@article {pmid42308119,
year = {2026},
author = {Holman, DB and Gzyl, KE and Kommadath, A and Määttänen, P},
title = {Multi-omic characterization of the sow colostrum and milk microbiome and proteome.},
journal = {Microbial genomics},
volume = {12},
number = {6},
pages = {},
doi = {10.1099/mgen.0.001726},
pmid = {42308119},
issn = {2057-5858},
mesh = {Animals ; *Colostrum/microbiology ; *Milk/microbiology ; Female ; *Proteome/genetics ; Multiomics ; *Microbiota/genetics ; Swine ; *Bacteria/classification/isolation & purification/genetics ; Metagenomics/methods ; Proteomics ; },
abstract = {Sow colostrum and milk provide essential nutrients, immune protection and one of the earliest microbial exposures for piglets. However, the microbial composition, functional potential and host interactions of these mammary secretions remain poorly characterized. Here, we combined culturomics, metagenomics and proteomics to comprehensively characterize the microbiome and proteome of sow colostrum and milk collected at farrowing and at 7 and 21 days postpartum. We recovered 132 bacterial isolates representing at least 42 species, including 15 putatively novel taxa. These isolates included both potentially pathogenic species, such as Sarcina perfringens and Streptococcus suis, and potentially beneficial bacterial species like Lactobacillus amylovorus and Lactiplantibacillus plantarum. The microbial composition and functional potential shifted significantly as the milk matured, with L. amylovorus, Limosilactobacillus reuteri and Rothia spp. among the most relatively abundant taxa. Several antimicrobial resistance genes, including erm(C), tet(K), tet(M), lnu(A), poxtA and fexB, were identified on contigs encoding plasmid replicons in the isolates, indicating potential for horizontal gene transfer. Functional annotation of isolate genomes indicated broad carbohydrate-active enzyme (CAZyme) repertoires, including β-galactosidase-associated families and other CAZyme families consistent with potential milk oligosaccharide utilization. The colostrum and milk proteome also shifted during lactation, reflecting declining immune-related proteins and increasing metabolic and structural proteins. Correlations between specific microbial taxa and host proteins, including Rothia spp. and immune proteins or glycoproteins, suggested potential host-microbe interactions during lactation. Together, these findings provide a multi-omic perspective on how mammary microbiome dynamics and host responses during lactation may influence neonatal microbial colonization and health.},
}

Animals
*Colostrum/microbiology
*Milk/microbiology
Female
*Proteome/genetics
Multiomics
*Microbiota/genetics
Swine
*Bacteria/classification/isolation & purification/genetics
Metagenomics/methods
Proteomics

@article {pmid42308338,
year = {2026},
author = {Ong, CJN and Nazari, R and Cabuhat, KSP and Ogaya, JB and Ahmed, MM and Shomuyiwa, DO and Musa, SS and Daberechi, OJ and Abdi, YH and Dulay, RMR and Lucero-Prisno, DE},
title = {The mobile resistome in the water-soil-air nexus: horizontal gene transfer and environmental dissemination of antimicrobial resistance genes.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiag064},
pmid = {42308338},
issn = {1574-6941},
abstract = {The rapid emergence and global dissemination of antimicrobial resistance pose a serious threat to public health, environmental sustainability, and economic development. Central to this crisis is the resistome, defined as the collection of all antimicrobial resistance genes present in pathogenic and non-pathogenic microorganisms across clinical, agricultural, and natural ecosystems. The environmental resistome plays a crucial role in the evolution and transmission of resistance, serving as both a reservoir and a conduit for ARG exchange through horizontal gene transfer. This review provides a comprehensive overview of the structure, diversity, and dynamics of the resistome, with emphasis on the interconnected water-soil-air continuum. Key mechanisms driving resistome dissemination, including mobile genetic elements such as plasmids, integrons, transposons, and bacteriophages, are discussed alongside the major routes of gene transfer, conjugation, transformation, and transduction. The review highlights anthropogenic drivers that intensify resistome expansion, including antibiotic misuse, wastewater discharge, agricultural runoff, and exposure to heavy metals, pesticides, and disinfectants, which promote co-selection. Advances in resistome profiling approaches, such as quantitative PCR, metagenomics, long-read sequencing, and functional metagenomics, are critically evaluated for their capacity to resolve ARG diversity, mobility, and host associations.},
}

@article {pmid42309504,
year = {2026},
author = {Barros, DC and de Freitas, LHK and Gomes, MP},
title = {Microbiome-Informed Pathways Linking Nature-Based Treatment Systems to Antimicrobial Resistance Outcomes.},
journal = {Environmental microbiology},
volume = {28},
number = {6},
pages = {e70358},
doi = {10.1111/1462-2920.70358},
pmid = {42309504},
issn = {1462-2920},
support = {001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; 302226/2022-2//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; BRD2024011000004//Fundação Araucária/ ; },
mesh = {*Microbiota ; *Drug Resistance, Bacterial ; *Anti-Bacterial Agents/pharmacology ; Wetlands ; *Bacteria/drug effects/genetics ; Rhizosphere ; *Drug Resistance, Microbial ; },
abstract = {Antimicrobial resistance (AMR) is a One Health challenge driven by clinical antibiotic use and environmental processes that shape microbial selection and genetic exchanges. Nature-based solutions (NbS), particularly constructed wetlands, are increasingly used to remove complex contaminant mixtures from aquatic systems. Although these systems often achieve considerable efficiencies, their effects on AMR dynamics remain unclear. This review synthesizes evidence on how aquatic rhizospheres function as microbiome-associated ecological reactors, in which contaminant mixtures, redox gradients and microbial interactions jointly influence resistance. We show that wetlands can function along a continuum between antimicrobial resistance attenuation, persistence, and dissemination, depending on the design, operation, and ecological context. Importantly, the removal of bioactive compounds does not necessarily translate to a reduced resistance risk, as selective pressures may persist within biofilms, sediments, and plant-associated compartments. We propose a microbiome-informed conceptual framework for interpreting AMR in nature-based systems. This perspective identifies potentially modifiable leverage points for understanding, interpreting, and potentially mitigating resistance-related risks and underscores the need for monitoring and risk assessment strategies that extend beyond conventional chemical metrics and incorporate the One Health exposure pathways. Together, these insights reposition wetlands as conditional solutions, whose sustainability depends on explicitly addressing antimicrobial resistance, alongside contaminant removal.},
}

*Microbiota
*Drug Resistance, Bacterial
*Anti-Bacterial Agents/pharmacology
Wetlands
*Bacteria/drug effects/genetics
Rhizosphere
*Drug Resistance, Microbial

@article {pmid42310306,
year = {2026},
author = {Ishimoto, N and He, S and Bogdanov, M and Smith, TK and Frankel, G and Beis, K},
title = {Phospholipid-independent biogenesis and function of the RP4 conjugation pilus.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-74409-x},
pmid = {42310306},
issn = {2041-1723},
abstract = {Bacterial conjugation, the process of horizontal gene transfer between bacteria, is initiated by mating pair formation (MPF) via a conjugative pilus. Conjugation of the IncP RP4 plasmid is mediated by short mating pili. Here, we report the cryo-EM structure of the RP4 pilus at 2.74 Å resolution. Uniquely, both the structural and quantitative mass spectral analyses revealed that the cyclic TrbC pilin subunit is not lipidated. Consistently, an E. coli pgsA mutant lacking phosphatidylglycerol (PG) can serve as a donor of RP4 but not of F- (pKpQIL), H- (R27) or W- (R388) pili, whose biogenesis and DNA transfer is PG-dependent. RP4 is the first example of a lipid-independent functional mating pilus. This discovery suggests that an amphipathic lipid moiety is not universally essential for the biogenesis of conjugative pili and MPF, providing an alternative model for their assembly and function. These data expand our understanding of the diverse bacterial mechanisms employ to transfer genetic material.},
}

@article {pmid42310404,
year = {2026},
author = {Typas, D},
title = {A horizontal gene-transfer-like mechanism in mammalian cells.},
journal = {Nature structural & molecular biology},
volume = {33},
number = {6},
pages = {896},
doi = {10.1038/s41594-026-01826-3},
pmid = {42310404},
issn = {1545-9985},
}

@article {pmid42311380,
year = {2026},
author = {Liang, L and Shang, Z and Liu, A and Lin, D and Wu, N and Jing, J and Yang, Z and Liu, W},
title = {Genomic characterization of a pathogenic Bacillus licheniformis strain LSDY01: deciphering its genetic diversity and virulence-associated traits.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1815181},
pmid = {42311380},
issn = {1664-302X},
abstract = {BACKGROUND: Bacillus licheniformis is an opportunistic pathogen in clinical settings. However, the emergence of clinical strains carrying horizontally acquired virulence determinants, including chromosomal genomic islands harboring yopX, a putative type IV secretion system (T4SS), and plasmids bearing toxin-antitoxin systems and additional virulence factors, poses a significant challenge to diagnosis and treatment. Moreover, the genetic basis of the pathogenicity of clinical isolates has not been comprehensively studied.

METHODS: A pathogenic B. licheniformis strain (LSDY01) isolated from a skin infection was subjected to whole-genome sequencing and comparative genomic analyses. Phylogenetic reconstruction, pan-genome analysis, and detailed characterization of plasmid and chromosomal virulence determinants were performed. Antimicrobial susceptibility testing was performed according to standardized guidelines. Biofilm formation assays were also conducted. The cytotoxic effect of LSDY01 on HEK293 cells was evaluated using a CCK-8 assay.

RESULTS: Strain LSDY01 belonged to B. licheniformis ST20, differing by only one allele from the prevalent ST3. Its closest relatives were the Daqu-derived strains CP143961.1 and CP143962.1. A unique horizontally acquired genomic island (~157 27 kb, GC 33.03%) and a putative type IV secretion system (T4SS) gene cluster were identified on the chromosome of this strain. A novel plasmid (pLSDY01), which is highly similar to environmental plasmids, harbors yopX, a toxin-antitoxin system, pilT, and a pistol ribozyme. LSDY01 was susceptible to imipenem and vancomycin but resistant to penicillin, erythromycin, and chloramphenicol. The CCK-8 assay revealed a non-significant trend toward reduced HEK293 cell viability after co-culture with LSDY01 (p = 0.0545 at 2 h of CCK-8 incubation).

CONCLUSION: Our findings suggest that horizontal gene transfer, including plasmid acquisition and potential phage integration, may have enabled B. licheniformis to evolve into a pathogen, highlighting the need to reassess the safety of traditionally non-pathogenic microbes.},
}

@article {pmid42313054,
year = {2026},
author = {Hikida, H and Zhang, R and Chen, J and Okazaki, Y and Ogata, H},
title = {Horizontal transfer of a 180-kbp genomic fraction among the largest viral genomes.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0010526},
doi = {10.1128/aem.00105-26},
pmid = {42313054},
issn = {1098-5336},
abstract = {Viruses are generally considered tiny biological entities with small genomes; however, some dsDNA viruses, known as giant viruses, have large genomes that are comparable to those of small bacteria. These viruses may have evolved from a small ancestor. During their evolution, virus-to-virus horizontal gene transfer has substantially contributed to the expansion of the genomic repertoire of giant viruses. In this study, we identified a horizontal transfer of a large fraction of the genome between viruses in pandoraviruses, a group of giant viruses with the largest genome sizes reaching 2.5 Mbp. We isolated a pandoravirus that belongs to a known viral species. However, its genome size was 200 kbp larger than that of other strains in the same species. Comparative genomics identified a 180-kbp genomic fraction with 168 genes in the newly isolated virus, which may have been horizontally transferred from a distantly related pandoravirus. The gene composition in the 180-kbp region further indicates that this region was already large at the time of the horizontal transfer. Our findings suggest that pandoraviruses can horizontally exchange a large portion of their genomes. This event presumably represents one mechanism for accelerating genomic evolution and gigantism in giant viruses.IMPORTANCEGiant viruses are double-stranded DNA viruses belonging to the phylum Nucleocytoviricota, characterized by large particles and genomes. Previous studies have suggested that these viruses may have evolved from a small ancestor, but the underlying mechanisms are not fully understood. In this study, we isolated one of the largest giant viruses, pandoravirus, which belongs to a known viral species but has a genome 200 kbp larger than that of other strains in the same species. Comparative genomics identified a 180-kbp genomic fragment containing 168 genes in the newly isolated virus that is absent from other strains of the same species. Further comparative analysis indicated that this 180-kbp region has been horizontally transferred from a distantly related pandoravirus. Our findings suggest that giant viruses can exchange a massive number of genes by a horizontal transfer of a large genomic fraction, which may have contributed to their gigantism.},
}

@article {pmid42313083,
year = {2026},
author = {Holtappels, D and Rickus, GEJ and Morgan, T and de Rezende, RR and Koskella, B and Alfenas-Zerbini, P},
title = {Erratum: Comparative genomics reveals high prophage diversity and horizontal gene transfer of effectors and phage defence systems in the Pseudomonas syringae complex.},
journal = {Microbial genomics},
volume = {12},
number = {6},
pages = {},
doi = {10.1099/mgen.0.001761},
pmid = {42313083},
issn = {2057-5858},
}

@article {pmid42313157,
year = {2026},
author = {Cardenas Alegria, OV and Torres, MC and Breyer, GM and Rebelatto, R and Wuaden, CR and Pastore, J and Lazzarotti, M and Ramos, RTJ and Dorn, M and Kich, JD and Siqueira, FM},
title = {Dynamics of Bacterial Communities and Resistomes Across Swine Waste Stabilization Ponds and Fertilized Soils.},
journal = {Current microbiology},
volume = {83},
number = {8},
pages = {},
pmid = {42313157},
issn = {1432-0991},
mesh = {Animals ; Swine ; *Bacteria/genetics/classification/drug effects/isolation & purification ; *Soil Microbiology ; *Manure/microbiology ; *Drug Resistance, Bacterial/genetics ; *Ponds/microbiology ; Interspersed Repetitive Sequences ; Anti-Bacterial Agents/pharmacology ; Fertilizers/analysis ; Soil/chemistry ; Metagenomics ; Genes, Bacterial ; *Microbiota ; },
abstract = {The environmental dissemination of antimicrobial resistance (AMR) through livestock waste represents a growing concern for human, environmental, and animal health. This study investigated how swine waste stabilization ponds (WSPs), and subsequent manure application to agricultural soils, influence bacterial community structure, antimicrobial resistance genes (ARGs), and mobile genetic elements (MGEs). Using shotgun metagenomics, we analyzed 80 samples from 20 swine farms, including waste collected before and after WSP treatment and soils with and without a history of manure application. Distinct microbial profiles were observed between waste and soil environments. Waste samples were dominated by Bacillota, Bacteroidota, and Pseudomonadota, whereas soils were enriched in Actinomycetota, particularly Streptomyces. WSP significantly reduced microbial diversity and caused shifts toward stress-tolerant taxa, indicating selective pressures during the process. Manure-fertilized soils exhibited altered community composition and enrichment of clinically relevant ARGs, including the fluoroquinolone resistance gene adeF. Waste management practices influenced resistome composition, with treated waste showing increased relative abundance of macrolide resistance genes (ermB and mefA). In soils, ARG profiles were associated with distinct MGE patterns, suggesting environment-specific mechanisms of gene mobility. Phage-associated elements were more prevalent in waste samples, whereas transposons were more prominent in soils, where ARG-MGE co-occurrence patterns indicated potential for horizontal gene transfer. Overall, our findings demonstrate that WSP management and soil application of swine manure shape both microbial communities and resistome configurations. These results underscore the importance of integrating waste treatment strategies into AMR surveillance frameworks and support a One Health approach to mitigate its dissemination in agroecosystems.},
}

Animals
Swine
*Bacteria/genetics/classification/drug effects/isolation & purification
*Soil Microbiology
*Manure/microbiology
*Drug Resistance, Bacterial/genetics
*Ponds/microbiology
Interspersed Repetitive Sequences
Anti-Bacterial Agents/pharmacology
Fertilizers/analysis
Soil/chemistry
Metagenomics
Genes, Bacterial
*Microbiota

@article {pmid42313295,
year = {2026},
author = {Asgharzadeh, S and Pourhajibagher, M and Bahador, A},
title = {Bacterial extracellular vesicles: emerging players in antimicrobial resistance and clinical translation.},
journal = {Molecular biology reports},
volume = {53},
number = {1},
pages = {},
pmid = {42313295},
issn = {1573-4978},
mesh = {*Extracellular Vesicles/metabolism/genetics ; Humans ; *Bacteria/metabolism/drug effects/genetics/pathogenicity ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Gene Transfer, Horizontal ; Animals ; Bacterial Infections/drug therapy/microbiology ; Drug Resistance, Multiple, Bacterial ; },
abstract = {Antimicrobial resistance (AMR) represents a critical and escalating global health challenge that extends beyond classical genetic mechanisms of resistance acquisition. Increasing evidence highlights extracellular vesicles (EVs) as key mediators of bacterial adaptation, intercellular communication, and resistance dissemination. Among these, bacterial extracellular vesicles (BEVs) play a central role by transporting diverse cargo, including antibiotic resistance genes, mobile genetic elements, antibiotic inactivating enzymes, and immunomodulatory factors. By facilitating horizontal gene transfer (HGT) and non-genetic resistance mechanisms such as antibiotic sequestration, extracellular neutralization, and biofilm reinforcement, BEVs contribute to the emergence and persistence of multidrug-resistant (MDR) infections. This review critically examines the biogenesis, cargo composition, and functional roles of BEVs in bacterial pathogenesis and AMR, while also discussing the complementary influence of host-derived EVs on infection dynamics and antimicrobial responses. We assess emerging evidence supporting EVs as non-invasive biomarkers for resistance surveillance and as adaptable platforms for vaccine development and targeted antimicrobial delivery. Finally, we highlight key unresolved challenges, including vesicle heterogeneity, limited understanding of cargo selection mechanisms, and the lack of standardized isolation and characterization protocols, which must be addressed to enable the clinical and translational integration of EV-based strategies in combating AMR.},
}

*Extracellular Vesicles/metabolism/genetics
Humans
*Bacteria/metabolism/drug effects/genetics/pathogenicity
*Drug Resistance, Bacterial/genetics
Anti-Bacterial Agents/pharmacology
Gene Transfer, Horizontal
Animals
Bacterial Infections/drug therapy/microbiology
Drug Resistance, Multiple, Bacterial

@article {pmid42299635,
year = {2026},
author = {Cunha da Silva, G and Rossi, CC},
title = {Global One Health genomics identify conserved virulence and mobile resistance in the opportunistic pathogen Staphylococcus saprophyticus.},
journal = {Future microbiology},
volume = {},
number = {},
pages = {1-10},
doi = {10.1080/17460913.2026.2688716},
pmid = {42299635},
issn = {1746-0921},
abstract = {AIMS: To define the global genomic landscape of Staphylococcus saprophyticus and evaluate the contribution of human, animal, food, and environmental strains to the dissemination of antimicrobial resistance and virulence traits within a One Health framework.

