularly those involved in horizontal gene transfer and DNA repair, was enhanced at the PND phase, accelerating ARG dissemination. Importantly, the process upgrade reduced the relative abundance of Streptococcus pyogenes, a high-risk pathogen, suggesting improved pathogen control. This study provides critical insights into optimizing LLTP processes to mitigate AMR risks and improve public health safety.},
}

@article {pmid40997562,
year = {2025},
author = {Duan, Y and Zhang, J and Petropoulos, E and Zhao, J and Chen, Y and Wang, L and Wang, X and Jia, R and Wu, F and Li, Y},
title = {Metagenomic profiling of antibiotic resistance genes in terrestrial ecosystems across China.},
journal = {Ecotoxicology and environmental safety},
volume = {304},
number = {},
pages = {119096},
doi = {10.1016/j.ecoenv.2025.119096},
pmid = {40997562},
issn = {1090-2414},
abstract = {Soil represents a significant reservoir of antibiotic resistance genes (ARGs), yet their distribution across diverse terrestrial ecosystems remains poorly characterized. To address this knowledge gap, we conducted a large-scale, cross-regional soil survey spanning 4300 km in China, collecting samples at 42 intervals across six distinct terrestrial ecosystems. High diversity (18 ARG types and 129 ARG subtypes) and abundance (mean value: 724.9 [coverage, ×/Gb]) of ARGs were observed in the topsoil (0-20 cm depth) across the six terrestrial ecosystems, with tetracycline resistance and efflux pump being the prevailing class and resistance mechanism respectively. Notably, only aac (6')-I ranked among the highest-risk ARGs (Rank I), indicating that merely 0.78 % of detected ARGs pose a severe pathogenic threat. Meanwhile, horizontal gene transfer (HGT) is likely the primary transmission mechanism for ARGs in these soils. While most ARGs currently present minimal direct public health risks, their high transmission potential warrants attention. Furthermore, stochastic processes dominate the spread of soil ARGs, though both stochastic and deterministic processes contribute to the spread of their hosts. Collectively, these results provide timely insights into the resistance mode of soil ARGs in terrestrial ecosystems.},
}

@article {pmid40988758,
year = {2025},
author = {Azad, RB and Kasfy, SH and Molla, K and Islam, T},
title = {Horizontal Gene Transfer in Plants and Implications for Biotechnology.},
journal = {Plant-environment interactions (Hoboken, N.J.)},
volume = {6},
number = {5},
pages = {e70087},
pmid = {40988758},
issn = {2575-6265},
abstract = {Horizontal gene transfer (HGT), a fundamental process long acknowledged in prokaryotic evolution, is increasingly recognized as a pivotal force in shaping the evolutionary trajectories of eukaryotes, including plants. Despite its established significance in prokaryotic adaptation, the role of HGT in eukaryotic evolution is still understudied. HGT plays a pivotal role in the evolution of eukaryotes, giving rise to novel features that allow organisms to exploit new environments and resources with reduced competition. Moreover, the coevolution of interacting organisms in any ecosystem is greatly influenced by HGT. Recent discoveries of HGT events among eukaryotic species such as gene transfers from fungi to plants and from plants to whiteflies highlight the importance of understanding this phenomenon in the context of plant biology. In this review, we provide an update of recent findings related to plant and associated organisms like microorganisms, insects, and critically discuss the profound implications of HGT for plant evolution and adaptation, probing into potential underlying mechanisms, highlighting the knowledge gap and discussing their implications. In particular, we explore the potential applications of the new knowledge of HGT in plant biotechnology, illuminating its pivotal role in shaping the future landscape of bioengineering.},
}

@article {pmid40986369,
year = {2025},
author = {Ratna, TA and Sharon, BM and Barros Velin, CA and Palmer, K},
title = {Factors affecting CRISPR-Cas defense against antibiotic resistance plasmids harboured by Enterococcus faecalis laboratory model strains and clinical isolates.},
journal = {Microbiology (Reading, England)},
volume = {171},
number = {9},
pages = {},
doi = {10.1099/mic.0.001601},
pmid = {40986369},
issn = {1465-2080},
mesh = {*Enterococcus faecalis/genetics/drug effects/isolation & purification ; *Plasmids/genetics ; *CRISPR-Cas Systems/genetics ; Gene Transfer, Horizontal ; Conjugation, Genetic ; Humans ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Multiple, Bacterial/genetics ; Gram-Positive Bacterial Infections/microbiology ; },
abstract = {Enterococcus faecalis is a Gram-positive bacterium and opportunistic pathogen that acquires resistance to a wide range of antibiotics by horizontal gene transfer (HGT). The rapid increase of multidrug-resistant (MDR) bacteria including MDR E. faecalis necessitates the development of alternative therapies and a deeper understanding of the factors that impact HGT. CRISPR-Cas systems provide sequence-specific defense against HGT. From previous studies, we know that E. faecalis CRISPR-Cas provides sequence-specific anti-plasmid defense during agar plate biofilm mating and in the murine intestine. Those studies were mainly conducted using laboratory model strains with a single, CRISPR-targeted plasmid in the donor. MDR E. faecalis typically possess multiple plasmids that are diverse in sequence and may interact with each other to impact plasmid transfer and CRISPR-Cas efficacy. Here, we altered multiple parameters of our standard in vitro conjugation assays to assess CRISPR-Cas efficacy, including the number and genotype of plasmids in the donor, and laboratory model strains as donor versus recent human isolates as donor during conjugation. We found that the plasmids pTEF2 and pCF10, which are not targeted by CRISPR-Cas in our recipient, enhance the conjugative transfer of the CRISPR-targeted plasmid pTEF1 into both WT and CRISPR-Cas-deficient (via deletion of cas9) recipient cells. However, the effect of pTEF2 on pTEF1 transfer is much more pronounced, with a striking 6-log increase in pTEF1 conjugation frequency when pTEF2 is also present in the donor and recipients are deficient for CRISPR-Cas (compared with 4-log for pCF10). Overall, this study provides insight about the interplay between plasmids and CRISPR-Cas defence, opening avenues for developing novel therapeutic strategies to curb HGT among bacterial pathogens and highlighting pTEF2 as a plasmid for additional mechanistic study.},
}