MATERIALS AND METHODS: A total of 975 publicly available genomes were analyzed using comparative genomics to characterize the resistome, virulome, and mobilome. Associations between antimicrobial resistance genes and mobile genetic elements were assessed. Ribosomal multilocus sequence typing (rMLST) was used to investigate population structure and lineage distribution across sources and geographic regions.

RESULTS: S. saprophyticus showed a global distribution across diverse hosts. A subset of rMLSTs (48500, 48501, 48492, and 48498) accounted for ~52% genomes and were widely distributed across countries and sources. Multidrug resistance was detected in all regions and frequently associated with plasmids, prophages, and integrative and conjugative elements, which together carried nearly half of resistance genes. In contrast, virulence determinants were largely chromosomal and conserved, supporting a stable pathogenic repertoire across ecological contexts.

CONCLUSIONS: These findings highlight the circulation of dominant lineages across multiple reservoirs and identify non-clinical environments as important contributors to the spread of clinically relevant resistance and virulence traits.},
}

@article {pmid42300741,
year = {2026},
author = {Mei, Z and Rodríguez, EA and Balcázar, JL},
title = {Plastic pollution and antimicrobial resistance: an emerging link with major implications.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0097326},
doi = {10.1128/aem.00973-26},
pmid = {42300741},
issn = {1098-5336},
abstract = {Plastic pollution and antimicrobial resistance are increasingly interconnected global threats. Micro- and nanoplastics create ecological hotspots that enhance microbial interactions and horizontal gene transfer, facilitating antimicrobial resistance dissemination. Here, we argue that the plastisphere acts as an evolutionary interface that reshapes microbial adaptation and resistome dynamics across ecosystems. Current antimicrobial resistance surveillance frameworks largely overlook the contribution of plastic pollution, highlighting the need to integrate plastisphere-mediated processes into One Health and environmental risk assessment strategies.},
}

@article {pmid42302690,
year = {2026},
author = {Li, X and Wen, S and Yu, C and Zhang, J and Xu, W and Yue, Z and Zhang, J},
title = {Dynamic evolution of the antibiotic resistome and mobilome on the microplastics of hospital wastewater.},
journal = {Journal of environmental management},
volume = {412},
number = {},
pages = {130243},
doi = {10.1016/j.jenvman.2026.130243},
pmid = {42302690},
issn = {1095-8630},
abstract = {Antimicrobial resistance is a major global health threat. Hospital wastewater serves as a significant reservoir for both microplastics (MPs) and antibiotic resistance genes (ARGs). MPs have recently been recognized not only as persistent pollutants but also as novel ecological niches for microbial colonization. However, the underlying mechanisms and key biological carriers driving MPs - mediated antimicrobial resistance transmission in hospital wastewater remain unclear. Here, we quantified the occurrence and characteristics of MPs in hospital wastewater and combined an incubation experiment with metagenomic sequencing to resolve the temporal dynamics of ARGs, mobile genetic elements (MGEs), and virulence factors (VFs) on MPs surfaces. MPs reached an abundance of 9.5 particles/L, with polyethylene (PE) dominating. Across the 28-day colonization period, with samples collected at 7, 14, 21, and 28 days, 68 ARGs, 443 MGEs and 414 VFs were detected, along with 129 prophage, highlighting the potential for enhanced horizontal gene transfer (HGT) in the plastisphere. We further reconstructed 360 metagenome-assembled genome (MAGs) spanning 16 phyla, and identified Pseudomonadota and Bacteroidota as core hosts of ARGs on MPs. Variance partitioning analysis revealed that MGEs were the major drivers of ARGs variation, independently explaining 44.4% of the dynamics. Our findings provide new insights into the ecological processes of antibiotic resistome of the MPs in the hospital wastewater.},
}

@article {pmid42303717,
year = {2026},
author = {Kamil, V and Yazdanmanesh, M and Tadayon, K and Khoshnood, S and Kalani, BS and Kazemian, H},
title = {Molecular characterization and antimicrobial resistance profiles of Shigella flexneri isolates from pediatric clinical cases in Ahvaz, Iran.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-57416-2},
pmid = {42303717},
issn = {2045-2322},
abstract = {Shigella is a highly invasive pathogen that causes dysentery and is associated with significant morbidity and mortality in children under five years of age. This agent is a major public health problem in developing countries. Multiple-locus variable-number tandem repeat (VNTR) analysis (MLVA) is a reliable, cost-effective typing method with high discriminatory power and reproducible results. The rise of drug resistance in Shigella strains is a growing global health threat. Despite the significance of Shigella in Iran, there is limited knowledge about genetic diversity and drug resistance profiles of local strains. Therefore, the purpose of this study was to characterize the genetic diversity and drug resistance profiles of Shigella strains isolated in Ahvaz, Iran. A total of 49 Shigella flexneri isolates were recovered from 500 stool samples of pediatric patients. Routine biochemical tests were used to identify all isolates. Antimicrobial susceptibility testing was performed, and resistance genes were detected by polymerase chain reaction (PCR). Extended-spectrum β-lactamases (ESBL), carbapenemase, and Metallo-β-lactamase (MBL) production were detected phenotypically using combination disk assays and confirmed by the CLSI-recommended modified Carbapenem inactivation method (mCIM) and EDTA-modified carbapenem inactivation method (eCIM). MLVA based on seven VNTR loci was performed to characterize the genetic diversity of the isolates. All 49 isolates were resistant to ceftazidime, trimethoprim/sulfamethoxazole, ampicillin, and ceftriaxone (100% each). High resistance rates were also observed for imipenem 36/49 (73.5%), meropenem 36/49 (73.5%), azithromycin 21/49 (42.9%), and ciprofloxacin 16/49 (32.7%). Furthermore, phenotypic testing revealed ESBL production in 46/49 (93.9%) isolates and carbapenemase activity in 36/49 (73.5%), of which 22/49 (44.9%) were MBL. PCR analysis identified blaCTX-M 38/49 (77.6%) and blaSHV 35/49 (71.4%) as the most prevalent ESBL genes, whereas blaNDM 14/49 (28.6%), and blaOXA-48 14/49 (28.6%) were the most common carbapenemase genes. MLVA typing divided the isolates into 22 different MLVA types, including 10 clusters and 12 singletons, and locus ms21 showed the highest discriminatory power. The isolates exhibited high genetic diversity with a non-clonal distribution of resistance, which indicates dissemination through horizontal gene transfer. Our results demonstrated that mCIM/eCIM and MLVA are viable methods for investigating Shigella species as they are cost-effective, provide quick results, and allow for easy sharing of numerical data between laboratories.},
}

@article {pmid42304007,
year = {2026},
author = {Alam, SA and Karmakar, D and Khan, B and Mandal, R and Bhattacharya, S and Ahmed, I and Maruyama, F and Saha, P},
title = {Polyphasic taxonomic characterization of Brachybacterium netajii sp. nov., a metabolically versatile bacterium isolated from the river Ganges, India.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-56775-0},
pmid = {42304007},
issn = {2045-2322},
abstract = {A comprehensive polyphasic taxonomic strategy was applied to the systematic characterization of strain DNPG3[T], which was isolated from the river Ganges, Hooghly, West Bengal, India. The Gram-positive, halotolerant, heavy-metal-tolerant strain exhibited the ability to degrade p-nitrophenol (PNP). Cellular fatty acid analysis revealed that the predominant components were anteiso-C15:0 (24.61%), C11:0 (21.06%), iso-C16:0 (11.89%), C16:0 (11.58%), and anteiso-C17:0 (11.24%). Notably, the presence of C11:0, C10:0 2-OH as major fatty acids differentiate strain DNPG3[T] from its closely related members of the genus Brachybacterium. The predominant respiratory quinone was identified as menaquinone-7 (MK-7). Analysis of 16S rRNA gene sequence indicated that B. zhongshanense strain JB[T] was the closest relative of DNPG3[T], sharing 97.08% sequence similarity. Genome-based ANI value calculated using the EzBioCloud server revealed that B. zhongshanense JCM 15471[T] was the closest genomic relative (85.49%). These values were further substantiated by digital DNA-DNA hybridization (dDDH) estimates calculated using the GGDC server. Taxonomic assignment using the GTDB database further indicated that strain DNPG3[T] constitutes a previously unrecognized species within the genus Brachybacterium. Genome analysis of strain DNPG3[T] identified eleven genomic islands, along with a rich repertoire of 194 carbohydrate-active enzyme (CAZyme) families, comprising 95 glycoside hydrolases and 53 glycosyltransferases. In addition, five biosynthetic gene clusters were detected. Collectively, these genomic features indicate the involvement of horizontal gene transfer events and highlighted the pronounced metabolic versatility of the strain, underscoring its potential for industrial enzyme production and secondary metabolite biosynthesis. Pan-genome analysis further indicates that the Brachybacterium pan-genome is open, reflecting substantial genetic diversity and ongoing gene acquisition within the genus. Comprehensive biochemical, physiological, chemotaxonomic, and phylogenetic analyses supported the assignment of strain DNPG3[T] to the genus Brachybacterium while clearly distinguishing it from all currently described species within the genus. Accordingly, strain DNPG3[T] was proposed to represent a novel species, for which the name Brachybacterium netajii sp. nov. is suggested. The type strain was DNPG3[T] (= MTCC13125[T]).},
}

@article {pmid42304249,
year = {2026},
author = {Whitehead-Tillery, CE and Waite, SE and Durand-Piña, GAE and Green, EK and Bell, JA and Zhang, L and Mansfield, LS},
title = {Genomic analysis reveals close genetic similarity between ESBL and other β-lactamase-producing E. coli isolates from humans and dogs, suggesting potential for inter-species transmission.},
journal = {BMC genomics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12864-026-13015-z},
pmid = {42304249},
issn = {1471-2164},
abstract = {BACKGROUND: Extended-spectrum β-lactamase-(ESBL)-producing Enterobacteriaceae are emerging in hospital and community settings as important causes of urinary tract infections. These plasmid-mediated enzymes have been identified in human and dog hosts, with blaCTX-M variants being the most prevalent ESBLs worldwide. Our objective was to identify horizontal gene transfer (HGT) events amongst human and dog-derived ESBL-producing bacteria by examining genetic relatedness of plasmid and bacterial whole genome sequences (WGS) associated with ESBLs and other β-lactamase genes. By understanding genetic relatedness, we aimed to provide insight into transmission dynamics of ESBLs and antibiotic resistance among humans and dogs in community-acquired settings.

RESULTS: Of 149 plasmids collected from humans (n = 125) and dogs (n = 24), 111 (74.5%) carried class A ESBL genes with blaCTX-M-14 (31.6%) predominating in human-derived plasmids and blaCTX-M-1 in dog-derived plasmids (29.6%). In addition, ESBLs and other β-lactamase genes, including blaTEM-1,were also identified in both populations. pMLST showed that IncF, IncI1, and IncN plasmids were the main groups contributing to the dissemination of ESBLs amongst human and dog populations. Neighbor-joining analysis revealed clustering of human and dog-derived plasmids carrying similar ESBL genes as well as other antibiotic-resistant genes. The maximum-likelihood tree revealed a high predominance of ST131 carried by E. coli serotypes O25:H4 in humans but not dogs. Virulence gene analysis revealed that ESBL-producing bacteria were not limited to UPEC.

CONCLUSIONS: The presence of conserved ESBLs, other β-lactamase genes and E. coli clones in both humans and dogs highlights widespread circulation of shared resistance elements. These findings support the need for broader One Health surveillance, particularly involving companion animals, to better track and mitigate ARG spread in community settings.},
}

@article {pmid42306866,
year = {2026},
author = {Roulet, ME and Ceriotti, LF and Gatica Soria, LM and Tulle, WD and Sanchez-Puerta, MV},
title = {A structural solution to functional HGT: gene chimaerism bypasses mitochondrial expression barriers in parasitic plants.},
journal = {Proceedings. Biological sciences},
volume = {293},
number = {2073},
pages = {},
doi = {10.1098/rspb.2025.2955},
pmid = {42306866},
issn = {1471-2954},
support = {//Fondo para la Investigación Científica y Tecnológica/ ; //Secretaría de Investigación, Internacionales y Posgrado, Universidad Nacional de Cuyo/ ; },
mesh = {*Gene Transfer, Horizontal ; *Genome, Mitochondrial ; *Genes, Mitochondrial ; Mitochondria/genetics ; },
abstract = {Horizontal gene transfer (HGT) in plant mitochondria is frequent, yet acquired genes are rarely functional due to expression barriers. The holoparasitic plant Lophophytum mirabile (Balanophoraceae) is an exceptional case, having functionally replaced numerous native mitochondrial genes with host-derived xenologues. This system provides a unique opportunity to investigate the mechanisms of functional HGT assimilation. Here, we assembled mitochondrial genomes of the sister species L. pyramidale and their mimosoid hosts and analysed expression data from both holoparasites. We show that this extensive functional integration occurred without the co-transfer of nuclear regulatory factors; Lophophytum relies entirely on its pre-existing native machinery. Our results demonstrate that the primary mechanism enabling Lophophytum to overcome the transcription barrier is structural: most functional xenologues are chimaeric and retain native 5' regions that probably place foreign coding sequences under the control of a recognizable native promoter. This structural solution is complemented by post-transcriptional flexibility, as the RNA editing machinery efficiently processes novel host-specific sites. However, functional replacement appears biased towards genes with inherently low editing requirements and no introns, highlighting a strong selective filter. Taken together, our results show that functional integration is driven by a combination of structural integration and the flexibility of the native regulatory system.},
}

*Gene Transfer, Horizontal
*Genome, Mitochondrial
*Genes, Mitochondrial
Mitochondria/genetics

@article {pmid42307236,
year = {2026},
author = {Liu, Y and Liu, Y},
title = {Gain and loss of plasmid-borne antibiotic resistance genes are associated with chromosomal resistance presence in Enterobacteriaceae.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0041226},
doi = {10.1128/msystems.00412-26},
pmid = {42307236},
issn = {2379-5077},
abstract = {Plasmids are central vehicles for the dissemination of antibiotic resistance genes (ARGs). They are among the most mobile and evolvable genetic elements, with broad host ranges and high rates of gene turnover, making them especially effective in spreading antibiotic resistance across bacterial lineages. Using the phylogeny-aware gene gain and loss model applied to 6,895 Enterobacteriaceae genomes, we quantified four evolutionary processes-gene gain, loss, expansion, and reduction-for plasmid-borne genes. We found that, overall, plasmid-borne ARGs (pARGs) exhibit similar gain rates compared with other plasmid genes, but significantly higher expansion and reduction rates. All four processes were strongly species-dependent, with only a minor influence of antibiotic class. Furthermore, bacterial clades harboring chromosomal ARGs (cARGs) showed significantly higher acquisition and lower loss of plasmid-borne resistance than did their sister clades lacking corresponding cARGs. Moreover, we found that the IncQ2 backbone was associated with qnrS2 and exclusively identified in Leclercia adecarboxylata, while Col(VCM04) plasmids carrying mprF were predominantly (71.4%) distributed within the Citrobacter genus. In summary, plasmid-mediated resistance is primarily species-dependent, and cARGs effectively mark lineages with a high capacity for plasmid-borne resistance acquisition.IMPORTANCEPlasmids play a central role in the spread of antibiotic resistance genes (ARGs), and the long-term evolutionary behavior of plasmid-borne ARGs (pARGs) could provide insights into the emergence of novel multidrug resistance. We studied nearly 7,000 Enterobacteriaceae genomes and show that pARGs evolve through the same gain processes as other plasmid genes but exhibit markedly higher and species-dependent copy number changes. Crucially, the strong association between chromosomal and plasmid ARGs reflect a lineage-level pattern of resistance retention, likely shaped by historical selective pressures or specific genomic backgrounds. Identifying such evolutionary lineages may provide a basis for predicting and monitoring the emergence of multidrug resistance.},
}

@article {pmid42296092,
year = {2026},
author = {Westley, J and Bedekar, P and Pursey, E and Szczelkun, MD and Recker, M and van Houte, S and Westra, ER},
title = {Eco-evolutionary feedbacks drive the co-occurrence of restriction-modification systems and antimicrobial resistance genes in bacteria.},
journal = {PLoS biology},
volume = {24},
number = {6},
pages = {e3003842},
doi = {10.1371/journal.pbio.3003842},
pmid = {42296092},
issn = {1545-7885},
abstract = {Bacterial pathogens commonly become drug resistant via horizontal acquisition of antimicrobial resistance genes (ARGs), which are often encoded on mobile genetic elements (MGEs). Although bacterial defence systems are typically considered barriers to horizontal gene transfer (HGT), previous studies revealed that bacteria with more restriction-modification (RM) systems (the most abundant bacterial defences) frequently carry more MGEs. It was suggested that this counterintuitive relationship might result from stronger selection for RM systems when exposure to costly MGEs increases. Here, we test this hypothesis using a combination of modeling and bioinformatics analysis of >40,000 bacterial genomes to better understand how eco-evolutionary feedbacks between selection for RM and acquisition of MGEs shape bacterial genome evolution. Our model predicts negative associations between HGT and RM, but only if RM diversity is high. By contrast, at low RM diversity, eco-evolutionary feedbacks drive the emergence of positive associations between HGT and RM. Consistent with these predictions, we identified negative relationships between acquired ARG counts and RM counts across species but positive relationships within individual species. Collectively, our work helps to understand how RM systems shape patterns of HGT of ARGs, which may offer opportunities for targeted surveillance of strains at higher risk of horizontally acquiring novel drug resistance alleles.},
}

@article {pmid42296180,
year = {2026},
author = {Hamelin, RC and Stewart, JE and Hadziabdic, D},
title = {Tree Killer, Qu'est-ce Que C'est? Insights From Forest Pathogen Genomes.},
journal = {Annual review of phytopathology},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-phyto-021621-114843},
pmid = {42296180},
issn = {1545-2107},
abstract = {Forests are central to planetary health but are increasingly challenged by emerging diseases driven by climate change, global trade, and anthropogenic disturbance. Despite the apparent resilience of long-lived, genetically diverse tree hosts, forest ecosystems have repeatedly experienced landscape-level pathogen-driven transformations. Advances in genomics, transcriptomics, and functional biology have transformed our understanding of how fungal and oomycete pathogens interact with their hosts across a continuum of lifestyles, from saprotrophy and necrotrophy to biotrophy. Here, we synthesize insights from comparative and population genomics and functional studies across diverse forest pathosystems to examine the traits that characterize successful tree pathogens. We highlight how lifestyle plasticity, adaptations to woody tissues, vector-mediated transmission, and biotrophic stealth enable pathogens to colonize perennial hosts and persist over long temporal scales. We further examine how genome plasticity, hybridization, and horizontal gene transfer generate adaptive potential that often outpaces host evolutionary responses under current environmental change. Finally, we discuss emerging genomic tools, including biosurveillance, machine learning-based classification, and genome editing, that are beginning to link genotype to phenotype and inform assessments of disease risk. By integrating genomic, ecological, and evolutionary perspectives, this review outlines general principles governing forest pathogen success and identifies priorities for future research aimed at improving understanding, early detection, and management of forest diseases in a changing world.},
}