*Enterococcus faecalis/genetics/drug effects/isolation & purification
*Plasmids/genetics
*CRISPR-Cas Systems/genetics
Gene Transfer, Horizontal
Conjugation, Genetic
Humans
Anti-Bacterial Agents/pharmacology
*Drug Resistance, Multiple, Bacterial/genetics
Gram-Positive Bacterial Infections/microbiology

@article {pmid40985733,
year = {2025},
author = {Romero, JL and Ratliff, JH and Carlson, CJ and Griffiths, DR and Miller, CS and Mosier, AC and Roane, TM},
title = {Community and functional stability in a working bioreactor degrading 1,4-dioxane at the Lowry Landfill Superfund Site.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0057425},
doi = {10.1128/aem.00574-25},
pmid = {40985733},
issn = {1098-5336},
abstract = {UNLABELLED: 1,4-dioxane (dioxane) is an emerging contaminant that poses risks to human and environmental health. Bacterial dioxane degradation is increasingly being studied as a method to remove dioxane from contaminated water. However, there is a lack of studies on microbial community structures and functions within efficient, large-scale, biodegradation-based remediation technologies. The Lowry Landfill Superfund Site (Colorado, USA) uses an on-site, pump-and-treat facility to remove dioxane from contaminated groundwater by biodegradation. Here, 16S rRNA gene and shotgun metagenomic sequencing were used to describe microbial community composition, soluble di-iron monooxygenase (SDIMO) alpha hydroxylases, and potential for dioxane degradation and horizontal gene transfer in bioreactor support media from the facility. Support media showed diverse microbial communities dominated by Nitrospiraceae, Nitrososphaeraceae, and Nitrosomonadaceae. Pseudonocardia was also detected, suggesting a potential presence of known dioxane-degraders. Candidate SDIMOs belonged mostly to Group V, followed by Groups IV, II, and I (based on read depth). The most abundant Group V clade contained 38 proteins that were phylogenetically related to DxmA-like proteins, including that of Pseudonocardia dioxanivorans CB1190 (a known dioxane degrader). Seventeen Lowry contigs containing DxmA-like proteins contained protein-coding genes potentially involved in chemical degradation, transcriptional regulation, and chemical transport. Interestingly, these contigs also included evidence of potential horizontal gene transfer, including toxin-antitoxin proteins, phage integrase proteins, putative transposases, and putative miniature inverted-repeat transposable elements. These findings improve our understanding of potential dioxane biodegradation mechanisms in a functioning remediation system. Further studies are needed to definitively confirm microbial activity and enzymatic activity toward dioxane removal in this site.

IMPORTANCE: As an environmental contaminant, 1,4-dioxane poses risks for water quality and human health. Used as a solvent and chemical stabilizer in a variety of manufacturing and industrial applications, microbiological methods of detoxification and mitigation are of interest. The degradation of 1,4-dioxane by the bacterium Pseudonocardia spp. is the best understood example; however, these studies are largely based on single isolate, bench-scale, or in silico experiments. Consequently, a knowledge gap exists on bacterial degradation of 1,4-dioxane at environmentally relevant concentrations using functioning remediation technologies at scale. This study addresses this gap directly by describing microbial taxa, enzymes, and potential horizontal gene transfer mechanisms associated with an active treatment plant located on a 1,4-dioxane-impacted U.S. Environmental Protection Agency (EPA) superfund site. As 1,4-dioxane contamination gains more attention, these findings may prove useful for future facilities aiming to promote and optimize removal by biodegradation.},
}

@article {pmid40804527,
year = {2025},
author = {Gavrilov, AA and Shamovsky, I and Zhegalova, I and Proshkin, S and Shamovsky, Y and Evko, G and Epshtein, V and Rasouly, A and Blavatnik, A and Lahiri, S and Rothenberg, E and Razin, SV and Nudler, E},
title = {Elementary 3D organization of active and silenced E. coli genome.},
journal = {Nature},
volume = {645},
number = {8082},
pages = {1060-1070},
pmid = {40804527},
issn = {1476-4687},
mesh = {*Escherichia coli/genetics/cytology ; *Genome, Bacterial/genetics ; Escherichia coli Proteins/metabolism/genetics ; *Chromosomes, Bacterial/genetics/chemistry/metabolism ; DNA-Binding Proteins/metabolism/genetics ; *Gene Silencing ; Nucleic Acid Conformation ; DNA, Bacterial/chemistry/genetics/metabolism ; Gene Transfer, Horizontal/genetics ; Molecular Chaperones ; },
abstract = {Unravelling how genomes are spatially organized and how their three-dimensional (3D) architecture drives cellular functions remains a major challenge in biology[1,2]. In bacteria, genomic DNA is compacted into a highly ordered, condensed state called nucleoid[3-5]. Despite progress in characterizing bacterial 3D genome architecture over recent decades[6-8], the fine structure and functional organization of the nucleoid remain elusive due to low-resolution contact maps from methods such as Hi-C[9-11]. Here we developed an enhanced Micro-C chromosome conformation capture, achieving 10-base pair (bp) resolution. This ultra-high-resolution analysis reveals elemental spatial structures in the Escherichia coli nucleoid, including chromosomal hairpins (CHINs) and chromosomal hairpin domains (CHIDs). These structures, organized by histone-like proteins H-NS and StpA, have key roles in repressing horizontally transferred genes. Disruption of H-NS causes drastic reorganization of the 3D genome, decreasing CHINs and CHIDs, whereas removing both H-NS and StpA results in their complete disassembly, increased transcription of horizontally transferred genes and delayed growth. Similar effects are observed with netropsin, which competes with H-NS and StpA for AT-rich DNA binding. Interactions between CHINs further organize the genome into isolated loops, potentially insulating active operons. Our Micro-C analysis reveals that all actively transcribed genes form distinct operon-sized chromosomal interaction domains (OPCIDs) in a transcription-dependent manner. These structures appear as square patterns on Micro-C maps, reflecting continuous contacts throughout transcribed regions. This work unveils the fundamental structural elements of the E. coli nucleoid, highlighting their connection to nucleoid-associated proteins and transcription machinery.},
}