@article {pmid42296358,
year = {2026},
author = {Ewart, KM and Adams, MWD and Zhang, Z and Baker, L and Fujiwara, K and Hayashi, Y and Featherstone, LA and Lu, OL and Helbling, JES and Moral, M and Maekawa, K and Rose, H and Jex, A and Ho, SYW and Lo, N},
title = {Uncovering thousands of endosymbiont DNA transfer events within single cockroach genomes.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {25},
pages = {e2604240123},
doi = {10.1073/pnas.2604240123},
pmid = {42296358},
issn = {1091-6490},
support = {FT160100463//Australian Research Council/ ; DP220103265//Australian Research Council/ ; },
mesh = {Animals ; *Gene Transfer, Horizontal ; *Cockroaches/genetics/microbiology ; *Symbiosis/genetics ; Phylogeny ; *Genome, Insect ; Evolution, Molecular ; },
abstract = {Horizontal gene transfer (HGT) between organisms can be a valuable source of genetic variation and innovation. Research on HGT in eukaryotes has hitherto focused on transfers of coding sequences; insertions of noncoding DNA remain poorly understood. Here, we investigated HGT in cockroaches, which have a long-standing evolutionary relationship with the transovarially transmitted endosymbiont Blattabacterium cuenoti, making them a valuable system for assessing the potential scale of HGT. We aligned 150-bp genomic fragments of B. cuenoti to 23 cockroach and termite genomes, including 8 genomes newly sequenced, and revealed pervasive endosymbiont DNA transfer events. Australian panesthiine and geoscapheine cockroaches were consistently found to harbor >3000 HGT inserts, more than an order of magnitude higher than the previous maximum estimate in other eukaryotes, excluding rotifers. Some inserts appear to have persisted for ≥28.7 million years in this group, which may reflect functional roles. We identified numerous chimeric inserts comprising up to nine short segments from different locations in the B. cuenoti genome. Our findings indicate pervasive HGT in eukaryote genomes, with potentially far-reaching implications for adaptation and speciation.},
}

Animals
*Gene Transfer, Horizontal
*Cockroaches/genetics/microbiology
*Symbiosis/genetics
Phylogeny
*Genome, Insect
Evolution, Molecular

@article {pmid42296904,
year = {2026},
author = {Ababii, M and Bohuon, V and Chane, A and Poc, CD},
title = {Atmospheric pollutants and airborne bacteria: adaptation mechanisms, virulence modulation, and public health implications.},
journal = {The Science of the total environment},
volume = {1044},
number = {},
pages = {181950},
doi = {10.1016/j.scitotenv.2026.181950},
pmid = {42296904},
issn = {1879-1026},
abstract = {Outdoor air pollution is a major public health issue. Many studies correlate ambient air pollution with acute and chronic pulmonary disease. However, its interactions with airborne bacteria remain insufficiently characterized. In particular, the mechanisms linking pollutants to microbial adaptation and pathogenicity are not clearly established. An increasing body of evidence shows that airborne bacteria respond actively to atmospheric pollutants. These responses affect their survival, behavior, and functional traits. However, a comprehensive synthesis of pollutant-driven microbial adaptation and its implications for virulence and public health, is still lacking. This review synthesizes current knowledge on the interactions between atmospheric pollutants and airborne bacteria within an integrative mechanistic and One Health framework. The nature and sources of major atmospheric pollutants are first outlined. The mechanisms by which these pollutants induce oxidative and nitrosative stress in bacteria are then analyzed, with a focus on the generation of reactive oxygen and nitrogen species and their cellular impacts. Bacterial adaptive responses to these stresses are subsequently discussed. These include antioxidant defenses, membrane remodeling, biofilm formation, and horizontal gene transfer. The potential contribution of these processes to bacterial persistence, virulence-associated traits, and antibiotic resistance is discussed. The implications for human and environmental health are then addressed. Particular attention is given to respiratory infections, the enrichment of airborne resistomes, and the emergence of opportunistic taxa in polluted environments. Finally, future research directions including key knowledge gaps are summarized.},
}

@article {pmid42297254,
year = {2026},
author = {Ma, R and Li, X and Tang, R and Liu, Y and Wang, J and Li, G and Li, S and Tian, S and Jiang, T and Chang, J and Yuan, J},
title = {Two-phase removal kinetics of antimicrobial resistance in collaborative composting: Thermophilic enhancement and rebound suppression.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135174},
doi = {10.1016/j.biortech.2026.135174},
pmid = {42297254},
issn = {1873-2976},
abstract = {Temperature significantly affects antimicrobial resistance (AMR) during composting, but its role in multi-material co-composting remains unclear. This study explored temperature effects on pathogen inactivation, antibiotic resistance gene (ARG) removal, and host dynamics. Three composting regimes were established based on temperature: thermophilic (TC, <65 °C), superthermophilic (SC, 65-75 °C), and hyperthermophilic (HC, >75 °C). Fecal coliforms were inactivated within 2 days at > 65 °C, compared to 3 days at 40-50 °C. Temperatures exceeding 65 °C accelerated pathogen elimination, achieving over 98% reduction by day 28. During the thermophilic phase, elevated temperatures (>65 °C) suppressed vertical gene transfer and removed 95%-97% of ARGs by day 28. In the maturation phase, maintaining moisture content (MC) below 40% mitigated ARG rebound by restricting horizontal gene transfer, bacterial activity, and mobile genetic elements (MGEs). Six high-risk ARGs (tetW, aadE, ermX, ermB, sul1, tetM) and their pathogenic hosts (Enterococcus, Escherichia, Streptococcus, Clostridium, Corynebacterium) were identified. By day 28, treatments exceeding 65 °C eliminated 96%-99% of pathogens, high-risk ARGs, and their hosts, with no ARG rebound detected in the final compost. Overall, maintaining composting temperatures above 65 °C for at least five consecutive days and controlling final MC below 40% constitutes an effective strategy for mitigating AMR risks in multi-material co-composting. This study provides both theoretical and technical foundations for managing antibiotic resistance risks during composting.},
}

@article {pmid42299085,
year = {2026},
author = {Ghafoor, M and Saqib, M and Ashfaq, K and Rehman, SU},
title = {Novel capsular diversity and antimicrobial resistance determinants of Staphylococcus aureus associated with bovine and bubaline mastitis.},
journal = {Polish journal of veterinary sciences},
volume = {29},
number = {2},
pages = {313-326},
doi = {10.24425/pjvs.2026.1277},
pmid = {42299085},
issn = {2300-2557},
mesh = {Animals ; *Staphylococcus aureus/drug effects/genetics ; Cattle ; *Mastitis, Bovine/microbiology/epidemiology ; Female ; *Staphylococcal Infections/veterinary/microbiology/epidemiology ; *Drug Resistance, Bacterial ; *Anti-Bacterial Agents/pharmacology ; *Buffaloes ; *Bacterial Capsules/genetics ; Gene Expression Regulation, Bacterial/physiology ; },
abstract = {In Pakistan, bovine mastitis has been identified as one of the biggest limitations to dairy production, and Staphylococcus aureus has been identified as one of the most enduring and economically relevant mastitogens. The current study was conducted to examine the capsular genotype and antimicrobial resistance (AMR) of S. aureus isolated from cases of clinical and subclinical mastitis in cows and buffaloes of the Punjab and Sindh provinces. One hundred and fifty S. aureus isolates (109 from cows and 41 from buffaloes) were isolated out of 87 dairy herds and verified using nuc gene-based PCR. Genotyping of capsular polysaccharide (CP) demonstrated that there were only cap5 (56%) and cap8 (44%) loci, but no cap1 and cap2. The cap5 was the most common among clinical (20.66%) and subclinical (35.33%) isolates, whereas cap8 had a frequency of 12.66% and 31.33% in clinical and subclinical isolates, respectively, suggesting that CP5 and CP8 are the common circulating types of capsular pathogens in the study areas. The antimicrobial susceptibility testing involving 13 routine antimicrobial agents revealed that 92% of isolates were resistant to one or more antimicrobials, and 63.3% of the isolates were multidrug-resistant (MDR). The greatest resistance was found with penicillin (72.66%), then amoxicillin (53.33%), and amoxicillin-clavulanic acid (37.33%). Those resistant to methicillin (3.33%) were mecA-positive MRSA, but no isolate was positive for mecC. Molecular screening showed that the prevalence of the blaZ gene (95.33%) was high and in line with the prevalence of resistance mediated by β-lactamase. The tetM (92.10%) and tetK (84.21%) were most common among the tetracycline-resistant isolates. The determinants of macrolide resistance were msrC (87.5%), ermB and ermC, and the aac-aphD aminoglycoside resistance gene was also present in 17.64% of resistant isolates. Resistance to critically important antimicrobials like vancomycin and linezolid was low, and optrA was not identified. Strong genotype-phenotype concordance was shown by correlation analysis to occur in 22 cases where 2 beta-lactam, tetracycline, and macrolide resistance determinants were genotyped and phenotyped, indicating the occurrence of co-selection and possible horizontal gene transfer. This study provides the first comprehensive molecular epidemiological insight in bovine and bubaline S. aureus capsular diversity, as well as AMR determinants of S. aureus, in Punjab and Sindh. The prevalence of CP5/CP8 is in favor of their inclusion in vaccine development, whereas high rate of MDR burden evidences the urgency of antimicrobial stewardship and long term molecular surveillance within one health paradigm.},
}

Animals
*Staphylococcus aureus/drug effects/genetics
Cattle
*Mastitis, Bovine/microbiology/epidemiology
Female
*Staphylococcal Infections/veterinary/microbiology/epidemiology
*Drug Resistance, Bacterial
*Anti-Bacterial Agents/pharmacology
*Buffaloes
*Bacterial Capsules/genetics
Gene Expression Regulation, Bacterial/physiology

@article {pmid40643607,
year = {2025},
author = {Soonsanga, S and Rungrod, A and Utamatho, M and Trakulnaleamsai, C and Paenpong, P and Pootakham, W and Phaonakrop, N and Roytrakul, S and Promdonkoy, B},
title = {Integrated genomic and proteomic analysis of local Bacillus thuringiensis isolates for targeted insect pest control and functional insight.},
journal = {Archives of microbiology},
volume = {207},
number = {9},
pages = {193},
pmid = {40643607},
issn = {1432-072X},
support = {P2351509//National Science and Technology Development Agency, Thailand/ ; P2351509//National Science and Technology Development Agency, Thailand/ ; P2351509//National Science and Technology Development Agency, Thailand/ ; P2351509//National Science and Technology Development Agency, Thailand/ ; P2351509//National Science and Technology Development Agency, Thailand/ ; P2351509//National Science and Technology Development Agency, Thailand/ ; P2351509//National Science and Technology Development Agency, Thailand/ ; P2351509//National Science and Technology Development Agency, Thailand/ ; P2351509//National Science and Technology Development Agency, Thailand/ ; },
abstract = {Bacillus thuringiensis (Bt) produces insecticidal crystal proteins and is widely used in pest control. Efficient strain selection for specific targets can be enhanced by integrating genomic and proteomic data. In this study, we sequenced 72 local Bt isolates and selected 12 for detailed proteomic and bioassay analyses. Expressed toxins were identified, and larval assays confirmed high toxicity in selected strains. Bt117 showed 16-fold higher toxicity against Spodoptera frugiperda compared to commercial strain B. thuringiensis serovar kurstaki, while Bt117 and Bt506 were similarly effective against Helicoverpa armigera. Comparative genomics revealed that vip3A expression is regulated by VipR, a finding confirmed experimentally. Phylogenetic analysis indicated that Bt117 and Bt202 are genomically divergent and more closely related to Bacillus cereus, suggesting horizontal gene transfer of pesticidal genes. Additionally, genes linked to plant growth-promoting traits (e.g., asbA, ipdC, and accd) were identified. This omics-guided strategy supports efficient Bt strain selection and broader application in sustainable agriculture.},
}

@article {pmid40856861,
year = {2025},
author = {Saif, M and Ahmed, V and Ahmed, S and Rizvi, SA and Yadav, RN and Haq, QMR},
title = {High prevalence of co-trimoxazole and carbapenem resistance among uropathogenic bacteria from a community hospital in New Delhi, India.},
journal = {Molecular biology reports},
volume = {52},
number = {1},
pages = {849},
pmid = {40856861},
issn = {1573-4978},
abstract = {BACKGROUND: Urinary tract infections (UTI) caused by multidrug-resistant bacteria are a serious concern worldwide. The problem is exacerbated by the rapid rise of resistance to antibiotics, including co-trimoxazole and carbapenem. This study investigates the prevalence of co-trimoxazole and carbapenem resistance among bacteria causing UTI from a community hospital in New Delhi. METHODS: Antibiotic susceptibility tests were carried out by Kirby-Bauer disc diffusion and broth microdilution method. Molecular detection of antibiotic-resistant genes was done by PCR. Plasmid-mediated horizontal gene transfer and biofilm studies were performed by conjugation assay and crystal violet assay, respectively. FINDINGS: Phenotypic screening of 141 non-duplicate bacterial isolates obtained from urine samples showed co-trimoxazole resistance in 72% isolates (n = 101). Among 101 co-trimoxazole resistant isolates, 63 were phenotypically positive for carbapenem resistance. The isolates were identified as Escherichia coli (n = 69), Klebsiella pneumoniae (n = 15), Streptococcus dysgalactiae (n = 5), Citrobacter spp. (n = 3), Pseudomonas aeruginosa (n = 3), Staphylococcus aureus (n = 3), Klebsiella oxytoca (n = 1), Serratia fonticola (n = 1) and Proteus mirabilis (n = 1). Co-trimoxazole resistant genes sul1, sul2, dfrA1, dfrA5, dfrA7, dfrA12, and dfrA17 were detected in 75, 28, 29, 23, 60, 63, and 8 isolates, respectively. Carbapenem resistance genes blaNDM, blaOXA-48, blaKPC, and blaIMP were amplified in 36, 77, 8, and 27 isolates, respectively using plasmid DNA as the template. CONCLUSION: This study provides useful data on an alarming rise in co-trimoxazole and carbapenem resistance among bacteria causing UTI. Conjugation assay confirmed horizontal transfer of plasmid-borne resistance genes. Furthermore, some of these isolates were resistant to nitrofurantoin and fosfomycin, the last resort antibiotics for treating UTI.},
}

@article {pmid41222715,
year = {2025},
author = {Almutawif, YA and Khan, NU},
title = {Gut microbiome dysbiosis and antimicrobial resistance in the Middle East: a converging public health crisis in conflict and fragile settings.},
journal = {Archives of microbiology},
volume = {208},
number = {1},
pages = {15},
pmid = {41222715},
issn = {1432-072X},
abstract = {The Middle East is confronting a converging public health crisis as gut microbiome dysbiosis and antimicrobial resistance (AMR) amplify in conflict and fragile settings, driven by war, displacement, and systemic healthcare collapse. This review examines the bidirectional relationship between disrupted gut microbiota and escalating AMR, particularly among vulnerable refugee populations and war-affected communities. Key findings reveal alarming resistance rates in ESKAPE pathogens (e.g., Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp), exacerbated by unregulated antibiotic use, malnutrition, and poor sanitation. Dysbiosis fosters AMR through loss of colonization resistance and horizontal gene transfer, while conflict-related healthcare breakdowns—such as empiric antibiotic overuse and absent diagnostics—accelerate resistance spread. Refugee camps, with overcrowding and contaminated water, emerge as critical AMR hotspots. Urgent interventions are needed, including microbiome restoration therapies (e.g., probiotics and faecal microbiota transplantation (FMT), rapid diagnostic tools, and integrated One Health surveillance. Moreover, the increasing trend of AMR is further amplified by the COVID-19 pandemic, which led to widespread antibiotic use and disrupted healthcare services. Review emphasises the importance of regional policy coordination, targeted humanitarian aid focused on microbiome health, and global advocacy to mitigate this crisis, which poses a threat to both local and international health security. Without action, the intersection of dysbiosis and AMR will deepen health inequities in conflict zones, with far-reaching consequences.},
}

@article {pmid41718947,
year = {2026},
author = {AlJerf, A and Maad, AH and Ukaogo, PO and Aljerf, L and Ajong, AB and Alajlani, M},
title = {Antimicrobial Armageddon: The Professional Guide to Conquering Antibiotic Resistance.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {41718947},
issn = {1867-1314},
abstract = {Antibiotic resistance has accelerated into a critical global health emergency, undermining the effectiveness of modern medicine and increasing the burden of severe, persistent, and difficult-to-treat infections. This review synthesizes current evidence on the biological, clinical, and public health dimensions of resistance and highlights the major drivers behind its rapid expansion. Recent epidemiological data reveal substantial increases in mortality associated with resistant bloodstream, respiratory, and intra-abdominal infections, emphasizing the urgency of coordinated intervention. Mechanistic analyses demonstrate how horizontal gene transfer (HGT), mutational adaptation, biofilm formation, efflux systems, and enzymatic drug modification collectively strengthen bacterial survival. In parallel, persistent and tolerant cell populations further complicate therapeutic outcomes by enabling recurrent and chronic infections. Despite these challenges, several promising countermeasures have emerged. Advances in antimicrobial stewardship, drug repurposing, bacteriophage-based strategies, immunotherapies, and nanotechnology offer new avenues to restore or enhance antimicrobial efficacy. Innovative approaches—such as targeting novel metabolic pathways, disrupting virulence networks, and employing engineered phage systems—represent a growing frontier in drug development. Collectively, these insights highlight the importance of integrating molecular innovation, optimized clinical practices, and global surveillance as complementary strategies to mitigate the progression of antimicrobial resistance. Finally, this review acknowledges limitations related to the focus on bacterial pathogens, while recognizing that antifungal and antiviral resistance present parallel, distinct challenges in global health.},
}

@article {pmid41805848,
year = {2026},
author = {Nada, MAL and Asejo, AB and Joloro, MJG and Chin, RAD and Reterta, MCC and Collado, ARG and Casidsid, JYO and Tejada, AJP and Ancla, JB and Gestuveo, RJ},
title = {Genome characterization and receptor-binding protein identification of Klebsiella phage vB_VIPKPNMC05, a member of a novel viral family Pituviridae.},
journal = {Archives of virology},
volume = {171},
number = {4},
pages = {},
pmid = {41805848},
issn = {1432-8798},
support = {LFP-EBD-2021-02//Department of Science and Technology Grants-In-Aid (GIA) Program/ ; },
abstract = {Klebsiella pneumoniae is an opportunistic pathogen and a leading cause of antimicrobial-resistant infections in the Philippines. Here, we report the genome sequence of Klebsiella phage vB_VIPKPNMC05, which targets a multidrug-resistant (MDR) K. pneumoniae strain with capsule type K8. VIPKPNMC05, isolated from environmental water, has a siphovirus morphology and exhibits a broad lytic activity against several strains of K. pneumoniae, K. quasipneumoniae, Pseudomonas aeruginosa, and Escherichia coli. The linear double-stranded DNA genome (34,476 bp; 51.0% G + C content) encodes 58 protein-coding sequences (CDS), 37 of which are involved in phage morphogenesis, DNA replication, transcription regulation, and host lysis. Notably, a receptor-binding protein (RBP) with a putative depolymerase (Dpo) was identified. Structural prediction using AlphaFold 3 showed that the tailspike protein (TSP19) forms a homotrimer structure with a conserved C-terminal pectin lyase domain. The TSP module is conserved among Enterobacteriaceae-infecting phages and may have been acquired through horizontal gene transfer. Whole-genome comparisons revealed 52–54% similarity to known phages, suggesting that VIPKPNMC05 represents a distinct lineage. Based on taxonomic analysis, we propose that VIPKPNMC05 belongs to a novel phage family, Pituviridae. The absence of virulence, toxin, and antimicrobial resistance genes, along with its broad host range and lytic lifestyle, suggests possible therapeutic and biotechnological potential of VIPKPNMC05. To our knowledge, this is the first report of a newly discovered phage family from the Philippines, underscoring the importance of local phage bioprospecting for therapeutic applications.},
}

@article {pmid41998453,
year = {2026},
author = {Harini, AC and Sundaresan, AK and Ramakrishnan, J},
title = {Klebsiella pneumoniae in the global AMR: resistance mechanisms and genomic adaptation.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {5},
pages = {},
pmid = {41998453},
issn = {1573-0972},
abstract = {Antimicrobial Resistance (AMR) represents a defining crisis of modern healthcare, severely limiting therapeutic options and driving a global increase in clinical mortality. Central to this crisis is Klebsiella pneumoniae, a ubiquitous gut commensal that has evolved into a formidable opportunistic pathogen through its remarkable ability to transition from a harmless organism to a hypervirulent, Multidrug-Resistant (MDR) threat. This review examines that pathogenic transition, emphasizing the dangerous convergence of virulence and resistance traits particularly within carbapenem-resistant lineages. The bacterium leverages an expansive “open” pangenome and immense genetic plasticity to act as a primary trafficker of AMR genes. We detail the molecular mechanisms underlying resistance across nearly all antibiotic classes including β-lactams, aminoglycosides, and last-resort polymyxins driven by enzymatic degradation, target modification, and sophisticated efflux systems. Beyond clinical antibiotic pressure, the review explores how non-antibiotic drivers, such as environmental stressors, biocide exposure, and heavy metals, accelerate AMR evolution through cross-resistance and novel epigenetic adaptations. The rapid dissemination of these resistance determinants is facilitated by a robust toolkit of Horizontal Gene Transfer (HGT), including transposons, integrons, plasmid replicons, and bacteriophage-mediated transduction. Finally, this review evaluates the current therapeutic landscape, addressing the challenges of the drug development pipeline while highlighting emerging interventions such as novel β-lactam/β-lactamase inhibitor combinations, phage therapy, and anti-virulence strategies. Understanding this interplay between genomic evolution and ecological drivers is critical for designing a unified stewardship framework and effective interventions to curb the global AMR crisis.},
}

@article {pmid42281424,
year = {2026},
author = {Garland, S and Orr, VT and Hall, JPJ and Harrison, E},
title = {Invasive plasmids as ecosystem engineers-from mechanism to application.},
journal = {Essays in biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1042/EBC20250040},
pmid = {42281424},
issn = {1744-1358},
support = {APP37189//UKRI | Biotechnology and Biological Sciences Research Council (AFRC)/ ; NE/X009971/1//UKRI | Natural Environment Research Council (NERC)/ ; MR/W02666X/1//UKRI | Medical Research Council (MRC)/ ; },
abstract = {Horizontal gene transfer, mediated by mobile genetic elements such as conjugative plasmids, is recognised as a major driver of bacterial innovation. While predominantly explored in the context of change within individual strains and species, the broad host ranges of many plasmids mean that they can invade not just lineages but communities. This has far-reaching implications for both the fate of the plasmid and our understanding of bacterial adaptation, as well as applications for the functional engineering of microbial communities. In comparison to single-strain systems, in which plasmid invasion is largely determined by a now well-defined set of parameters-conjugation rate, fitness cost of carriage, and segregation loss-the spread of plasmids into communities is vastly more complex: governed by the wide range of dynamics within strains, but also by community dynamics, spatial heterogeneity, and the interactions between strain- and community-level selection. Here, we review the processes by which plasmids can invade communities and discuss how community complexity both constrains and facilitates plasmid spread. We further explore how this mechanistic understanding can be harnessed to enhance microbial community function.},
}

@article {pmid42283811,
year = {2026},
author = {Costanzo, M and Di Gregorio, L and Tabacchioni, S and Bevivino, A and Visca, A},
title = {Mobile Genetic Elements as Key Drivers of Bacterial Evolution and Adaptation in Agroecosystems.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02803-5},
pmid = {42283811},
issn = {1432-184X},
abstract = {Mobile genetic elements (MGEs), including plasmids, transposons, integrative and conjugative elements, and phage-derived sequences, are central drivers of bacterial evolution in agroecosystems. By enabling horizontal gene transfer, MGEs allow soil- and plant-associated bacteria to rapidly acquire complex functional traits, facilitating adaptation to fluctuating environmental conditions and different agricultural management practices. In agricultural soils, MGEs underpin key microbial functions such as nutrient acquisition and cycling, stress tolerance, rhizosphere competence, and interactions with plant hosts, thereby influencing soil fertility and crop performance. Selective pressures in agroecosystems extend beyond antimicrobial exposure and include fertilizers, pesticides, plant defense compounds, recurrent biotic and abiotic stress, as well as high-yielding crop varieties. These pressures generate co-selection dynamics that shape mobilome composition and activity, linking traits such as resistance, pathogenicity, and biocontrol to broader ecological functions relevant to plant health. Rather than acting as exceptional genetic entities, MGEs form a dynamic and environmentally responsive genetic network that enables rapid ecological tuning while preserving core genome stability. Comparative genomics has revealed that major lifestyle transitions in agroecosystem-associated bacteria, from free-living to commensal, mutualistic, or pathogenic states, are frequently mediated by the gain and loss of genomic islands and other MGEs. This review synthesizes the latest research on the ecological functions and evolutionary dynamics of MGEs in agroecosystems and explores how mobilome-informed approaches can support microbial-based strategies for sustainable agriculture.},
}

@article {pmid42284196,
year = {2026},
author = {Benigno, V and Carraro, N and Gardet, M and Budny, H and van der Meer, JR},
title = {Horizontal transfer of ICEclc-like elements in Pseudomonas aeruginosa clinical isolates.},
journal = {Journal of bacteriology},
volume = {},
number = {},
pages = {e0000926},
doi = {10.1128/jb.00009-26},
pmid = {42284196},
issn = {1098-5530},
abstract = {Integrative and conjugative elements (ICEs) are widespread autonomous mobile DNA within bacterial chromosomes. ICEs contain the genes necessary for excision from the chromosome, conjugative transfer to a new recipient cell, and chromosomal reintegration. They can also carry accessory genes that, while not essential for transfer, confer adaptive phenotypes to the host, contributing to host survival under stressful or changing conditions. Genome studies have indicated that Pseudomonas aeruginosa clinical isolates carry a wide range of related ICEs with adaptive genes enriched for heavy metal resistance and efflux systems; however, their mobility has remained understudied. Here, we studied the activation and transfer mechanisms of a representative subset of ICEclc-type elements. We found that ICE excision could be induced in P. aeruginosa by ectopic expression of BisDC, the known master regulator of ICEclc activation, pointing to a similar regulatory cascade. A number of elements could be transferred to P. putida, where they conferred increased tolerance to specific heavy metals. We also assessed ICE excision rates in response to different classes of stressors using qPCR-based quantification. Sub-lethal copper exposure significantly increased ICE excision rates in several P. aeruginosa strains, although this response was strongly strain-dependent and absent in isolates with enhanced copper tolerance, highlighting the importance of host background. Despite elevated excision, copper did not stimulate ICE transfer or induce conjugation gene expression, indicating that ICE excision and conjugation can be uncoupled processes. Transcriptomic analyses revealed strain-specific regulatory responses to copper stress, including differential activation of metal-responsive regulators, oxidative stress pathways, and virulence-associated systems.IMPORTANCEIntegrative and conjugative elements (ICEs) play a major role in bacterial adaptation by mediating horizontal gene transfer; however, the environmental cues governing their activation remain poorly understood. Here, we demonstrate that ICEclc-type elements in Pseudomonas aeruginosa are transferable at low frequencies and that their excision rates can be selectively increased by specific stress conditions, notably copper exposure and hypoosmotic stress. Our findings reveal that ICE excision and conjugative transfer can be uncoupled and are strongly influenced by host genetic background, underscoring the complexity of ICE regulation. This work aimed to explore whether clinical conditions or antimicrobial treatment could inadvertently promote ICE-mediated gene transfer, with implications for understanding the evolution of antibiotic resistance and virulence.},
}

@article {pmid42286276,
year = {2026},
author = {Wójcicki, M and Cieślik, M and Górski, A and Jończyk-Matysiak, E},
title = {Giving Antibiotics a Second Chance: Evolutionary Trade-Offs and Phage-Driven Restoration of Antibiotic Susceptibility.},
journal = {BioDrugs : clinical immunotherapeutics, biopharmaceuticals and gene therapy},
volume = {},
number = {},
pages = {},
pmid = {42286276},
issn = {1179-190X},
abstract = {Antimicrobial resistance poses a critical and escalating threat to global public health, driven by the widespread and often unjustified use of antibiotics and the rapid dissemination of resistance determinants. With the antibiotic discovery pipeline largely depleted, alternative and complementary strategies are urgently needed to preserve the effectiveness of existing antimicrobials. Bacteriophages-viruses that specifically infect bacteria-have re-emerged as promising tools not only for direct bacterial eradication but also for reshaping bacterial evolutionary trajectories. This review examines the concept of phage-driven restoration of antibiotic susceptibility, focusing on evolutionary trade-offs that arise when bacteria adapt to phage pressure. Resistance to bacteriophages frequently involves modifications of surface structures, capsules, or efflux systems, changes that often incur fitness costs manifested as reduced virulence, impaired biofilm formation, or increased antibiotic sensitivity. Experimental studies and clinical case reports demonstrate that phage-antibiotic synergy can suppress bacterial growth more effectively than monotherapy, limit resistance emergence, and resensitize multidrug-resistant pathogens to previously ineffective antibiotics. Particular attention is given to mechanisms involving efflux pump targeting, capsule loss, biofilm disruption, and temperate phage-antibiotic interactions. In addition, emerging strategies that combine bacteriophages with CRISPR-Cas systems enable precise targeting and removal of resistance genes, offering a highly selective means to restore antibiotic efficacy and curb horizontal gene transfer. Together, these findings highlight bacteriophages as powerful evolutionary and therapeutic tools capable of giving antibiotics a "second chance". Integrating phage-based approaches into antibiotic stewardship frameworks may represent a sustainable path forward in combating multidrug-resistant bacterial infections.},
}

@article {pmid42287895,
year = {2026},
author = {Yao, Z and Lin, G and Liu, Y and Zhang, J},
title = {Mechanisms for the phytohormone-elevated performance of a continuous-flow baffled cyanobacterial photo-bioreactor for antibiotic removal and lipid production.},
journal = {Water research},
volume = {303},
number = {},
pages = {126283},
doi = {10.1016/j.watres.2026.126283},
pmid = {42287895},
issn = {1879-2448},
abstract = {A mixture of Synechococcus sp., Chroococcus sp., and Synechocystis sp. was immobilized in indole-3-acetic acid (IAA)-supplemented calcium alginate beads and then placed into a four-compartment baffled photo-bioreactor. A 30-day continuous-flow treatment of secondary effluent wastewater using this system achieved removal rates of 74.08-85.12% for COD, 87.52-96.89% for TN, 95.36-99.26% for TP, 84.02-88.36% for cefalexin, 67.15-75.57% for erythromycin, 91.17-96.05% for oxytetracycline, and 74.76-78.87% for norfloxacin. Chroococcus sp. contributed the most to pollutant removal, with its abundance negatively correlated with the concentrations of all pollutants. Bacterial colonization within cyanobacterial beads, upregulated genes involved in signal transduction, quorum sensing, and biofilm formation, as well as correlations between cyanobacteria and seven bacterial genera (Acidovorax, Chitinophaga, Massilia, Algoriphagus, Chryseobacterium, Comamonas, and Candidatus) together confirmed the formation of a cyanobacteria-bacteria consortium. Efficient pollutant removal was attributed to the high cyanobacterial biomass stimulated by IAA and the activation of genes related to stress response, the TCA cycle, oxidative phosphorylation, and pollutant metabolism in bead microorganisms. Reduced abundances of antibiotic resistance genes in the effluent may result from activated mismatch repair pathway and suppressed horizontal gene transfer. Antibiotics, the symbiotic bacterium Azospirillum, and IAA jointly stimulated cyanobacterial growth and lipid accumulation, contributing to a high cyanobacterial lipid productivity of 47.59-51.82 mg/(L·d), mainly through the upregulation of genes involved in the Calvin cycle, pentose phosphate pathway, and fatty acid biosynthesis. Overall, this study provides a sustainable strategy integrating pollutant removal, resistance control, and resource recovery.},
}

@article {pmid42287910,
year = {2026},
author = {Li, H and Li, Y and Zhang, Z and Li, X and Zhao, K and Fan, Z and Liu, K},
title = {The ablation cycle drives glacier microbiome dynamics and downstream dissemination risk of the resistome.},
journal = {Journal of hazardous materials},
volume = {514},
number = {},
pages = {142686},
doi = {10.1016/j.jhazmat.2026.142686},
pmid = {42287910},
issn = {1873-3336},
abstract = {Glacial ecosystems on the Tibetan Plateau undergo pronounced hydrological shifts across the glacial ablation cycle, driven by the onset and retreat of the Indian summer monsoon. To elucidate how transitions between four distinct hydrological ablation stages (pre-ablation, early ablation, late ablation, and frozen) shape microbial community structures and antibiotic resistance gene (ARG) profiles, we analyzed 112 samples collected across four stages from multiple glacier catchments on the southeastern Tibetan Plateau using metagenomic sequencing. Our results indicated that warmer stages favored thermotolerant Proteobacteria and reduced overall community diversity and evenness. ARG abundances exhibited ablation-dependent fluctuations, with Betaproteobacteria identified as predominant potential hosts. Furthermore, ARGs and virulence factors associated with mobile genetic elements were enriched during early and late ablation stages relative to the frozen stage, suggesting elevated potential for horizontal gene transfer coinciding with peak meltwater discharge. Notably, while upstream meltwaters generally exhibited higher ARG abundances, the upstream-downstream disparity tended to diminish from the pre-ablation to the late ablation stage, likely reflecting enhanced microbial mixing driven by glacier melt. Together, these findings reveal that glacier meltwater microbiomes are primarily shaped by ablation dynamics rather than spatial heterogeneity. More importantly, dynamics across the glacial ablation cycle drive shifts in meltwater hydrology that facilitate the downstream environmental mobility of glacial resistomes, posing growing antimicrobial resistance risks within the One Health framework.},
}

@article {pmid42291119,
year = {2026},
author = {Park, J and Jang, KB and Kang, MG and Kyung, J and Yoon, J and Ryu, S and Kim, Y},
title = {Comparative pangenome analysis of methanogenic archaea from diverse ecosystems reveals potential targets for methane mitigation in rumen microbiome.},
journal = {Journal of animal science and technology},
volume = {68},
number = {3},
pages = {935-953},
pmid = {42291119},
issn = {2055-0391},
abstract = {Rumen methanogenesis is a major biological contributor to methane emissions in ruminants, yet the extent to which functional markers align with taxonomic relationships and how genome content varies across habitats, remains poorly resolved. In this study, we integrated broad phylogenetic frameworks with pangenome-resolved analysis to characterize methanogenic archaea from diverse ecosystems, including seawater, freshwater, sewage, rumen, human gut, soil, and cockroach sources. By combining these insights with pangenome reconstruction and KEGG-based pathway mapping of methanogenesis, we reveal key evolutionary and functional patterns. Notably, phylogenies based on 16S rRNA and mcrA genes showed limited concordance: only two clades exhibited overlap between trees, with most clustering patterns lacking environmental specificity. This discrepancy reflects the deep conservation of 16S rRNA compared with the evolutionary plasticity of mcr genes, shaped by lateral gene transfer, gene loss, and pathway modularity. The pangenome comprised of 8,695 orthogroups across 71 genomes, with core and soft-core genes enriched in translation, amino acid metabolism, and coenzyme biosynthesis, while the shell contained many poorly annotated orthogroups, highlighting annotation gaps in archaeal genomes. KEGG analysis revealed habitat-specific signatures: rumen methanogens were notably depleted in genes of the acetyl-CoA pathway, whereas human gut methanogens lacked key cofactor biosynthesis modules, including those for coenzymes M, B, F420, and methanofuran. From rumen-derived shotgun metagenomes, we identified 53 methane-producing, 4 canonical methanogenic, 10 potential competitor, and 1 methanotrophic metagenome-assembled genomes based on functional gene content. Competitor candidates included nitrate-reducing and Wood-Ljungdahl pathway-utilizing acetogens, suggesting hydrogen redirection under high-hydrogen or inhibitor conditions. These findings support a functional marker strategy that integrates 16S rRNA with pathway-specific genes and a pangenome framework to enhance ecological interpretations of methanogens and to prioritize potential targets for methane mitigation in ruminants.},
}

@article {pmid42292220,
year = {2026},
author = {Ge, J},
title = {Functional redundancy as a stabilizing principle in bacterial communities under antibiotic perturbation: mechanisms, trade-offs, and emerging frameworks.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1834295},
pmid = {42292220},
issn = {2296-858X},
abstract = {The widespread use of antibiotics has severely disrupted the structure of microbial communities, but the responses of these communities vary in different environments. Interestingly, even when the species composition changes, some microbial communities can still maintain crucial functions, a phenomenon known as "decoupling of structure and function." Among them, functional redundancy (FR) - the characteristic that multiple microorganisms perform the same ecological function - is the key mechanism for maintaining this stability. This review focuses on how functional redundancy may enhance microbial community resilience under antibiotic perturbation. We first start from the insurance hypothesis and the YAS (yield - acquisition - stress) framework to explain the ecological principles behind functional redundancy, and explain how microorganisms allocate resources and make trade-offs in different environments. We systematically analyze the multi-level defense strategies of microorganisms at five levels, including: ecological niche differentiation at the species level, horizontal transfer of resistance genes at the genetic level, cross-feeding reconstruction of metabolic networks, dormancy strategies at the temporal dimension (seed bank), and population regulation mediated by bacteriophages. Methodologically, we review metatranscriptomic approaches for distinguishing active signals from residual DNA, structural entropy algorithms for inferring FR, and AI-based tools for identifying latent resistance genes. Evidence from ecosystems such as the gut, respiratory tract, soil, and wastewater suggests the broad relevance of functional redundancy, although its stabilizing effect depends on antibiotic type, exposure duration, initial community composition, and ecological context. Finally, we explore the application prospects of this principle in the construction of synthetic communities and the optimization of fecal microbiota transplantation, and point out the evolutionary costs that may accompany maintaining functional redundancy, which is an important challenge that future research needs to address.},
}