*Escherichia coli/genetics/cytology
*Genome, Bacterial/genetics
Escherichia coli Proteins/metabolism/genetics
*Chromosomes, Bacterial/genetics/chemistry/metabolism
DNA-Binding Proteins/metabolism/genetics
*Gene Silencing
Nucleic Acid Conformation
DNA, Bacterial/chemistry/genetics/metabolism
Gene Transfer, Horizontal/genetics
Molecular Chaperones

@article {pmid40985701,
year = {2025},
author = {Boehlein, SK and Hennen-Bierwagen, TA and Shuler, SL and Tracy, WF and Hannah, LC and Resende, MFR and Myers, AM},
title = {Interactions of separately conserved α-(1→6) glucosidases that participate in maize endosperm starch biosynthesis.},
journal = {Plant physiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/plphys/kiaf417},
pmid = {40985701},
issn = {1532-2548},
abstract = {Chloroplast-containing species possess two α-(1→6)-glucosidases that share a common ancestor but were independently acquired by horizontal gene transfer from separate eubacterial donors. The pullulanase-type enzyme (CAZy subfamily GH13_13) and the isoamylase-type enzyme (CAZy subfamily GH13_11) both hydrolyze branch linkages in α-polyglucans. Thus, both enzyme types function as debranching enzymes (DBE) in starch metabolism. As both enzyme types are conserved, distinct selectable functions are expected. This study describes the functional interactions between maize (Zea mays L.) pullulanase1 (ZPU1) and the isoamylase-type enzyme complex comprising the paralogous proteins isoamylase1 (ISA1) and isoamylase2 (ISA2). Mutation of ISA1 or ISA2 caused reduced ZPU1 activity in developing endosperm extracts, and the addition of ISA1 to ZPU1-expressing yeast (Saccharomyces cerevisiae) cells caused increased ZPU1 activity. Specific amino acid substitutions in ISA1 resulted in altered ZPU1 mobility in SDS-PAGE. In vivo protein-protein interaction tests and co-immunoprecipitation revealed that ZPU1 and ISA1 interact in multi-subunit complexes. Maize lines harboring ISA1 mutations, exhibiting a classical low-starch, high-phytoglycogen-accumulation phenotype, were altered by recurrent selection so that kernel appearance reverted to near normal. Extragenic suppression indicated the requirement for ISA1/ISA2 activity had been bypassed. These results are consistent with a functional overlap between the GH13_11 and GH13_13 DBE types and raise the possibility that multiple GH13 proteins, namely ZPU1, ISA1 and ISA2, act together to physically coordinate their hydrolytic activities on precursor α-polyglucans.},
}

@article {pmid40983639,
year = {2025},
author = {Dirick, L and Liu, Y and Dong, S and Yu, J and Ouerdane, L and Storti, M and Alboresi, A and Curie, C and Goffinet, B},
title = {Multiple independent acquisitions of a metallophore-synthesis gene by plants through horizontal microbial gene transfer.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {8339},
pmid = {40983639},
issn = {2041-1723},
support = {DEB-1753811//National Science Foundation (NSF)/ ; ANR-19-CE20-0009//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-2021-CE20-0022-03//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-2021-CE20-0022-03//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-19-CE20-0009//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-2021-CE20-0022-03//Agence Nationale de la Recherche (French National Research Agency)/ ; 202005//Urban Management Bureau of Shenzhen Municipality/ ; 202203//Urban Management Bureau of Shenzhen Municipality/ ; },
mesh = {*Gene Transfer, Horizontal ; Phylogeny ; Evolution, Molecular ; *Plants/genetics ; *Bryophyta/genetics ; Fungi/genetics ; },
abstract = {The evolution of land plants is marked by major innovations enhancing their vegetative and reproductive fitness. Despite their extensive adaptations to terrestrial habitats, plants rely on ecological interactions with microbes for various physiological processes. Beyond their role as critical partners in the conquest of, and diversification on land, fungi and bacteria also serve as sources of genetic tools. Analyses of the gene space of land plant model organisms suggest that such transfers are unique and ancient. However here, using genomic data spanning the diversity of mosses, we demonstrate that a metallophore-synthesis gene was acquired independently from distinct microbial donors by at least five plant lineages. Furthermore we find that the first NAS gene acquired by mosses was later replaced by another fungal copy, transferred to another major moss lineage. Such a complex history of acquisition of a gene may reflect a more general pattern of highly dynamic gene exchange across the tree of life.},
}

*Gene Transfer, Horizontal
Phylogeny
Evolution, Molecular
*Plants/genetics
*Bryophyta/genetics
Fungi/genetics

@article {pmid40982302,
year = {2025},
author = {Liu, Z and Ma, C and Teng, X and Yu, K and Li, J},
title = {Emergence of Pediatric Sepsis Caused by a Klebsiella pneumoniae Strain Coharboring blaNDM-1, blaOXA-1, and Mcr-9 in China.},
journal = {Microbial drug resistance (Larchmont, N.Y.)},
volume = {},
number = {},
pages = {},
doi = {10.1177/10766294251380517},
pmid = {40982302},
issn = {1931-8448},
abstract = {This study reports the discovery of a Klebsiella pneumoniae (KPN) strain carrying the blaNDM-1, blaOXA-1, and mcr-9 genes in China for the first time. This strain was isolated from the blood of a 2-year-old pediatric patient with acute lymphoblastic leukemia and sepsis. The strain exhibited high resistance to various antibiotics, including β-lactams, carbapenems, and ceftazidime-avibactam. Through whole-genome sequencing and comparative genomic analysis, we found that these resistance genes coexisted on the transferable IncHI2/IncHI2A-type plasmid pK708696_1, which showed high similarity to plasmid pK710429_2 from strain KPN710429 previously identified in our hospital, indicating their potential for rapid spread through horizontal gene transfer. We also performed conjugation experiments to verify the transferability of the plasmid. The results show that the resistance of this strain to traditional antibiotics significantly limited clinical treatment options, thereby posing a serious threat, especially for pediatric leukemia patients with compromised immune systems. This study provides important scientific evidence and new therapeutic approaches for combating carbapenem-resistant Klebsiella pneumoniae infections and highlights the urgency of developing new antibiotics and alternative therapies.},
}

@article {pmid40980877,
year = {2025},
author = {Eriksson, H and Schlegel, S and Koskiniemi, S},
title = {A delivered DNase toxin creates population heterogeneity through transient intoxication of siblings.},
journal = {mBio},
volume = {},
number = {},
pages = {e0208325},
doi = {10.1128/mbio.02083-25},
pmid = {40980877},
issn = {2150-7511},
abstract = {UNLABELLED: Population heterogeneity is important for multicellular behavior, as well as bet-hedging strategies. Recent findings suggest a role for bacterial toxin delivery in generating population heterogeneity, but the molecular mechanisms by which this occurs are not well understood. Here, we address if and how delivery of bacterial CdiA toxins generates heterogeneity in an isogenic population of Escherichia coli (E. coli) cells. Using a DNase toxin as a proxy, we find that E. coli populations able to deliver the toxin show a heterogeneous expression of the SOS-response gene sulA, whereas those incapable of kin-delivery remain homogeneous. Heterogeneity results from excessive delivery of toxin into some cells, which become intoxicated due to insufficient immunity. A low level of intoxication by this toxin is transiently reversible, and intoxicated cells can be rescued by the de novo synthesis of cognate immunity protein. The fraction of cells experiencing toxicity is increased by liberating the receptor responsible for toxin import from its tasks in outer-membrane biogenesis, suggesting that kin-intoxication is limited by receptor availability. Expression of sulA is regulated by both DNA damage and redox status. Interestingly, kin-delivery changes redox status, whereas intoxicated non-kin cells induce the SOS DNA damage response. The former results in changed expression of metabolic genes, whereas the latter induces prophage excision, which may promote horizontal gene transfer. In conclusion, we identify a molecular mechanism by which heterogeneity is generated through toxin delivery among kin, and some of the consequences of said heterogeneity.

IMPORTANCE: Population heterogeneity is important for multicellularity, as well as for bet-hedging strategies. A heterogeneous population allows cells with the same genotype to respond differently to environmental cues and stresses. For multicellularity, heterogeneity originates from coordinated signaling, whereas bet-hedging strategies can arise stochastically due to cell-to-cell variation in the concentration of signaling molecules. However, recent advances suggest a role for bacterial toxin delivery in the generation of population heterogeneity. How toxins mediate heterogeneity mechanistically is, however, unclear. Here, we show that kin cells transiently intoxicate each other with CdiA toxins, resulting in physiological changes. These changes are specific to the toxic activity, i.e., other toxins with different activities are likely to give rise to other responses. Thus, we find that the arsenal of toxins that bacteria harbor could affect their ability to participate in bet-hedging strategies, as well as in multicellular behavior.},
}

@article {pmid40980327,
year = {2025},
author = {Mosca Angelucci, D and Piergiacomo, F and Donati, E and Pagani, L and Minuti, E and Brusetti, L and Tomei, MC},
title = {Combined effects of ciprofloxacin and microplastics on alpine spring water microbiota: evidence from glacier-fed microcosm experiments.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1654589},
pmid = {40980327},
issn = {1664-302X},
abstract = {INTRODUCTION: Emerging contaminants such as microplastics (MPs) and antibiotics pose increasing environmental and public health risks due to their persistence and incomplete removal by wastewater treatment processes. MPs can act as vectors for antibiotics, facilitating their environmental spreading and supporting biofilm formation, which can enhance horizontal gene transfer and antibiotic resistance. This study investigates the combined effects of ciprofloxacin (CIP) and polyethylene terephthalate (PET) MPs on microbiota in alpine spring water (SW) sourced from a rock glacier.

METHODS: Four experimental scenarios (Control, CIP, PET, CIP + PET) were established to assess the sorption dynamics of CIP onto PET particles and the consequent microbial responses. A multidisciplinary analytical approach combining ultra-performance liquid chromatography, microscopy, quantitative PCR, and metabarcoding was applied.