@article {pmid42292747,
year = {2026},
author = {Fan, F and Shi, Q and Chen, G and Zhan, H and Deng, S and Peng, Y and Wei, L},
title = {Meropenem stress drives lipid remodeling and resistance gene dissemination via outer membrane vesicles in carbapenem-resistant Klebsiella pneumoniae.},
journal = {Current research in microbial sciences},
volume = {11},
number = {},
pages = {100616},
pmid = {42292747},
issn = {2666-5174},
abstract = {Carbapenem-resistant Klebsiella pneumoniae (CRKP) has emerged as a critical global health threat, fueled by escalating antibiotic resistance rates among clinical isolates. This study investigates the adaptive responses of CRKP to meropenem, a last-line β-lactam antibiotic, with a focus on the role of outer membrane vesicles (OMVs) in resistance evolution. Under meropenem stress, CRKP exhibited significant upregulation of total lipid content within OMVs (CRKP-OMVs), particularly enriched in glycerophospholipids and sphingolipids to enhance bacterial membrane integrity. Notably, CRKP-OMVs function as critical vehicles for the carbapenemase gene bla KPC-2 . Furthermore, meropenem exposure significantly augments their horizontal gene transfer (HGT) efficiency. Compared to control OMVs, these drug-induced vesicles facilitated a 3.52-fold and 12.08-fold increase in bla KPC-2 dissemination into carbapenem-susceptible K. pneumoniae and Escherichia coli recipients, respectively. Proteomic profiling revealed meropenem-driven upregulation of efflux machinery (e.g., PET family inner membrane protein YccS, multidrug resistance outer membrane channel MdtQ) and lipid transporters (LptB, LplT, phospholipid-lipopolysaccharide ABC transporter). These findings demonstrate that meropenem exposure modulates OMVs' proteolipid composition and enhances biofilm formation, while simultaneously promoting OMV-mediated dissemination of resistance genes through their function as mobile genetic vectors under therapeutic pressure, suggesting a potential defensive mechanism against antibiotic penetration.},
}

@article {pmid42294647,
year = {2026},
author = {Guzel, M and May, F and Buchan, A},
title = {Mobile genetic elements shape the evolution and adaptation of the marine Sulfitobacter genus.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0047926},
doi = {10.1128/msystems.00479-26},
pmid = {42294647},
issn = {2379-5077},
abstract = {UNLABELLED: Mobile genetic elements (MGEs) are essential for facilitating horizontal gene transfer and play crucial roles in the evolution and adaptive capabilities of bacterial species. Here, we analyzed closed genomes from the marine Sulfitobacter genus to assess plasmid contributions to ecological adaptability and evolutionary diversification. Our analysis of 153 Sulfitobacter plasmids from 36 strains representing 8 species shows extensive plasmid conservation within species (e.g., >95% nucleotide identity for flagellar plasmids) alongside significant mosaicism across 60% of plasmids. Insertion sequences (IS) elements are nearly ninefold more concentrated on plasmids relative to chromosomes, suggestive of active genetic exchange in this replicon class. Network analysis identified 14 primary plasmid clusters, with species-specific conservation patterns and evidence of inter-species gene transfer. In Sulfitobacter pontiacus strain CB2047, we discovered chromosomal integration of a 280 kb plasmid encoding a toxin-antitoxin system, rrn operon, as well as a chromosomal partitioning system. These findings demonstrate that plasmids function as key drivers of evolution and adaptation in Sulfitobacter, serving as both repositories of conserved adaptive traits and platforms for ongoing genetic innovation.

IMPORTANCE: Plasmids are increasingly recognized as crucial drivers of bacterial evolution and adaptation, yet their roles in shaping marine microbial communities are poorly understood. Here, we provide a comprehensive analysis of plasmid diversity and evolution within Sulfitobacter, a broadly distributed and metabolically versatile marine bacterial genus, in which ~15% of genome content is plasmid-encoded. We propose that Sulfitobacter plasmids serve dual evolutionary roles: maintaining highly conserved species-specific traits essential for survival (such as flagellar motility and biofilm formation), while simultaneously functioning as platforms for genetic innovation through extensive horizontal gene transfer. The discovery of a large plasmid integrated into the chromosome of one strain highlights that episomal elements can transition to stable chromosomal inheritance in this genus. These findings advance our understanding of how marine bacteria balance genomic stability with adaptive flexibility, providing insights applicable to microbial evolution in dynamic ocean environments.},
}

@article {pmid42294719,
year = {2026},
author = {Regan, MR and McDevitt, CJ and Robinson, LR and Issifou, S and Wadsworth, CB},
title = {Put your money where your mouth is: surveillance of antibiotic resistance within the commensal Neisseria.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0072526},
doi = {10.1128/spectrum.00725-26},
pmid = {42294719},
issn = {2165-0497},
abstract = {Commensal Neisseria species are major reservoirs of adaptive genetic variation, including antimicrobial resistance, for their pathogenic relatives, yet they remain poorly characterized. This gap limits our ability to anticipate resistance mechanisms that may ultimately emerge in Neisseria gonorrhoeae and Neisseria meningitidis. Here, we analyzed 166 novel commensal Neisseria isolates collected from 31 study participants and measured minimum inhibitory concentrations (MICs) for seven antimicrobials: azithromycin, cefixime, ceftriaxone, ciprofloxacin, doxycycline, penicillin, and gentamicin. Resistance, defined using the Clinical and Laboratory Standards Institute guidelines, was highly prevalent for azithromycin (76%) and doxycycline (52%), while no resistance to gentamicin was observed. High-level doxycycline resistance was always associated with the inheritance of tetM. Reduced susceptibility to azithromycin was linked to an MtrD K823E substitution, and reduced susceptibility to ciprofloxacin was associated with GyrA T91I (Neisseria subflava) or S91V (Neisseria mucosa). Across all antimicrobials, MICs varied widely, indicating the presence of additional modulating mutations. Finally, the genetic determinants underlying low-level doxycycline resistance and reduced penicillin susceptibility remain unresolved. Overall, here, we continue to build on the foundation of surveillance efforts in the commensal Neisseria and continue to flesh out what is known and unknown about this early warning system-or canary in the coal mine-for emerging resistance and clinically consequential evolution in pathogenic Neisseria.IMPORTANCECommensal Neisseria species constitute a vast and dynamic reservoir of genetic diversity that can be exchanged with pathogenic relatives, Neisseria gonorrhoeae and Neisseria meningitidis. However, these commensals remain substantially undercharacterized, limiting our ability to anticipate the evolutionary trajectories of antimicrobial resistance in clinically important species. By systematically analyzing commensal isolates and defining phenotypic resistance patterns alongside their genetic determinants, this study, and others like it, function as an early warning system for the emergence and spread of antimicrobial resistance. The high prevalence of azithromycin and doxycycline resistance, identification of specific mutations associated with reduced susceptibility, and evidence of additional unexplained contributors to minimum inhibitory concentration variation highlight both known and cryptic pathways of adaptation. These findings underscore the necessity of integrating commensal surveillance into resistance monitoring frameworks, improving our capacity to forecast clinically consequential evolution and to inform stewardship, diagnostics, and therapeutic development before resistance becomes entrenched in pathogenic Neisseria.},
}

@article {pmid42294728,
year = {2026},
author = {Mao, Z and Jiang, M and Zhao, Z and Xu, S and Wang, H and Chen, K and Duan, J and Chen, Z and He, D and Xing, P and Wu, QL},
title = {Biofilm-forming traits enrich the plasmid diversity and functional potential in particle-attached bacteria in coastal ecosystems.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0046026},
doi = {10.1128/spectrum.00460-26},
pmid = {42294728},
issn = {2165-0497},
abstract = {UNLABELLED: Planktonic microorganisms play a central role in aquatic biogeochemical processes and are commonly divided into particle-attached (PA) and free-living (FL) fractions. Although these two lifestyles differ in ecological strategy, the contribution of plasmids to their niche differentiation remains poorly resolved. Here, we conducted a plasmid-centric metagenomic analysis of two anthropogenically impacted coastal ecosystems in South China, the Pearl River Estuary (PRE), and Daya Bay (DYB), to determine the environmental and biological drivers of plasmid diversity, and their functional potenitial. We found that plasmid diversity was jointly shaped by different fractions and environmental stressors. The PA fraction contained significantly higher plasmid abundance and richness than the FL fraction, and was enriched in multifunctional and conjugative plasmids. These plasmids were associated with genes adapting to the PA lifestyle or microenvironments, suggesting linkage between particle attachment and plasmid maintenance. Structural equation modeling indicated that different fractions shaped plasmid diversity primarily through biofilm-forming genes. Along an anthropogenic gradient from DYB to PRE, increasing pollution levels were accompanied by higher plasmid diversity and greater abundances of antibiotic and metal resistance genes. Plasmid diversity was strongly correlated with resistance gene abundance. The enrichment of transferable plasmids in the PA fraction, where cell densities are high and intercellular distances are close, suggested that particle-associated habitats favor genetic exchange and the persistence of resistance traits. Together, these results demonstrate that particle-associated microbial communities represent key reservoirs of plasmid diversity and resistance potential in coastal ecosystems and highlight the combined influence of lifestyles and anthropogenic stress on plasmid-mediated microbial adaptation.

IMPORTANCE: Plasmids play an important role in microbial adaptation by mediating horizontal gene transfer, yet the ecological contexts that favor their persistence and diversification in natural environments remain poorly understood. This study showed that particle-attached microbial communities in coastal waters harbored substantially higher plasmid diversity and resistance potential than free-living communities, and that this enrichment is strongly linked to biofilm-associated traits. By demonstrating how particulate habitats and pollution gradients jointly shape plasmid diversity and resistance gene abundance, our findings identify particle-associated microenvironments as critical reservoirs for plasmid-mediated functions in coastal ecosystems. These results advance understanding of how microbial lifestyle and human activities influence microbial evolution and the environmental dissemination of resistance traits.},
}

@article {pmid42294936,
year = {2026},
author = {Lombardino, JM and Falbel, TG and Dewey, CN and Burton, BM},
title = {High-resolution genomic analysis reveals abundant mosaic outcomes of bacterial natural transformation independent of MutS-mediated mismatch repair.},
journal = {mBio},
volume = {},
number = {},
pages = {e0044426},
doi = {10.1128/mbio.00444-26},
pmid = {42294936},
issn = {2150-7511},
abstract = {The nature and breadth of horizontal gene transfer outcomes specific to natural transformation remain elusive. We present a genome-scale analysis of location-specific information associated with single-round transformation events in Bacillus subtilis. Using distributed selectable markers to remove location bias, we found transformant genomes often contained multiple discontinuous segments of donor sequence in close proximity. These highly mosaic sites span multiple length scales, with an abundance of shorter segments. We found that the small segments scale with the length of the nearest stretch of perfect homology, and these segments defy minimal, efficient homologous recombination rules. Sites of transformation and their associated intervening recipient sequences were not distinguished by overall percent identity, GC content, or median gene expression. Mismatch repair activity by MutS also failed to explain the breadth and frequency of mosaic patches. High-resolution mapping of donor and recipient alleles across sites of transfer demonstrates that natural transformation can contribute a breadth of allelic diversity, especially within short, clustered patches of genetic exchange. These observations point to a need to further investigate the complex mechanisms that drive distinct outcomes of natural transformation.IMPORTANCESeveral works have suggested the potential for discontinuity for donor DNA in transforming DNA. This work developed robust bioinformatic and genomic approaches to assess the full breadth of exchange between divergent genomes during natural transformation. The results demonstrate that simplistic sequence and expression-based associations are not sufficient to explain highly variable transformation outcomes. Similarly, transformant genomes are frequently incongruent with previously defined rules for homology-mediated recombination. MutS-mediated mismatch repair, a frequently proposed contributor to mosaic recombination, is also insufficient to explain discontinuity. Therefore, widespread molecular mechanisms intrinsic to recombination have the potential to generate significant genetic diversity during transformation, ranging from the scale of individual alleles to full operons. These results further reinforce the role of natural transformation in shaping genetic diversity within bacterial populations.},
}

@article {pmid42295605,
year = {2026},
author = {Olymon, K and Bhattacharjee, I and Roy, N and Rs, S and Dey, U and Teronpi, V and Kumar, A},
title = {Genome-wide analysis of biosynthetic gene clusters reveals hidden metabolic diversity in bacterial fish pathogens.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {7},
pages = {},
pmid = {42295605},
issn = {1573-0972},
mesh = {*Multigene Family ; Animals ; *Fishes/microbiology ; *Genome, Bacterial ; *Bacteria/genetics/metabolism/classification ; Phylogeny ; *Biosynthetic Pathways/genetics ; Secondary Metabolism/genetics ; Siderophores/genetics ; *Fish Diseases/microbiology ; Gene Transfer, Horizontal ; Peptide Synthases/genetics ; },
abstract = {Fish-pathogenic bacteria threaten global aquaculture, yet their biosynthetic capacity for secondary metabolites remains unexplored at the genomic scale. We present the first cross-genus atlas of biosynthetic gene clusters (BGCs) in prokaryotic fish pathogens, analyzing 1,855 genomes across 12 families and 14 genera. Using antiSMASH and BiG-SCAPE, we identified 13,626 BGCs encoding NRPS, PKS, RiPPs, terpenes, and siderophores, organized into 2,842 gene cluster families. Strikingly, 1,724 families (61%) lack close MIBiG reference homologs (designated here as MIBiG-distant clusters), representing potentially underexplored enzymatic diversity. Genus-level analyses revealed pronounced specialization: Pseudomonas, Mycobacterium, and Nocardia harbor NRPS/PKS-rich repertoires (> 5 BGCs/genome), while Streptococcus and Enterococcus exhibit streamlined RiPP-dominated profiles. Network analysis identified cross-taxon BGC sharing patterns consistent with horizontal gene transfer among aquatic lineages and massive within-genus expansions, with Flavobacterium RiPP families averaging 69 members. Genome-wide correlations linked GC content to BGC density (r = 0.41, p < 0.001), with genus-specific relationships ranging from r = 0.77 (Chryseobacterium) to r = -0.84 (Lactococcus), revealing compositional constraints on metabolic evolution. BGC distribution patterns reflected ecological lifestyle and suggested potential roles in iron acquisition, interspecies competition, and host colonization. This molecular inventory establishes fish-pathogenic bacteria as a strategic frontier for natural product discovery, providing a phylogenetically resolved roadmap for isolating antimicrobials, siderophores, and biofilm modulators with applications in sustainable aquaculture disease management.},
}

*Multigene Family
Animals
*Fishes/microbiology
*Genome, Bacterial
*Bacteria/genetics/metabolism/classification
Phylogeny
*Biosynthetic Pathways/genetics
Secondary Metabolism/genetics
Siderophores/genetics
*Fish Diseases/microbiology
Gene Transfer, Horizontal
Peptide Synthases/genetics

@article {pmid42026459,
year = {2026},
author = {Holman, DE and Klein, A and Keyster, M},
title = {Whole-genome characterization and analysis of Pantoea agglomerans R6: a genomic insight into its pathogenicity and resistance as a potential opportunistic plant pathogen.},
journal = {BMC genomics},
volume = {27},
number = {1},
pages = {},
pmid = {42026459},
issn = {1471-2164},
abstract = {UNLABELLED: Pantoea agglomerans is a Gram-negative bacterium increasingly recognised as an opportunistic pathogen, yet the molecular basis underpinning its host-interaction capacity remains poorly understood. Here, we report the whole-genome sequencing and integrative characterisation of P. agglomerans strain R6, isolated from Lactuca serriola. The 4.7 Mb draft genome (GC content 55.6%) encodes 4,349 genes, including secretion system components, siderophore clusters, adhesins, and multidrug efflux pumps. Comparative genomic analysis against previously characterised Pantoea strains revealed an open pan-genome shaped by horizontal gene transfer, with multiple genomic islands harbouring putative virulence- and resistance-associated loci. Notably, homologues of type VI secretion system components, iron acquisition systems, and stress response pathways suggest adaptive potential during host colonisation. Complementary phenotypic assays supported these genomic predictions, demonstrating swarming motility, biofilm formation, extracellular polysaccharide production, and enzymatic activities associated with host interaction in related strains. While R6 displayed susceptibility to β-lactams, its genomic repertoire indicates potential for adaptive resilience under selective pressure. This integrative genomic and phenotypic characterisation identifies candidate molecular features associated with opportunistic behaviour and highlights the genomic potential of R6, rather than experimentally validated causal determinants of pathogenicity.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-026-12875-9.},
}

@article {pmid42262838,
year = {2026},
author = {Deventer, AT and Sutherland, A and Biernacka, D and Johnston, PR and Stevens, CE and Kaczorowska, AK and Boraston, AB and Hobbs, JK},
title = {Clinical Rel mutations that increase basal (p)ppGpp promote conjugal transfer of staphylococcal resistance plasmids.},
journal = {Microbiology (Reading, England)},
volume = {172},
number = {6},
pages = {},
pmid = {42262838},
issn = {1465-2080},
mesh = {*Staphylococcus aureus/genetics/drug effects/metabolism ; *Plasmids/genetics/metabolism ; *Conjugation, Genetic ; Mutation ; *Guanosine Tetraphosphate/metabolism ; *Guanosine Pentaphosphate/metabolism ; *Drug Resistance, Bacterial/genetics ; *Bacterial Proteins/genetics/metabolism ; Anti-Bacterial Agents/pharmacology ; Staphylococcal Infections/microbiology ; Gene Expression Regulation, Bacterial ; Humans ; Gene Transfer, Horizontal ; },
abstract = {Conjugative transfer of plasmids represents a major route through which antibiotic resistance genes are spread. In the case of the prevalent and deadly pathogen Staphylococcus aureus, more than 90% of clinical isolates carry at least one plasmid. While plasmid-encoded mechanisms [e.g. plasmid copy number (PCN)] can influence conjugation frequency, host factors and environmental stimuli can also affect transmission. In particular, stress responses like the stringent response have been associated with increased movement of mobile genetic elements. We have previously shown that clinical mutations in the stringent response controller, Rel, lead to elevated levels of the alarmones guanosine tetra- and pentaphosphate [(p)ppGpp] and antibiotic tolerance in S. aureus. Here, we report that elevated (p)ppGpp in these strains promotes the conjugal transfer of diverse staphylococcal resistance plasmids. We observed that clinical Rel mutations promote donation, but not receipt, of plasmids from the three families of staphylococcal plasmid and a mobilizable plasmid. This increased conjugation frequency could also be induced by chemical induction of the stringent response by mupirocin. Intriguingly, detailed experimental analysis revealed that the effect of elevated (p)ppGpp on plasmid donation was not due to CodY derepression, SOS response induction or increased PCN. Furthermore, comparative transcriptomics of wild-type and mutant donor did not highlight any putative plasmid- or host-derived mechanisms to explain this observation. Further investigations are required to explore the mechanistic link between (p)ppGpp and conjugation, given the pervasive transcriptional and post-translational effects of (p)ppGpp. Overall, the association between Rel mutation and increased plasmid donation is alarming, especially as Rel mutations are being increasingly identified among clinical isolates.},
}