RESULTS: CIP exhibited progressive sorption onto PET, accompanied by a time-dependent increase in biofilm formation, most pronounced in the CIP + PET condition. qPCR revealed elevated copy numbers of resistance genes qnrA and qnrB in CIP + PET, suggesting synergistic effects between antibiotics and MPs in promoting resistance. CIP was the dominant driver of microbial compositional shifts, favoring known CIP-degrading taxa. A shared core microbiome of 216 amplicon sequence variants was detected across all conditions, but specific taxa were differentially enriched under varying exposures. The combined CIP + PET test induced the strongest community shifts, while CIP alone shared fewer taxa with controls, indicating selective pressure for resistant microorganisms like Achromobacter. PET MPs also shaped distinct microbial assemblages, possibly by offering niches favoring biofilm-associated genera such as Luteolibacter. Biodiversity metrics showed highest richness and evenness in CIP-free conditions (Control and PET), while CIP significantly reduced alpha diversity, favoring resistant taxa, as confirmed by NMDS and lower Shannon and Simpson indices. Effects of MPs were still noticeable.

CONCLUSION: These findings demonstrate the disruptive effects of CIP on alpine freshwater microbial communities and highlight the additional, though more moderate, influence of MPs. The combined presence of MPs and antibiotics may exacerbate resistance spreading by enhancing persistence and providing favorable conditions for resistant biofilms. A mechanistic understanding of these interactions is essential for accurate risk assessment and the development of effective mitigation strategies in alpine and other vulnerable freshwater ecosystems.},
}

@article {pmid40980325,
year = {2025},
author = {Lu, Y and Wen, Z and Liu, X and Zhang, T and Liu, M and Zhang, L and Qiu, J and Wang, M},
title = {Research progress on bacterial outer membrane vesicles in antibiotic resistance and clinical anti-infective therapy.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1670307},
pmid = {40980325},
issn = {1664-302X},
abstract = {In recent years, bacterial outer membrane vesicles (OMVs)-nanoscale, bilayered membrane structures secreted by Gram-negative bacteria-have attracted considerable attention for their involvement in antibiotic resistance and potential in clinical anti-infective strategies. OMVs encapsulate diverse biomolecules, including proteins, lipids, toxins, and nucleic acids, thereby serving as critical mediators of communication between bacteria and host cells. They contribute to horizontal gene transfer, signal transduction, and biofilm formation, ultimately enhancing bacterial adaptability and resistance. Clinically, OMVs are regarded as promising therapeutic platforms owing to their excellent biocompatibility and intrinsic immunogenicity, with ongoing investigations exploring their roles in vaccine development, targeted drug delivery, and immune modulation. This review highlights the participation of OMVs in resistance mechanisms across common pathogenic bacteria and discusses their emerging applications in infection control. By elucidating the biogenesis and functional mechanisms of OMVs, novel antibacterial strategies may be developed, offering new avenues to address the escalating global challenge of antibiotic resistance.},
}

@article {pmid40979677,
year = {2025},
author = {Phuadraksa, T and Choominthong, Y and Wichit, S and Yainoy, S},
title = {Emergence of Klebsiella pneumoniae ST14 co-harboring bla NDM-1, bla OXA-232 , mcr-1.1, and a novel IncI1 tet(X4) plasmid, with evidence of ColKP3 mobilization under antibiotic pressure.},
journal = {Current research in microbial sciences},
volume = {9},
number = {},
pages = {100466},
pmid = {40979677},
issn = {2666-5174},
abstract = {Companion animals and environmental niches act as interconnected reservoirs of antimicrobial resistance (AMR) genes, facilitating their persistence and horizontal transfer across hosts and ecosystems. Pet-associated environments, within the One Health framework linking human, animal, and environmental health, remain an underrecognized source of AMR dissemination. Pet grooming facilities generate wastewater containing bacteria from animal skin, fecal matter, and contaminated surfaces, potentially acting as factors that facilitate environmental contamination and zoonotic transmission. Here, we describe the isolation and complete genomic characterization of an extensively drug-resistant Klebsiella pneumoniae strain from wastewater at a pet grooming facility in Bangkok, Thailand. Whole-genome sequencing identified the isolate as sequence type (ST) 14, a globally disseminated high-risk clone associated with multidrug resistance and clinical outbreaks. The strain harbored four clinically significant resistance genes, bla NDM-1, bla OXA-232, mcr-1.1, and tet(X4), each located on distinct plasmids. To our knowledge, this is the first report of tet(X4) in K. pneumoniae ST14. The gene was found on a novel IncI1-type plasmid with a composite transposon, suggesting recent acquisition through horizontal gene transfer. Conjugation assays confirmed high transfer efficiency and phenotypic tigecycline resistance. In this study, although bla OXA-232 was carried on a non-conjugative ColKP3-type plasmid, colistin selection facilitated its transfer with plasmid size expansion, indicating antibiotic-driven mobilization. These findings highlight the evolutionary adaptability of K. pneumoniae ST14 and the risk posed by pet-associated wastewater as a reservoir for clinically important AMR genes. Integrated genomic surveillance and targeted One Health interventions are urgently needed to prevent environmental and zoonotic spread.},
}

@article {pmid40974529,
year = {2025},
author = {Tian, C and Tang, Z and Zhang, X and Yao, X and Li, Y and Zhuang, D and Luo, Y and Li, T and Bai, L and Zhao, F and Zhu, L and Shi, G and Jiang, P and Gong, Q and Zhou, H and Gao, H and Wu, Q and Sang, J and Liu, X and Li, X and Yu, L and Zhang, Z},
title = {Uncovering the gut microbiome and antibiotic resistome of mammals on the Tibetan Plateau.},
journal = {Science China. Life sciences},
volume = {},
number = {},
pages = {},
pmid = {40974529},
issn = {1869-1889},
abstract = {The mammalian species on the Tibetan Plateau are diverse and abundant, yet our understanding of their gut microbiome and antibiotic resistome remains limited. Here, we used metagenomics to analyse the gut microbiota of 2,561 mammals from the Tibetan Plateau, covering 14 species across six orders. Using de novo metagenome assembly, we reconstructed a total of 112,313 high- to medium-quality metagenomic assembly genomes (MAGs), representing 21,902 microbial species, 86% of which were unclassified. More than 8,000 nonredundant antibiotic resistance genes (ARGs) encompassing 28 types were identified in the gut microbiome of Tibetan Plateau mammals. We further conducted a risk assessment of these ARGs, identifying 334 nonredundant ARGs with high-risk characteristics related to human health. Importantly, seven cross-species horizontal gene transfer events involving high-risk ARGs were identified, three of which occurred between human and nonhuman mammalian gut microbiota. Additionally, we found that the abundance of ARGs in human gut microbiomes on the Tibetan Plateau was greater than that in those from eastern China, Europe, and the United States, whereas the abundance of ARGs in livestock gut microbiomes from the Tibetan Plateau was lower than that in livestock gut microbiomes from those regions. This study reveals that the gut microbiota of Tibetan Plateau mammals is a largely unexplored resource and a significant reservoir of ARGs, offering crucial insights into microbiome research and demonstrating potential public health implications.},
}

@article {pmid40527433,
year = {2025},
author = {Zhu, C and Han, Y and Lu, Z and Yao, H},
title = {Impacts of particle size and surface charge of ZnO on horizontal transformation of antibiotic resistance genes.},
journal = {NanoImpact},
volume = {39},
number = {},
pages = {100571},
doi = {10.1016/j.impact.2025.100571},
pmid = {40527433},
issn = {2452-0748},
mesh = {*Zinc Oxide/chemistry/pharmacology ; *Escherichia coli/genetics/drug effects ; Particle Size ; Surface Properties ; Plasmids/genetics ; *Gene Transfer, Horizontal/drug effects ; Anti-Bacterial Agents/pharmacology/chemistry ; *Drug Resistance, Microbial/genetics ; *Drug Resistance, Bacterial/genetics ; Nanoparticles/chemistry ; *Transformation, Bacterial/drug effects ; },
abstract = {The ever-growing antibiotic resistance in bacteria poses an enormous threat to public health and the environment. The horizontal transfer of antibiotic resistance genes (ARGs) is a major pathway for disseminating antibiotic resistance. As an inexpensive, nontoxic, and biocompatible material, ZnO with diverse sizes and surface properties have been prepared for widespread use. However, the effects and mechanisms of ZnO particles with different structural properties on the horizontal transfer of ARGs are not comprehensively understood. In this study, two groups of ZnO particles, one with the same size (93 nm) and different charge types (-9.5 and + 17.4 mV), and the other homogeneously positively charged but of different sizes (93, 215, and 2381 nm), were prepared. Their impacts on the horizontal transformation of ARGs mediated by plasmid pUC19 into E coli DH5α were investigated. In the positively charged group, the smallest ZnO nanoparticles at concentrations of 0.1-100 μg/mL induced 1.04-1.35 and 1.37-1.71-fold increases in transformation frequency when compared with that of the medium-sized and largest particles, respectively. In the similar-sized groups, positive ZnO promoted 1.06-1.32-fold increases than negative ZnO. Further investigation suggested that smaller and positive ZnO adsorbed more plasmids and correspondingly increased the uptake by recipient bacteria than that of larger and/or negative ZnO. In addition, the enhanced bacterial membrane permeability, ATP synthesis, and DNA replication were also accounted for the increased transformation. These results suggest that smaller-sized and positive ZnO poses a high environmental risk of spreading antibiotic resistance.},
}

*Zinc Oxide/chemistry/pharmacology
*Escherichia coli/genetics/drug effects
Particle Size
Surface Properties
Plasmids/genetics
*Gene Transfer, Horizontal/drug effects
Anti-Bacterial Agents/pharmacology/chemistry
*Drug Resistance, Microbial/genetics
*Drug Resistance, Bacterial/genetics
Nanoparticles/chemistry
*Transformation, Bacterial/drug effects

@article {pmid40973782,
year = {2025},
author = {Morimoto, D and Usutani, R and Tateishi, N and Funaoka, Y and Takahashi, M and Nagasaki, K},
title = {Co-infection of phylogenetically distinct nucleocytoviruses in Acanthamoeba castellanii cells.},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnaf087},
pmid = {40973782},
issn = {1574-6968},
abstract = {Nucleocytoviruses have extraordinarily large double-stranded DNA genome, including a set of highly conserved genes for viral reproduction. Meanwhile, nucleocytoviruses supposedly acquire new genes from cellular organisms and different lineages of nucleocytovirus, leading to their evolution. Although horizontal gene transfer among nucleocytoviruses is thought to occur in the cell simultaneously infected by distinct nucleocytoviruses, it remains unknown which combination of lineages can co-infect host cell. Here, we performed co-infection experiments using cedratvirus, megavirus, mollivirus, and pandoravirus. By transmission electron microscopy, we observed Acanthamoeba castellanii cells incorporating two distinct viral species in all six combinations. Furthermore, A. castellanii cell incorporating all four viral species was observed. In these experiments, a simultaneous increase in viral particles was observed for the combination of mollivirus and pandoravirus, pandoravirus and cedratvirus, mollivirus and cedratvirus, and megavirus and cedratvirus. Furthermore, transcription levels of cedratvirus and megavirus genes in the co-infected culture were significantly lower than those in the mono-infected culture based on time-course experiments, suggesting that distinct nucleocytoviruses may compete for viral reproduction. This is the first report experimentally demonstrating that co-infection of distinct nucleocytoviruses occurs in A. castellanii cell.},
}