*Staphylococcus aureus/genetics/drug effects/metabolism
*Plasmids/genetics/metabolism
*Conjugation, Genetic
Mutation
*Guanosine Tetraphosphate/metabolism
*Guanosine Pentaphosphate/metabolism
*Drug Resistance, Bacterial/genetics
*Bacterial Proteins/genetics/metabolism
Anti-Bacterial Agents/pharmacology
Staphylococcal Infections/microbiology
Gene Expression Regulation, Bacterial
Humans
Gene Transfer, Horizontal

@article {pmid42275600,
year = {2026},
author = {Matrougui, I and Oukkal, S and Musset, K and Orieux, E and Drezen, JM and Charlat, S and Gilbert, C},
title = {Horizontal transfers of polydnavirus segments extend the known range of parasitoid attacks to stick insects and orthopterans.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msag145},
pmid = {42275600},
issn = {1537-1719},
abstract = {Horizontal gene transfer occurs beyond anecdotal frequencies in metazoans. Among insects, some parasitoid wasps even carry gene delivery agents called polydnaviruses (PDVs). These domesticated viral elements mediate the integration of wasp genes into the genome of parasitized hosts, thereby protecting developing larvae from immune defenses. The frequency of PDV-mediated transfers is sufficiently high that it could be exploited to better characterize the range of organisms attacked by parasitoid wasps. Here, we apply this rationale by screening for the specific molecular footprints of these transfers in 6,814 protostome genomes. We found a total of 6,556 PDV-mediated integrations, all of which were in insects. The distribution of these integrations is highly consistent with the known host range of PDV-encoding parasitoid wasps. Most were found in lepidopterans (6,260 integrations in 303 species) - the main hosts of PDV-encoding wasps - and a few were retrieved in sawflies (139 integrations in 14 species) and leaf beetles (4 integrations in 2 species), also known to be parasitized by some of these wasps. Remarkably, we found a total of 232 integrations in 3 species of stick insects and one integration in an orthopteran, two insect lineages that have never been reported to be attacked by PDV-encoding wasps. We show that these integrations are mostly recent and that stick insects and sawflies were attacked recurrently, by multiple wasp lineages. Overall, our study warrants accounting for stick insects and orthopterans as possible new targets of parasitoid attacks, both in community ecology and in assessments of biological control strategies.},
}

@article {pmid42275669,
year = {2026},
author = {Sun, EG and Ventura, A},
title = {Seeing is Believing: Intercellular Transfer of DNA between human cells.},
journal = {Cancer research},
volume = {},
number = {},
pages = {},
doi = {10.1158/0008-5472.CAN-26-2540},
pmid = {42275669},
issn = {1538-7445},
abstract = {Genomic insults in the form of DNA damage and mitotic errors can result in mis-localization of nuclear DNA into the cytoplasm in the form of micronuclei or as fragmented chromosomal elements. Recent work from the Ly lab has demonstrated that cytoplasmic DNAs can undergo intercellular transfer via nanotube-like connections. Using a variety of cell lines, the authors demonstrate the transfer of DNA through nanotubes and that various sources of genome instability can promote this phenomenon. Crucially, the transferred DNA can be incorporated into the nucleus of recipient cells and intermix with host chromosomes. Additionally, the transferred DNA molecules are functional and can provide a fitness advantage to recipient cells. These findings uncover a novel horizontal gene transfer mechanism in human cells, which could have profound implications in human disease and biology.},
}

@article {pmid42276346,
year = {2026},
author = {Harith-Fadzilah, N and Iskandar Sahran, MS and Bin Khairil, MF and Ahmad, HF},
title = {In Silico Identification and characterisation of putative biphenyl degradation mechanism in gut-Derived Pediococcus pentosaceus.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125000},
doi = {10.1016/j.envres.2026.125000},
pmid = {42276346},
issn = {1096-0953},
abstract = {Polychlorinated biphenyls (PCBs) persist in the environment and bioaccumulate through the food chain. Probiotic microorganisms offer a potential strategy to reduce PCB uptake in livestock guts. This study aimed to identify and characterise potential biphenyl degradation capabilities in Pediococcus pentosaceus QS-GN03_1, isolated from the gut of the cockroach, Periplaneta americana for application as a PCB-detoxifying probiotic feed additive. Whole-genome sequencing yielded an approximately 1.86 Mbp assembly with 98.3 % BUSCO completeness. Genomic annotation revealed the presence of a putative biphenyl-2,3-diol 1,2-dioxygenase (BphC; PPBPHCIII) homologue. Compositional analysis surrounding this gene identified atypical genomic singatures and nearby IS481/ISNCY insertion sequence which suggests this gene locus was acquired through horizontal gene transfer independent of other bph genes. Promoter analysis affirmed PPBPHCIII possesses promoter elements and adopts a structure highly similar to functional BphC enzymes from the Protein Data Bank (RMSD 1.357 Å against Pseudomonas BphC PDB ID: 1EIR benchmark). Molecular docking and 100 ns averaged molecular dynamics (MD) simulations indicated stable binding of 2,3-dichlorobiphenyl ligand within a conserved active site coordinated by Fe (II), primarily via electrostatic and hydrophobic interactions. However, the free ligand binding energy calculations predicted a weaker binding affinity for PPBPHCIII compared to the functionally verified 1EIR complex which the difference was primarily due to fewer hydrogen bonds formations. While QS-GN03_1 lacks independent PCB mineralisation capabilities, the isolated presence of a highly ameliorated bphC gene suggests and ancient horizontal acquisition of a larger Bph operon, followed by reductive evolution due to lack of selective pressure. The discovery of native IS30-family insertion sequences within its genome offers synthetic biology opportunity for chromosomal integration of a complete Bph operon, allowing the generation of QS-GN03_1 with complete PCB degradation capability.},
}

@article {pmid42276819,
year = {2026},
author = {Zhang, Q and Lin, R and Zhao, Y and Zhan, P and Zhao, X and Zou, W},
title = {Biofilm-mediated antibiotic tolerance in bacterial pathogens: Integrated molecular networks and novel therapeutic avenues.},
journal = {Virulence},
volume = {},
number = {},
pages = {2687214},
doi = {10.1080/21505594.2026.2687214},
pmid = {42276819},
issn = {2150-5608},
abstract = {The stable structure of biofilms and the characteristics of the bacteria within them make biofilms an important barrier for bacteria to resist external stress, and a key factor contributing to the difficulty of eradicating clinical infections. This article reviews the multi-stage formation process of biofilms, the various mechanisms of antibiotic tolerance and resistance (such as physical barriers, metabolic adaptations, horizontal gene transfer, etc.), as well as the integrated regulatory roles of molecular networks like quorum sensing (QS) and cyclic diguanosine monophosphate (c-di-GMP). These multiple protective mechanisms in biofilms compose a closed "structure-function" loop system. In the past few years, the emergence of new anti-biofilm intervention approaches (matrix-degrading enzymes, phage therapy, nanomaterials, gene editing, etc.) revealed the possibility to break the limitations of conventional antibiotics by compromising structural integrity or interfering with signaling pathways, providing new ideas for drug-resistance infection control.},
}

@article {pmid42277643,
year = {2026},
author = {Rahimian, M and Aghazadeh-Soltan-Ahmadi, M},
title = {Evolutionary interplay: virulence, endolysin-like hydrolases, and defense correlations in the Erwinia amylovora pangenome.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05295-y},
pmid = {42277643},
issn = {1471-2180},
abstract = {Erwinia amylovora, the causative agent of fire blight, poses a significant threat to global pome fruit production. This study presents a comprehensive genomic analysis of 317 E. amylovora strains and 227 Erwinia phages to elucidate virulence evolution, phage-host dynamics, and the genomic signatures of the co-evolutionary arms race. Our analysis suggests that a substantial portion of E. amylovora's virulence factors (VFs) share evolutionary origins with diverse plant, human, and animal pathogens, underscoring widespread horizontal gene transfer. We identified bacterial phage hydrolases‑like proteins that share phylogenetic and domain-level similarities with phage endolysins. These observations are consistent with the possibility that some bacterial hydrolases originated from phage-derived ancestors, although functional repurposing remains to be experimentally validated. Crucially, our analysis identifies systematic, non-random associations between bacterial defense systems (e.g., RM, CRISPR-Cas, TA) and mobile anti-defense genes. Statistical correlations show strong patterns of co-occurrence and mutual exclusivity, which are consistent with an ongoing phage-bacteria arms race. These patterns provide a genomic basis for generating hypotheses about co-evolutionary dynamics. These findings may advance our understanding of E. amylovora pathogenicity and phage interactions, offering foundational insights for developing targeted phage-based biocontrol strategies against this devastating plant pathogen. Experimental validation of the predicted virulence factors and defense correlations is warranted to confirm their biological roles.},
}

@article {pmid42278533,
year = {2026},
author = {Ramadan, YN and Bukhari, SQ and Alatawi, Z and Oriquat, G and Ellah, NHA and Mohamedosman, EHA and Ahmed, R and Hetta, HF},
title = {Evolutionary Genomics of Human Gut Bacteria: Ecological Plasticity Across the Mutualism-Pathogenicity Spectrum.},
journal = {International journal of molecular sciences},
volume = {27},
number = {11},
pages = {},
doi = {10.3390/ijms27115009},
pmid = {42278533},
issn = {1422-0067},
abstract = {The human gut microbiome comprises a diverse community of bacteria whose interactions with the host range from beneficial mutualism to opportunistic pathogenicity. These interactions are shaped by genomic plasticity and ecological pressures that influence whether microbes support host health, remain conditionally harmless, or contribute to disease. Understanding the mechanisms underlying these shifts is essential for clarifying the balance between cooperation and pathogenicity within the gut ecosystem. This review explores the genomic and evolutionary mechanisms that shape microbial adaptation across the mutualism-pathogenicity spectrum in the human gut. Key processes, including horizontal gene transfer (HGT), host-mediated selection, and niche specialization, enable microbes to acquire, regulate, or retain traits that influence colonization, metabolic function, and virulence. These adaptive mechanisms allow gut bacteria to respond dynamically to ecological pressures such as inflammation, antibiotic exposure, and dietary change, resulting in context-dependent microbial behaviors. The review also considers how concepts from insect endosymbiosis may provide insight into gut microbial adaptation. While both systems exhibit host specialization, major differences in transmission mode, ecological flexibility, and genome evolution limit direct comparisons. Rather than following a fixed progression toward parasitism, gut microbes exhibit flexible adaptive strategies shaped by host and environmental conditions. By integrating ecological and evolutionary perspectives, this review presents a balanced framework for understanding how genomic adaptation influences microbial behavior in the gut. This perspective improves our understanding of dysbiosis and microbial pathogenesis and may support the development of microbiome-informed therapeutic strategies for maintaining host health.},
}

@article {pmid41991117,
year = {2026},
author = {Kreins-Irle, M and Berger, M and Solti-Hodován, Á and Mukherjee, K and Singh, R and Greune, L and Bányai, K and López, RF and Dersch, P and Schneider, G and Dobrindt, U},
title = {Investigating the role of novel alphatectiviruses in reducing carriage and transfer of antimicrobial resistance plasmids.},
journal = {International journal of antimicrobial agents},
volume = {67},
number = {7},
pages = {107806},
doi = {10.1016/j.ijantimicag.2026.107806},
pmid = {41991117},
issn = {1872-7913},
mesh = {*Plasmids/genetics ; Animals ; *Escherichia coli/virology/genetics ; *Drug Resistance, Bacterial/genetics ; Host Specificity ; *Gene Transfer, Horizontal ; Conjugation, Genetic ; *Bacteriophages/physiology ; Anti-Bacterial Agents/pharmacology ; },
abstract = {OBJECTIVE: To identify suitable phage isolates and the characterization of factors that define their host range and interactions with bacteria, which are of major importance for optimizing their use in reducing antimicrobial resistance (AMR).

METHODS: We characterized two novel conjugation apparatus-specific alphatectiviruses that target plasmids of the incompatibility groups IncW, N, and P. We show that ɸ4187/61 and ɸ4187/77 specifically target plasmid-harbouring bacteria in mixed bacterial populations, thereby reducing overall plasmid carriage and transfer.

RESULTS: Occurring phage resistance was associated with plasmid loss or greatly reduced plasmid transfer efficiency, further supporting the desired reducing effect of phage treatment on AMR plasmid dissemination. The host range of the two alphatectiviruses was not only determined by the type of the plasmid-encoded conjugation apparatus but also by other properties related to the conjugative plasmid, bacterial host, or phage. Treatment of Galleria mellonella larvae force-fed with Escherichia coli MG1655 carrying plasmid RP4 with ɸ4187/77 significantly reduced the RP4 transfer frequency and total number of RP4-harbouring bacteria in the G. mellonella gut.

CONCLUSIONS: Alphatectiviruses such as ɸ4187/61 and ɸ4187/77 are promising candidates for approaches to combat AMR by phage-dependent reduction of plasmid carriage and transfer.},
}

*Plasmids/genetics
Animals
*Escherichia coli/virology/genetics
*Drug Resistance, Bacterial/genetics
Host Specificity
*Gene Transfer, Horizontal
Conjugation, Genetic
*Bacteriophages/physiology
Anti-Bacterial Agents/pharmacology

@article {pmid42263430,
year = {2026},
author = {Fatima, H and Viejo-Borbolla, A and Krey, T},
title = {Architecture and evolution of viral complement evasion.},
journal = {Current opinion in virology},
volume = {76},
number = {},
pages = {101563},
doi = {10.1016/j.coviro.2026.101563},
pmid = {42263430},
issn = {1879-6265},
abstract = {The complement system constitutes a powerful antiviral defense, centered on C3b-mediated amplification that drives opsonization, inflammation, and membrane attack complex formation. To persist in the eukaryotic host, viruses must neutralize this amplification step, and strikingly diverse evolutionary lineages have converged on inhibiting C3b-mediated amplification. In this review, we compare host and viral regulators of complement activation (RCAs) to reveal the structural and mechanistic principles underlying C3b control. Human RCAs achieve complement regulation through modular assemblies of complement control protein domains whose multivalency, linker-encoded geometry, and domain-specific dynamics enable efficient decay acceleration and factor I cofactor activity. Viruses have independently replicated these principles through distinct evolutionary routes. Poxviruses and gammaherpesviruses acquired host-derived RCA genes via horizontal gene transfer, followed by lineage-specific refinement on extensively different time scales. In contrast, alphaherpesviruses evolved structurally unrelated complement inhibitors, exemplified by glycoprotein C, which suppresses C3b via a binding interface distinct from that used by RCAs. Despite profound structural divergence, most viral strategies converge on inhibition of the C3b amplification loop. This convergence highlights C3b suppression as an evolutionary bottleneck imposed by complement and reveals a fundamental asymmetry between structural innovation and functional constraint. Understanding how viruses repeatedly solve this invariant problem identifies complement regulation as a durable vulnerability and suggests therapeutic strategies resilient to viral diversity and mutation-driven escape.},
}

@article {pmid42263997,
year = {2026},
author = {Singh, S and Tripathi, V and Srivastava, P and Pandey, D and Roy, A and Sillanpää, M},
title = {Chemical and biological cargo on microplastics: current evidence for the Trojan-horse pathway to human exposure.},
journal = {Environmental research},
volume = {},
number = {},
pages = {124996},
doi = {10.1016/j.envres.2026.124996},
pmid = {42263997},
issn = {1096-0953},
abstract = {Microplastics (MPs) are increasingly recognised not as inert litter, but as chemically and biologically active interfaces that interact dynamically with environmental contaminants and microbial communities. Environmental weathering processes, including photochemical oxidation and mechanical abrasion, increase MP surface roughness and oxygen-containing functional groups by 2-10-fold, enhancing sorption capacity and eco-corona formation. These eco-coronas, composed of natural organic matter, biomolecules, and extracellular polymers, alter MP physicochemical properties and promote microbial colonisation. The resulting "plastisphere" facilitates microbial succession and antibiotic resistance gene (ARG) enrichment by 10-100-fold relative to surrounding environments through enhanced horizontal gene transfer. MPs also act as vectors for co-contaminants through the "Trojan-horse" effect, accumulating PFAS, PAHs, and heavy metals and amplifying oxidative stress and genotoxicity. Key findings indicate that: (1) weathered MPs exhibit enhanced contaminant adsorption and transport potential; (2) eco-corona formation governs pollutant binding and microbial attachment; (3) nanoplastics (<100 nm) show increased cellular uptake and bioavailability; (4) co-exposure to MPs and contaminants increases reactive oxygen species generation by 30-300% in biological models; and (5) MPs have been detected in human tissues, including lungs (∼7.1 μg g[-1]), blood (∼77% detection frequency), placenta (up to 790 μg g[-1]), and feces (10-20 particles g[-1]). Despite rapid advances, methodological and regulatory gaps continue to limit accurate risk assessment. Collectively, these findings establish MPs as dynamic ecological interfaces requiring integrated mitigation and regulatory strategies.},
}

@article {pmid42264341,
year = {2026},
author = {Zhu, K and Sun, W and Wang, Z and Zha, Y and Qu, X and Wang, B and Zhang, H},
title = {Environmental ubiquity but limited host taxonomic distribution of co-occurring metal(loid)-resistance genes and persistent organic pollutant-transformation genes in global inland waters.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {128552},
doi = {10.1016/j.envpol.2026.128552},
pmid = {42264341},
issn = {1873-6424},
abstract = {Human activities have transformed inland waters into reservoirs of co-contamination by heavy metals and persistent organic pollutants, driving microbial adaptation through metal-resistance genes (MRGs) and POP-transformation genes (POPTGs). However, the global biogeography and ecological drivers of these co-occurring functional genes and their hosts remain unresolved. Here, leveraging 1,593 metagenomes, we investigate the global distribution, microbial hosts, co-occurrence patterns, and drivers of MRGs and POPTGs in inland waters. Key MRG subtypes (e.g., ruvB, pstB, arsB) and POPTGs (e.g., hdt, linJ, bphA) co-occurred in phylogenetically constrained hosts-predominantly Proteobacteria (e.g., Pseudomonas, Acidovorax)-exhibiting dual resistance to Cr/Cu and transformation of aromatic/chlorinated POPs. The positive correlations linked MRG-POPTG to mobile genetic elements, suggesting horizontal gene transfer accelerates multi-pollutant resistance. Our findings highlight known POPTGs and MRGs occur together, which is ubiquitous in the environment but restricted to a limited number of taxa (approximately 3.8% ratio of the total 4129 non-redundant MAGs). Finally, a global map of MRG-POPTG-carrying MAGs (MPCMs) abundance is generated, where climatic and anthropogenic factors explained MPCMs hot spots in South Asia, Southeast Asia, South America.},
}