@article {pmid40972972,
year = {2025},
author = {Marcy, E and Chiek, S and Hidé, M and Hak, S and Ma, C and Lem, M and Delvallez, G and Bañuls, AL and Cheng, S and Hayer, J},
title = {Hybrid Sequencing of Chromosome and Plasmids from Multidrug Resistant Escherichia coli Isolated in Cambodia: Are Megaplasmids Vectors of Antibiotic Resistance Genes?.},
journal = {Journal of global antimicrobial resistance},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jgar.2025.09.003},
pmid = {40972972},
issn = {2213-7173},
abstract = {OBJECTIVES: The prevalence of Antimicrobial Resistance (AMR) in Escherichia coli infections in Cambodia is high and increasing, yet data distinguishing plasmid- and chromosome-mediated AMR-spread remain limited. The aim of this study was to characterise chromosomal and plasmid structures in clinically relevant E. coli resistant strains to investigate mechanisms driving the spread of Antibiotic Resistance Genes (ARGs) in Battambang Province, Cambodia.

METHODS: Hybrid genome assembly was performed using short- and long-read sequencing of six Extended Spectrum Betalactamase (ESBL)- and Carbapenemase Producing (CP) E. coli isolates collected from patients at Battambang Provincial Hospital, Cambodia. Detailed bacteriological analyses were conducted, as well as comprehensive genomic investigations to characterise Sequence Types (STs), plasmids, resistance mechanisms, and phylogenetic relationships among the strains, and to perform pairwise comparisons of plasmid sequences.

RESULTS: Chromosome and plasmid sequences were successfully recovered for each strain. Five STs were identified: ST1193 (two strains), ST131, ST205, ST405 and ST4204. All strains displayed a megaplasmid carrying ARGs, and one to five regular-sized plasmids without ARGs. Four distinct megasplasmids sequences were identified, including one shared by two ST1193 strains and one shared by ST131 and ST205 strains.

CONCLUSIONS: The identification of megaplasmids carrying ARGs and shared by different strains highlights their potential role in the spread of antimicrobial resistance through horizontal gene transfer (HGT) in Cambodia. This study also confirms the circulation of the high-risk multidrug-resistant (MDR) clones ST131 and ST1193 in Battambang province, Cambodia, and underscores the importance of hybrid genome assembly to study plasmid structure and identify their role in AMR spread.},
}

@article {pmid40972703,
year = {2025},
author = {Bao, Y and Liu, G and Yao, H},
title = {Microplastic aging mediates bacterial and antibiotic resistance gene composition in plastisphere and the associated soil solution.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {127134},
doi = {10.1016/j.envpol.2025.127134},
pmid = {40972703},
issn = {1873-6424},
abstract = {Microplastics (MPs) and antibiotic resistance genes (ARGs) are emerging contaminants that have garnered significant attention due to their prevalence in soil. Although many studies have already highlighted the effects of MPs on soil microbial communities and ARGs spread, their differential variation in both habitats (plastisphere and surrounding soil solution) and the effect of aging degree of MPs has not been clarified. Herein, we conducted a microcosm experiment to investigate the effects of aged-treated MPs on microbiome and antibiotic resistome of the plastisphere and the surrounding soil solution. The results showed that MPs with different aging degree altered bacterial community compositions. The plastisphere was enriched more unique bacterial species compared to its surrounding solution, particularly for 7d-aged MPs. MPs aging promoted certain ARGs dissemination, which depends on habitats, ARGs types and their aging degree. MPs always promoted the enrichment of Proteobacteria as the top host, especially aged MPs, which explained the enhanced ARGs dissemination after aged MPs addition. The primary hosts of most ARGs shifted from surrounding soil solution to the plastisphere. In addition to these individual host species, population hosts, including key taxa within co-occurrence network modules and functional bacterial populations, also contributed to ARGs dissemination. Unique bacteria from the plastisphere were included in network key modules and promoted ARGs dissemination, but not in the solution. Bacterial functions and pathways both played pivotal roles in ARGs dissemination. Interestingly, the influence of these population-level hosts, along with associated bacterial functions and metabolic pathways, on ARG spread was more pronounced in the surrounding soil solution than in the plastisphere. According to variance partitioning analysis, horizontal gene transfer via MGEs plays an important role in ARGs dissemination with 54-78% contribution in two habitats. Overall, these findings provide the differential processes and driving mechanisms of ARGs dissemination between the plastisphere and surrounding soil solution.},
}