@article {pmid42265319,
year = {2026},
author = {Gionchetta, G and Lee, J and Hansen, O and Beck, K and Bürgmann, H},
title = {Invasion dynamics of antimicrobial-resistant E. coli in river biofilms: impacts on the resistome, microbiomes, and horizontal gene transfer.},
journal = {npj antimicrobials and resistance},
volume = {},
number = {},
pages = {},
doi = {10.1038/s44259-026-00232-5},
pmid = {42265319},
issn = {2731-8745},
support = {ID 100010434//La Caixa Foundation/ ; 186531/SNSF_/Swiss National Science Foundation/Switzerland ; },
abstract = {River biofilms are frequently exposed to invasion by antibiotic-resistant bacteria (ARB) due to episodic or chronic wastewater inputs, yet the ecological processes governing the fate of invaders and their resistance plasmids remain poorly understood. We experimentally exposed river-grown biofilms from sites differing in microbial diversity and wastewater impact to a genetically tagged ARB Escherichia coli carrying a transferable IncPα plasmid with the nptII resistance gene. Over two weeks, we tracked invader and plasmid dynamics using qPCR and plasmid-to-genome ratios as a proxy for horizontal gene transfer (HGT), complemented by 16S rRNA gene sequencing and metagenomics. Both quantification approaches yielded consistent results: the invader transiently established in all biofilms, peaking within 48 h and declining to near-background levels after 14 days. Decreasing plasmid-to-genome ratios indicated limited HGT and progressive plasmid loss. Biofilms impacted by wastewater showed slower declines, suggesting greater plasmid persistence in disturbed environments and increased abundance of specific indigenous antimicrobial resistance genes of public health concern. While the overall resistome exhibited short-lived shifts, and indigenous resistomes remained largely stable. These findings demonstrate that invader-biofilm interactions are dynamic and shaped by community context, supporting the One Health framework and highlighting how environmental conditions modulate antimicrobial resistance risks in freshwater ecosystems.},
}

@article {pmid42269300,
year = {2026},
author = {Lo, HY and Hsiao, YT and Wu, YJ and Whang, LM and Chen, WH and Tung, HH},
title = {Persistence and dynamics of antibiotic resistome in a drinking water supply system with booster chlorination.},
journal = {Journal of hazardous materials},
volume = {514},
number = {},
pages = {142622},
doi = {10.1016/j.jhazmat.2026.142622},
pmid = {42269300},
issn = {1873-3336},
abstract = {Due to the extensive use of antibiotics worldwide, the prevalence of antibiotic resistance genes (ARGs) in aquatic environments has become a major public health concern. This study investigated the ARGs in a drinking water supply system, with particular emphasis on booster chlorination in the distribution network. To elucidate the dynamics of the antibiotic resistome, environmental DNA was extracted from water collected from five different sections, and the resistome profiles were subsequently reconstructed with metagenome assembly. Our findings revealed that 35 core ARGs persisted but decreased in concentration during water treatment and early distribution, with genes resistant to bacitracin, multidrug, and rifamycin being the most prominent. However, a notable surge of ARGs was observed at the terminal distribution segment. This increase was linked to changes in the resistome structure, which were primarily associated with shifts in the microbial community and, within the DWDS specifically, also linked to horizontal transfer mediated by mobile genetic elements (MGEs) under chlorine stress from booster chlorination. Microbial communities within the drinking water distribution system (DWDS) shifted distinctly from those in the water treatment plant. Under re-chlorination pressure, the chlorine-tolerant Mycobacteriales and the biofilm-forming Hyphomicrobiales and Rhodobacterales became the predominant taxa. Additionally, metagenome-assembled genomes (MAGs) reconstruction further identified that Hyphomicrobium and Mycobacterium were the main ARG carriers in the DWDS, with the latter as the main putative host for the core ARGs. Overall, this study demonstrated that booster chlorination in the water distribution system while controlling microbial regrowth, may simultaneously facilitate ARG dissemination. These findings highlight the need to optimise re-chlorination practices to balance microbial growth control while minimising ARG proliferation in DWDS.},
}

@article {pmid42270613,
year = {2026},
author = {Deng, C and Cai, H and Luo, K and Liu, S and Chen, Q and Sun, W and Ni, J},
title = {Nitrate-reducing bacteria bridge nitrogen cycling and antibiotic resistance in river ecosystems.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-74161-2},
pmid = {42270613},
issn = {2041-1723},
support = {U2240205//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {River ecosystems, crucial components of the global nitrogen cycle, are increasingly affected by antibiotic pollution. However, the mechanistic interplay between nitrogen cycling and antibiotic resistance genes (ARGs) dissemination remains poorly understood, limiting effective ecological risk assessments. Here, we identify nitrate-reducing bacteria (NRBs), key drivers of denitrification and greenhouse gas mitigation, as dual-functional hubs that co-regulate nitrogen turnover and ARG dissemination under antibiotic stress. By integrating 173 metagenomes and 10 metatranscriptomes from the Yangtze River, we reconstruct 4200 metagenome-assembled genomes (MAGs) and find that NRBs harbor ~69% of actively transcribed ARGs in river microbiomes, with antibiotic pressure as the dominant ecological driver. Simulated microcosms exposed to antibiotic gradients reveal a hormetic response, where environmentally relevant concentrations enhanced both NRB-driven denitrification efficiency and ARG dissemination. Multi-omics analyses further reveal antibiotic-driven horizontal gene transfer as the predominant selective force co-shaping ARG and nitrate reduction gene dynamics, accelerating both nitrogen cycling and ARG spread. These findings establish NRBs as central hubs bridging antibiotic resistance and nitrogen metabolism, providing a mechanistic framework for predicting co-selection dynamics and mitigating cascading ecological impacts. Our work highlights the need to integrate microbial co-metabolic functions into pollution control strategies and redefine ecological risk assessments in antibiotic-polluted ecosystems.},
}

@article {pmid42270740,
year = {2026},
author = {Masum, MHU and Chamonara, K and Uddin, MS and Hossain, I and Roy, SC and Hossain, MI and Hosen, MR and Siddiqua, A and Al Mukarrom, A},
title = {Comprehensive genomic analysis of avian Escherichia coli from Noakhali uncovers multidrug resistance, metal resistance, and zoonotic signatures.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-54331-4},
pmid = {42270740},
issn = {2045-2322},
abstract = {Colibacillosis caused by avian pathogenic Escherichia coli (APEC) results in significant poultry losses and financial constraints globally, particularly in Bangladesh, emphasizing the urgent need for effective surveillance and control strategies. The present study employed whole-genome sequencing (WGS) of E. coli isolates from avian hosts and their surroundings to obtain genomic and evolutionary insights. Subsequently, the strains exhibited high genome completeness (> 99%) and coarse consistency scores (> 98) for genome assembly metrics. Further, genome annotation profiles showed a broad range of antimicrobial resistance (AMR) determinants, including resistance-nodulation-division (RND), major facilitator superfamily (MFS), and small multidrug resistance (SMR) multidrug efflux pumps. The coexistence of such AMR determinants within mobile genetic elements (MGEs) indicates a pattern of horizontal gene transfer and a possible dissemination pathway for the multidrug resistance phenotype. Several virulence-associated gene (VAG) clusters in the genomes suggest potential virulence profiles. A significant number of genes conferring heavy metal resistance and detoxification were identified in the genomes, including arsenic, copper, magnesium, tellurite, and zinc resistance, indicating extensive metal stress tolerance in the strains. Subsequent pangenome and phylogeny analyses uncovered significant similarities between strains derived from avian and human clinical isolates, suggesting a potential for zoonotic transmission. The findings highlight genetic association and potential public health implications of APEC and environmental E. coli (EEC) strains from poultry.},
}

@article {pmid42270862,
year = {2026},
author = {Pereira, MF and Rossi, CC and Borghi, M and Januário, BD and Andrade-Oliveira, AL and Bazzolli, DMS and de Almeida, LGP and de Vasconcelos, ATR and Nicolás, MF and Schuenck, RP},
title = {Genomics of Hospital-Associated Brazilian Multidrug-Resistant Klebsiella pneumoniae: Abundance of Resistance and Virulence Genes and Mosaicism of the blaKPC-2 Genetic Context Among Enterobacterales.},
journal = {Current microbiology},
volume = {83},
number = {8},
pages = {},
pmid = {42270862},
issn = {1432-0991},
abstract = {The emergence of carbapenem-resistant Klebsiella pneumoniae (CRKP) poses a critical threat to global public health due to limited therapeutic options. This situation is magnified by CRKP strains with elevated virulence. This study aimed to characterize the virulome, resistome, and blaKPC genetic context of CRKP strains exhibiting increased virulence from hospital-associated infections in southeastern Brazil, focusing on their molecular evolution and clinical impact. Despite being classified as classical variants, the strains displayed a dense virulome, averaging 14 ± 0.55 virulence genes, many linked to mobile genetic elements and co-occurring with heavy metal resistance genes. Notably, the colicin-encoding cci gene, reported for the first time in ST147, illustrates unique adaptations in this lineage. Diversity was observed in K- and O-loci, including the rare K-locus 150, identified in an ST11 strain featuring a rearrangement involving the virulence-associated fucose synthesis gene gmb. The pan-resistome included 51 acquired resistance genes (ARGs), with an average of 14.7 ± 2.8 per strain, enabling resistance to multiple antibiotic classes. The colocalization of ARGs suggests horizontal gene transfer as a driver of resistance dissemination. All blaKPC-2-carrying strains also contained ESBL genes, with the blaKPC-2 gene typically located on IncN or IncM1-type plasmids within Tn4401, a conserved genetic context. However, an unusual blaKPC-2 context, associated with Tn5403 and suggesting a putative recombination event between plasmids from different Proteobacteria, was found in an ST11 (CC258) strain. These findings highlight the urgent need for genomic surveillance in hospitals to monitor and understand the evolution of resistance and virulence in CRKP.},
}

@article {pmid42271057,
year = {2026},
author = {Bernabeu, M and Manzano-Morales, S and Marcet-Houben, M and Gabaldón, T},
title = {Gene ancestries reveal diverse microbial associations during eukaryogenesis.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {42271057},
issn = {1476-4687},
abstract = {The origin of eukaryotes remains a central enigma in biology[1]. Continuing debates agree on the pivotal role of a symbiosis between an alphaproteobacterium and an Asgard archaeon[2,3]. However, the nature, timing and contributions of other potential bacterial partners[4-6] and the role of interactions with viruses[7-9] remain contentious. To address these questions, we used advanced phylogenomic approaches and comprehensive datasets spanning the known diversity of cellular life and viruses. Our analysis provided a revised reconstruction of the last eukaryotic common ancestor (LECA) proteome, in which we traced the phylogenetic origin of each protein family. We found compelling evidence for multiple waves of horizontal gene transfer from diverse bacterial donors, with some likely to have preceded mitochondrial endosymbiosis. We inferred plausible traits of the major donors and their functional contributions to the LECA. Our findings support a contribution of horizontal gene transfers to shaping the proteomes of pre-LECA ancestors and suggest a facilitating role of Nucleocytoviricota viruses. Taken together, our results suggest that ancient eukaryotes may have originated within complex microbial ecosystems through a succession of diverse associations that left a footprint of horizontally transferred genes.},
}

@article {pmid42273047,
year = {2026},
author = {Androsiuk, L and Tal, S},
title = {Rethinking the plasmid paradox: when plasmid costs do not affect fitness.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1836467},
pmid = {42273047},
issn = {1664-302X},
abstract = {Plasmids frequently impose measurable fitness costs on their bacterial hosts, yet they remain abundant across clinical and environmental microbiomes. This apparent contradiction, known as the plasmid paradox, has traditionally been explained through mechanisms such as horizontal gene transfer, compensatory evolution, addiction systems, and fluctuating selection. Here we suggest that part of the paradox may arise from implicit physiological assumptions embedded in most empirical measurements-specifically, the assumption that growth rate is a direct proxy for fitness and that plasmid burden necessarily reduces it. We argue that these assumptions may not hold under many ecological conditions. We formalize cell division time as the maximum of several required cellular modules, including cytoplasmic biosynthesis and membrane or envelope synthesis. If plasmid carriage primarily increases cytoplasmic demand, its cost will be expressed only when cytoplasmic processes constitute the dominant bottleneck for growth. When other modules limit division, plasmid-associated burdens may be physiologically real yet evolutionarily silent. More broadly, equating fitness with maximal exponential growth rate overlooks well-established growth-survival trade-offs in bacteria, suggesting that plasmid costs measured under optimized laboratory conditions may systematically overestimate ecological selection against plasmid carriage.},
}

@article {pmid42274492,
year = {2026},
author = {Zhu, H and Zhang, L and Hao, Z and Chen, E and Wang, Y and Jin, H and Zhou, Y},
title = {Stress-Driven Accelerated Evolution and Ecological Network Reconfiguration in Extremophilic Microbial Communities.},
journal = {Biology},
volume = {15},
number = {11},
pages = {},
pmid = {42274492},
issn = {2079-7737},
abstract = {Persistently high levels of abiotic stress define extreme environments. Even for adapted extremophiles, we argue this stress remains a continuous physiological challenge, necessitating energetically costly homeostasis. Crucially, this persistent pressure drives a self-reinforcing feedback loop across biological scales: it accelerates genomic evolution and concurrently reshapes ecological network architecture. Genomic innovations provide new traits for network reconfiguration, while the restructured network acts as a selective filter guiding subsequent evolution. This loop underpins extreme ecosystem resilience-the capacity for stress-induced adaptive restructuring. We synthesize mechanisms of this stress-adaptation interplay, propose testable hypotheses and outline experimental evolution approaches to validate this predictive framework for microbial responses to global change.},
}

@article {pmid42275032,
year = {2026},
author = {Yuan, S and Tan, D and Zhu, D and Balcazar, JL and Wang, H and Friman, VP and Sun, M and Hu, F},
title = {Global transmission and distribution of phage-encoded cholera toxin genes constrained by toxin-repression genes and anti-phage defense systems.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag139},
pmid = {42275032},
issn = {1751-7370},
abstract = {Cholera is a severe diarrheal disease caused by toxigenic Vibrio cholerae, whose virulence depends on lysogenic infection by CTXφ bacteriophages encoding the cholera toxin genes (ctxA and ctxB) and associated accessory genes (ace and zot). However, the global distribution and transmission dynamics of phage-encoded cholera toxin genes across environments remain poorly understood. To address this, we performed a large-scale bioinformatic analysis of publicly available whole genomes. We show that both phages and bacteria carrying toxin genes are globally distributed across human-associated, freshwater, fish, and mammalian habitats, with Vibrio and Aeromonas being the dominant bacterial taxa and Inoviridae is the most prevalent phage family. Phage-mediated horizontal gene transfer (HGT) of toxin genes occurred in both Vibrio and non-Vibrio species, with the highest transfer between Inoviridae and V. cholerae occuring predominantly among bacteria from the same habitat. Temporal analysis revealed an increase in candidate HGT events after 2000, peaking at 377845 events during 2010-2019. HGT events negatively correlated with the presence of CRISPR-Cas system and toxin-repression genes (hns, hapR, and tsrA) in host bacteria. Experimental validation indicated that H-NS and HapR inhibit phage infection by repressing phage release. Together, our results suggest that CRISPR-Cas phage defense system and toxin-repression mechanisms could constrain the spread of toxin-carrying phages, with potential implications for the occurrence and severity of cholera outbreaks worldwide.},
}

@article {pmid42259126,
year = {2026},
author = {Sharma, P and De, I and Chaudhary, N and Singh, G and Kumar, D and Ghosh, K and Singh, M},
title = {Comparative toxicity of nickel titanate and calcium manganite perovskite nanomaterials in human and bacterial systems: Implications for environmental and health risks.},
journal = {Chemosphere},
volume = {407},
number = {},
pages = {144975},
doi = {10.1016/j.chemosphere.2026.144975},
pmid = {42259126},
issn = {1879-1298},
abstract = {Perovskite nanomaterials are increasingly used in energy storage, catalysis, and sensing, but their effects on human health and the environment remain poorly understood, especially for newer types. This study presents the first direct comparison of two emerging perovskites, nickel-titanate (NiTiO3) and calcium-manganite (CaMnO3) tested simultaneously in human epithelial cells (A549) and Escherichia coli bacteria, providing a dual-host perspective on their biological impact. The materials differed notably in shape and size: NiTiO3 formed smooth, spherical-like particles (∼367 nm), while CaMnO3 had irregular, sharp-edged structures (∼588 nm). Neither caused destruction of red blood cells up to 400 μg/mL, although CaMnO3 induced visible deformation. In human cells, CaMnO3 was more toxic, causing oxidative stress, DNA damage, and activation of inflammatory and cell-death pathways. In bacteria, both nanomaterial increased cell membrane permeability, oxidative stress, with CaMnO3 showing stronger bactericidal effects. Metabolomic analysis of bacterial and human cells via NMR revealed NiTiO3 disrupted amino acid and energy metabolism primarily. Surprisingly, CaMnO3 caused broader but moderate metabolic changes., whereas NiTiO3 caused greater metabolic disruption despite being less lethal, suggesting that cell death and metabolic harm are not always correlated. Notably, both nanomaterials significantly enhanced horizontal gene transfer between bacteria, especially via outer membrane vesicles, raising concerns about accelerating antibiotic resistance spread. Overall, small differences in composition and shape led to vastly different biological outcomes. This study establishes a cross-species testing framework for nanomaterial safety and underscores the importance of biosafety considerations in developing next-generation perovskites. Environmental implication: This study highlights important environmental concerns associated with the growing use of perovskite nanomaterials. Once released into air, water, or soil, NiTiO3 and CaMnO3 may interact with human cells and beneficial microbial communities. CaMnO3 showed higher toxicity in human cells and bacteria, while both nanomaterials significantly increased horizontal gene transfer, which may accelerate the spread of antibiotic resistance in the environment. Such changes can affect ecosystem balance and public health. These findings emphasize the need for responsible production, controlled disposal, and rigorous environmental risk assessment before the large-scale application of perovskite nanomaterials.},
}

@article {pmid42262111,
year = {2026},
author = {Cheng, X and Liu, H and Qiu, X and Wu, W and Hu, H and Xu, P and Tang, H},
title = {Systemic trade-offs between core and accessory genomes govern stress adaptation in Rhodococcus erythropolis.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0013726},
doi = {10.1128/msystems.00137-26},
pmid = {42262111},
issn = {2379-5077},
abstract = {The genus Rhodococcus is a premier biotechnological chassis for organic pollutant bioremediation and natural product biosynthesis, yet the systemic genetic basis of its stress resilience remains poorly defined. Here, we elucidate adaptive strategies in Rhodococcus erythropolis by integrating pangenomics with multi-omics and phenotypic analyses. We refined R. erythropolis taxonomy using average nucleotide identity across 671 genomes and constructed a high-quality pangenome that exhibits an open architecture, with continuous expansion of the accessory cloud genome via horizontal gene transfer to enable environmental adaptation. Using R. erythropolis strain XP as a representative model, we confirmed broad physiological robustness, including tolerance to multiple heavy metals [Ni(II), Zn(II), Pb(II), Cu(II), and Cr(VI); minimum inhibitory concentrations, 2-7 mM], wide pH ranges (5-11), and high salinity (1.5 M NaCl). Integration of comparative transcriptomics with weighted gene co-expression network analysis revealed the transcriptional basis of this resilience. A key growth-regulatory module (ME1), dominated by evolutionarily conserved core genes (68.8%), including essential cell division components, was identified. Under severe stress, this core module is strongly downregulated, coinciding with stress-induced filamentation. These results expose a fundamental evolutionary trade-off: repression of vertical propagation via core functions enables preferential deployment of accessory cloud genes that confer resistance. Collectively, this study links pangenome plasticity to physiological trade-offs and provides a conceptual framework for optimizing R. erythropolis in industrial applications.IMPORTANCEMicroorganisms must continually balance rapid growth with survival under stress, yet the genomic architecture underlying this trade-off remains unclear. By analyzing 671 genomes to refine the taxonomy of the biotechnologically important bacterium Rhodococcus erythropolis and integrating multi-omics data, we demonstrate that this physiological balance is mirrored by an evolutionary division of labor. The conserved core genome predominantly governs growth, whereas the horizontally acquired accessory cloud genome drives stress resistance. Under severe stress, the bacterium downregulates core cell division machinery to prioritize resources for activating its accessory defense repertoire. This work establishes a direct link between pangenome evolution and cellular fitness, offering theoretical guidance for engineering robust microbial chassis.},
}