@article {pmid40971805,
year = {2025},
author = {Neupane, DP and Bearson, BL and Bearson, SMD},
title = {Localization of the origin of transfer (oriT) for Salmonella Genomic Island 4 (SGI-4) from Salmonella enterica serovar I 4, [5],12:i:.},
journal = {DNA research : an international journal for rapid publication of reports on genes and genomes},
volume = {},
number = {},
pages = {},
doi = {10.1093/dnares/dsaf023},
pmid = {40971805},
issn = {1756-1663},
abstract = {Salmonella enterica serovar I 4, [5],12:i:- (serovar I 4, [5],12:i:-) is one of the most frequent multidrug-resistant (MDR) Salmonella serovars associated with food-animal production globally, and strains often contain Salmonella genomic island-4 (SGI-4), an integrative conjugative element (ICE) encoding metal tolerance for copper, silver, and arsenic. Horizontal gene transfer (HGT) of SGI-4 from serovar I 4, [5],12:i:- to recipient bacteria results in enhanced metal tolerance for the transconjugants; however, the origin of transfer (oriT) for SGI-4 mobilization is unknown. In this study, the oriT within SGI-4 of MDR serovar I 4, [5],12:i:- strain USDA15WA-1 was identified by: a) cloning an internal region of SGI-4 into a non-mobilizable plasmid and demonstrating HGT to a bacterial recipient, and b) deleting the predicted oriT region of SGI-4 from strain USDA15WA-1 and abolishing SGI-4 transfer. Sequence similarity to oriTSGI-4 was identified in other Enterobacteriaceae, and conjugation of SGI-4 occurred from USDA15WA-1 to Salmonella serovars from serogroups C-E as well as Escherichia coli and Citrobacter. Localization of the SGI-4 oriT enhances our understanding of a DNA region involved in HGT of an ICE in a frequent MDR Salmonella serovar, thereby providing a model to investigate HGT of SGI-4 and dissemination of metal tolerance genes in the food-animal production environment.},
}

@article {pmid40971384,
year = {2025},
author = {Cuesta-Morrondo, S and Garita-Cambronero, J and Cubero, J},
title = {Unraveling the genomic complexity of secretion systems in the most virulent Xanthomonas arboricola pathovars.},
journal = {PloS one},
volume = {20},
number = {9},
pages = {e0332834},
doi = {10.1371/journal.pone.0332834},
pmid = {40971384},
issn = {1932-6203},
mesh = {*Xanthomonas/genetics/pathogenicity ; *Bacterial Secretion Systems/genetics ; *Genome, Bacterial ; Virulence/genetics ; Plant Diseases/microbiology ; Bacterial Proteins/genetics/metabolism ; Genomics ; Phylogeny ; },
abstract = {Xanthomonas arboricola pathovars pruni (Xap), juglandis (Xaj), and corylina (Xac) are phytopathogenic bacteria that infect Prunus spp., walnut, and hazelnut trees, respectively. In this study, the understanding of the differences among these pathovars was improved with the aim of elucidating their host range and uncovering distinct virulence mechanisms. A comparative genomic analysis was conducted focusing on secretion system clusters across high-quality genomes from two strains of each pathovar. The results revealed that the RaxABC type I secretion system was absent in all analyzed strains. However, the HlyDB type I secretion system was present in both Xap and Xac, with a putative HlyDB effector identified in each Xac strain. Additionally, Xap strains contained a putative PctAB type I secretion system, while only one of the Xac harbored a putative PctAB. Notably, the genomic region surrounding pctA and pctB lacked pctP, suggesting the presence of a novel type I secretion system rather than the canonical PctAB. In contrast, Xaj lacked all the studied type I secretion systems. While the core components of type II and type III secretion systems were highly conserved across strains, significant variation was observed in their substrates. Interestingly, only Xap carried two pathovar-specific type III effectors. Regarding type V secretion systems, complete homologs of EstA, YapH, and XadA were found in all strains, except for one Xac strain, which contained a frameshifted YapH. Additionally, homologs of the XacFhaB/XacFhaC system were found in both Xap strains. However, both Xaj strains and one Xac strain carried an incomplete XacFhaB subunit, while the other Xac strain lacked this system entirely. Finally, analysis of the genomic regions surrounding these secretion system clusters strongly suggests that horizontal gene transfer has played a crucial role in their acquisition, likely contributing to the diversification, emergence and specialization of distinct X. arboricola pathovars.},
}

*Xanthomonas/genetics/pathogenicity
*Bacterial Secretion Systems/genetics
*Genome, Bacterial
Virulence/genetics
Plant Diseases/microbiology
Bacterial Proteins/genetics/metabolism
Genomics
Phylogeny

@article {pmid40970135,
year = {2025},
author = {Gutiérrez-Escobar, AJ and Srinivasan, M and Muñoz-Ramirez, ZY and Vale, FF and Wang, D and Sandoval-Motta, S and Dekker, JP and Thorell, K and Camargo, MC and Yamaoka, Y and Fischer, W},
title = {Global diversity of integrating conjugative elements (ICEs) in Helicobacter pylori and their influence on genome architecture.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.08.25.671524},
pmid = {40970135},
issn = {2692-8205},
abstract = {Integrating conjugative elements (ICEs) are mobile genetic elements conferring a wide range of beneficial functions upon their bacterial hosts. Generally, they can be activated from their integrated states to undergo horizontal gene transfer via conjugation. In the case of the human gastric pathogen Helicobacter pylori , a paradigm for extensive genetic diversity, highly efficient natural transformation and recombination processes may superimpose canonical transfer of its two ICEs termed ICE Hptfs3 and ICE Hptfs4 , and thus shape their composition substantially. Here, as a part of the Helicobacter pylori Genome Project (Hp GP) initiative, we have analyzed high-quality genome sequences from 1011 clinical strains with respect to their ICE content and variability. We show that both elements are highly prevalent in all H. pylori populations, but have a strong tendency for gene erosion. ICE sequence variations reflect the population structure and show a clear signature of increased horizontal transfer. A detailed map of ICE integration sites revealed local preferences, but also how recombination processes result in hybrid elements or genome rearrangements. Population-specific differences in ICE cargo genes might reflect distinct requirements in the biological functions provided by these mobile elements.},
}