@article {pmid42262123,
year = {2026},
author = {Zhou, J and Yang, J and Li, K and Shi, H and Gao, K and Zhao, P and Xu, L and Zhang, D and Zhen, M},
title = {Carbapenem resistance mediated by blaNDM-13 in a highly drug-resistant Salmonella Stanley ST29 strain in China.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0320724},
doi = {10.1128/spectrum.03207-24},
pmid = {42262123},
issn = {2165-0497},
abstract = {The rise of carbapenem-resistant Enterobacterales presents a substantial global public health challenge. While carbapenem-resistant Salmonella is rarely reported in clinical settings, this study characterizes a carbapenem resistance mediated by blaNDM-13 Salmonella Stanley strain SAL22057, isolated from the fecal sample of a pediatric patient with diarrhea and fever. We determined antimicrobial susceptibility, conducted genomic characterization, and assessed plasmid conjugation. Antimicrobial susceptibility testing showed that SAL22057 was resistant to meropenem (minimum inhibitory concentration [MIC] 32 μg/mL) and imipenem (MIC 16 μg/mL). Genotyping analysis identified SAL22057 as belonging to ST29, and it was found to be multidrug-resistant and to carry numerous virulence genes. Whole-genome sequencing and plasmid analysis identified that blaNDM-13 was located on pSAL22057-NDM (IncI1α), while a distinct plasmid, pSAL22057-OXA (IncHI2), harbored multiple antimicrobial resistance genes, including blaOXA-10. Conjugation experiments revealed that blaNDM-13 was transferable to Escherichia coli C600. We show that IS1294 likely mediates blaNDM-13 mobilization, with its insertion influencing gene transfer. Furthermore, the consistent flanking of several resistance genes by IS26 elements indicates that IS26-mediated horizontal gene transfer is a key mechanism driving the dissemination of these determinants and genomic rearrangements within Enterobacteriaceae.IMPORTANCEThe emergence of carbapenem-resistant Enterobacterales poses a global health threat. This study identified a carbapenem-resistant Salmonella Stanley strain, SAL22057, from a pediatric patient, which carried the carbapenemase gene blaNDM-13. The genotyping revealed that SAL22057 is ST29, displaying a concerning multidrug-resistant phenotype along with several virulence determinants. Alarmingly, this strain exhibits high-level resistance to meropenem (minimum inhibitory concentration [MIC] 32 μg/mL) and imipenem (MIC 16 μg/mL). Conjugation experiments confirm that blaNDM-13 is transferable to Escherichia coli C600, signaling a clear pathway for resistance dissemination among Enterobacteriaceae. We demonstrate that IS1294 likely mobilizes blaNDM-13, while IS26 consistently flanks multiple resistance genes, providing mechanistic evidence that IS26-mediated transposition is accelerating the spread of resistance genes in clinical pathogens.},
}

@article {pmid42262436,
year = {2026},
author = {Alvi, AA and Hussain, M and Noureen, S and Malik, ZA and Zahoor, S and Jamil, A and Mohsin, MA and Azeem, A and Javaid, H and Hassan, Z},
title = {CRISPR-based gene editing for antimicrobial resistance control in human medicine.},
journal = {Archives of microbiology},
volume = {208},
number = {9},
pages = {},
pmid = {42262436},
issn = {1432-072X},
abstract = {Antimicrobial resistance (AMR) has already become one of the most urgent threats to the public health of this century. In 2019 alone, it directly causes about 1.27 million deaths and it was estimated that 1.91 million people will die yearly by 2050 should present trends persist. The traditional antibiotic development pipelines have been shown to be structurally insufficient to meet the rate at which bacterial populations have developed, diversified and spread resistance determinants, typically by horizontal gene transfer. In this context, CRISPR-Cas gene editing has become a focused antimicrobial approach that can selectively target resistance genes, virulence factors, and mobile genetic elements without the broad-spectrum collateral damage associated with conventional antibiotics. The review assesses CRISPR-Cas systems, namely Cas9, Cas12a, Cas3, and Cas13 in the context of two complementary mechanistic strategies namely selective killing of pathogens and antibiotic resensitization by the targeted disruption of gene resistance. We compare the impact of key delivery systems, such as bacteriophage vectors, lipid nanoparticles, and conjugative plasmids, evaluating them based on their therapeutic activity, host selectivity, and possible translation. The present state of clinical translations is discussed, including the two most advanced clinical-stage candidates SNIPR001 (Phase I/II, NCT05277350) and LBP-EC01 (Phase 2/3, NCT05488444). We also address the open issues that include off-target editing, host immune reactions, bacterial counter-resistance, regulatory ambiguity, and scalability of manufacturing. Lastly, we provide priority research directions, such as the combination antimicrobial strategies, AI-assisted CRISPR design, and next-generation delivery engineering, none of which will be resolved before routine clinical application of CRISPR-based antimicrobials is achieved.},
}

@article {pmid42254714,
year = {2026},
author = {Davies, KM and Albert, NW and Yorker, RM and Schwinn, KE and Zhou, Y},
title = {The Biosynthesis and Functions of Flavonoids: Recent Advances From Studies Across Land Plant Diversity.},
journal = {Journal of the Royal Society of New Zealand},
volume = {56},
number = {3},
pages = {e70057},
pmid = {42254714},
issn = {1175-8899},
abstract = {Over the last decade there have been significant advances in genome sequencing and model species development for ferns, lycophytes, and the bryophyte lineages-mosses, liverworts, and hornworts. This has facilitated research on the biosynthesis and function of flavonoids in these non-seed land-plant lineages. Most studies have been on the liverwort model species Marchantia polymorpha (Marchantia). There has been extensive characterisation of biosynthetic and regulatory genes of the Marchantia flavonoid pathway, including generation of loss-of-function mutant lines to examine flavonoid contribution to tolerance of abiotic stresses and pathogen infection. Notably, the red pigments of liverworts were shown to be a new class of flavonoids, named 'auronidins'. There are relatively few studies on mosses, lycophytes, or ferns. Yet these lineages also contain distinct red pigment structures not found in seed plants. They also contain novel enzymatic activities, unique horizontal gene transfer events, and expanded gene families for proteins such as the polyphenol oxidases. Additionally, the hornworts have been shown to have lost the flavonoid pathway during lineage-specific evolution. Indeed, evidence suggests that aspects of flavonoid biosynthesis may have been lost and regained on multiple occasions, in different lineages, during land plant evolution. In this review, we summarise recent advances in understanding of flavonoid biosynthesis in non-seed plants and examine how this informs theories of the evolution of the flavonoid pathway across the land-plant lineages.},
}

@article {pmid42258181,
year = {2026},
author = {Shetty, VP and Rai, P and Karunasagar, A and Deekshit, VK},
title = {Integron-mediated gene cassette dynamics in Enterobacterales under selective antibiotic pressure.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxag135},
pmid = {42258181},
issn = {1365-2672},
abstract = {AIM: Antimicrobial resistance among Enterobacterales is an urgent global crisis, with horizontal gene transfer being one of the major driving forces behind it. The integrons play a significant role in this process. Here, we present the investigation of gene cassette dynamics of integrons among the Enterobacterales under selective antibiotic pressure.

METHODS AND RESULTS: We analysed Escherichia coli (n = 214), Klebsiella pneumoniae (n = 210), and Salmonella Typhi (n = 70) isolates for antibiotic susceptibility, and performed Sanger sequencing for the integron region of multidrug-resistant isolates. The evolution assay was carried out to determine the gene cassette rearrangement under stress. RT-qPCR was performed to investigate the gene expression on exposure to trimethoprim and streptomycin. All the E. coli and K. pneumoniae isolates were MDR, and showed the highest resistance to ampicillin (94%) and ceftazidime (95.2%), respectively. Integron screening revealed a higher abundance of class 1 integrons followed by class 2 integrons in both isolates. Sequencing revealed the presence of trimethoprim and streptomycin-resistant gene cassettes within integrons. The phenotypic assays revealed that integron-positive isolates carried more resistance to antibiotics than integron-negative isolates. The combination of 2 antibiotics (trimethoprim + streptomycin) showed gene upregulation in the isolates, depicting the synergistic activity of the antibiotics. The evolution assay revealed a change of the gene cassette arrangement from dfrA12-aadA2 to dfrA17-aadA5 after streptomycin treatment in K. pneumoniae.

CONCLUSIONS: The prevalence of integrons thus enhanced the antibiotic resistance, even under antibiotic pressure. These findings highlight the potential role of integrons in antimicrobial resistance among the studied clinical isolates and suggest that monitoring integron-associated resistance may be useful in clinical settings.},
}

@article {pmid42258293,
year = {2026},
author = {Pellegrinetti, TA and Hammond, C and Pérez-López, E and Muirhead, K and Bennypaul, H and Sanderson, D and Dumonceaux, TJ},
title = {Pseudogenization of the chaperonin system in 'Candidatus Phytoplasma pruni' revealed by genome sequencing and comparative genomics.},
journal = {Microbial genomics},
volume = {12},
number = {6},
pages = {},
pmid = {42258293},
issn = {2057-5858},
abstract = {GroE is a chaperonin folding system consisting of GroEL (Cpn60, a 60 kDa chaperonin), and the smaller co-chaperonin GroES (Cpn10). Many 'client' proteins require GroE to fold properly, including several that are essential for cell viability. GroE is found in nearly all bacteria and eukaryotes. Mollicutes are the only micro-organisms that lack GroE in almost all cases. Only two clades of Mollicutes have retained the ancestral GroE system, or perhaps reacquired one; these exceptions include the family Acholeplasmataceae, consisting of the genera Acholeplasma and 'Candidatus Phytoplasma'. The role of GroEL in these unique Mollicutes is a source of speculation, given how many non-canonical 'moonlighting' roles have been ascribed to this protein. GroEL has been suggested to play a role in pathogenesis in plant and animal pathogenic Mollicutes by binding to host cells and facilitating invasion. However, in one further layer of exception, the phytopathogenic taxon 'Candidatus Phytoplasma pruni' (ribosomal group 16SrIII) was reported in 2012 to lack a GroE system. This study confirms the lack of a functional GroE system in 16SrIII by providing two new, high-quality, non-fragmented genome assemblies, as well as a thorough survey of other 16SrIII genomes for genes encoding GroEL/GroES, including those that may not resemble phytoplasma GroEL (i.e. acquired by horizontal gene transfer, HGT). We discuss the implications of a clearly phytopathogenic, invasive group of Mollicutes that nevertheless lacks GroE, in light of the presumed role of GroEL for this species. We determined that multiple genomes of 16SrIII contain short, non-functional groEL pseudogenes, while most of the reported genomes lack any semblance of a GroE system. Examination of the new assemblies allowed us to rule out HGT as a means of GroE acquisition.},
}

@article {pmid42250573,
year = {2026},
author = {Tomás-Tomás, M and Arias-Giraldo, LF and Velasco-Amo, MP and Marco-Noales, E and Landa, BB and Domingo-Calap, P},
title = {Genomic Analysis of Prophage Distribution in Xylella fastidiosa Reveals Extensive Diversity and Horizontal Gene Transfer.},
journal = {Phytopathology},
volume = {},
number = {},
pages = {},
doi = {10.1094/PHYTO-04-25-0141-R},
pmid = {42250573},
issn = {0031-949X},
abstract = {Xylella fastidiosa is a plant pathogenic bacterium responsible for significant agricultural and environmental impact. Prophages, genetic elements of viral origin integrated into bacterial genomes, play a key role in bacterial evolution by facilitating horizontal gene transfer and recombination, processes that drive host and environmental adaptation. In this study, we analyzed the diversity and distribution of prophages across 89 X. fastidiosa strains representing the three main subspecies: fastidiosa, multiplex and pauca, as well as the two proposed subspp. sandyi and morus, representative of 28 sequence types (ST). A total of 410 prophages were identified as PHASTEST-intact candidates, with a notable prevalence in strains of the subspp. sandyi and multiplex. Comparative analyses of the high-confidence prophage regions revealed 105 unique prophages, highlighting their role in enhancing genetic diversity through horizontal gene transfer and recombination. While some prophages were strain-specific, others were shared across multiple strains of the same subspecies or ST, suggesting clonal propagation. Genomic comparisons showed clear distinctions between prophages and lytic phages and highlighted similarities among prophages from different subspecies, reflecting shared evolutionary processes. These findings will support future studies on the functional roles of specific prophage genes, their contributions to X. fastidiosa virulence and host range, and their potential applications in phage-based biocontrol.},
}

@article {pmid42251392,
year = {2026},
author = {Krysińska, M and Barua, D and Muszewska, A},
title = {Glomhopper-a subfamily of DUF3504-encoding CryptonA elements in Glomeromycota.},
journal = {Mobile DNA},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13100-026-00404-0},
pmid = {42251392},
issn = {1759-8753},
support = {2023/49/N/NZ2/03440//Narodowe Centrum Nauki/ ; 2021/41/B/NZ2/02426//Narodowe Centrum Nauki/ ; },
abstract = {BACKGROUND: Transposable elements drive genomic changes and are mobilized by specific nucleases. Among them are tyrosine recombinases (YRs), which mediate DNA cleavage and rejoining. YR-encoding elements, such as DIRS, Ngaro, Crypton, and Starships, occur in diverse eukaryotes and display characteristic terminal repeat structures that enable their mobility. Their activity in fungi results in large-scale chromosomal rearrangements, horizontal gene transfer, and the movement of genes for pathogenicity, symbiosis, and secondary metabolism. Other YR-elements underwent domestication giving rise to ZMYM transcriptional regulators in animals.

RESULTS: We identify and characterize the fungal members of the CryptonA lineage of tyrosine recombinase-encoding transposons, which we name Glomhoppers. These elements encode a DUF3504 domain that retains the conserved catalytic residues characteristic of active YRs. In contrast, many domesticated animal DUF3504 homologs lack key catalytic residues, whereas active CryptonA transposon-derived DUF3504 elements have also been reported in animals. Structural modeling suggested the presence of a putative DNA-binding groove, and phylogenetic analyses placed Glomhoppers as a well-supported subclade within the CryptonA lineage, together with domesticated ZMYM-like derivatives. Across 72 Glomeromycota genomes, ~ 1,800 Glomhopper copies were identified, representing a subset of DUF3504-containing loci, mostly truncated or intronized, but ~ 25% lacked introns and maintained intact catalytic motifs, consistent with potential mobility. Genomic context analysis revealed their frequent localization within highly repetitive compartments, often alongside other transposon families. Expression data indicated that intronless variants respond to stress, reaching several-fold higher expression levels than intron-containing forms, especially in Gigaspora species. This is consistent with the possibility that a subset of Glomhoppers remains transcriptionally active and potentially mobilizable, although direct evidence of transposition is lacking.

CONCLUSION: Our findings establish Glomhoppers as a novel subfamily of DUF3504-encoding CryptonAs. The lineage-specific distribution, intron variation, and stress-responsive expression of Glomhoppers suggest divergent evolutionary trajectories, potentially including both mobility and domestication. These elements expand the known diversity of YR transposons and highlight DUF3504 as a candidate domain for further functional and evolutionary studies.},
}

@article {pmid42251689,
year = {2026},
author = {Tao, M and Zhang, Z and Dai, L and Zeng, Y and Zhang, X},
title = {Metagenomic insights into potential horizontal transfer of resistance/virulence genes in gut microbiota from patients with Crohn disease.},
journal = {Inflammatory bowel diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/ibd/izag090},
pmid = {42251689},
issn = {1536-4844},
support = {2025JJ50123//Hunan Provincial Natural Science Foundation of China/ ; 32101368//National Natural Science Foundation of China/ ; 1053320242393//Fundamental Research Funds for the Central Universities of Central South University/ ; },
abstract = {BACKGROUND: Unraveling the potential horizontal transfer of resistance genes/virulence genes (RGs/VGs) in gut microbiota from patients with Crohn disease (CD) is an interesting but poorly characterized issue.

METHODS: Quantitative assessment was performed to estimate the relative abundance and diversity of RGs/VGs/mobile genetic elements (MGEs). Differential analysis was applied to identify the CD-specific enriched genetic subtypes. A species-RGs/VGs/MGEs association network was constructed to explore possible co-occurrence patterns of these genetic elements across potential microbial hosts. Integrated with topological metrics and Zi-Pi computational modeling, co-occurrence network analysis was conducted to characterize potential associations among RGs, VGs, and MGEs.

RESULTS: Comparative metagenomic analyses indicated that the microbiome in group CD exhibited significantly higher relative abundance of RGs compared to that in healthy controls (HC; P = .040), with 131 specific RG/VG subtypes (eg, acrA/T6SS) exhibiting marked enrichment (P < .05). The co-occurrence network revealed intensified interconnectivity between RGs/VGs and MGEs in group CD, in which MGEs accounted for 71% of network nodes (vs 60.80% in HC), and 99.14% of the edges were positively correlated (vs 93.60% in HC). Network topology and Zi-Pi analysis further suggested reduced modularity (0.709 vs 0.979 in HC) and enhanced intergene connectivity (average degree: 12.288 vs 2.156; average weighted degree: 23.359 vs 3.688 in HC). There were no network hubs (0 vs 5 in HC) but abundant modular hubs (60 vs 25 in HC), peripheral nodes (2317 vs 1549 in HC), and connectors (61 vs 36 in HC), which may reflect conditions favorable for enhanced gene transfer potential. Cross-species transfer events were predicted across clinical-environmental-commensal boundaries, exemplified by tet(M) dissemination between Clostridioides difficile and Bacteroides sp., probably implying progressive erosion of ecological barriers.

CONCLUSIONS: Collectively, we inferred that the gut microbiome of CD patients might represent a high-risk reservoir for the horizontal transfer of pathogenic determinants, which may pose a potential threat for public health and biosecurity.},
}

@article {pmid42252411,
year = {2026},
author = {Li, K and Yan, F and Feng, Z and Zhang, P and Duan, Z and Gong, Q and Adelson, DL and Wei, C},
title = {Horizontal gene transfer is widespread in diverse eukaryotes.},
journal = {BMC genomics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12864-026-12958-7},
pmid = {42252411},
issn = {1471-2164},
support = {22ZR1433600//Natural Science Foundation of Shanghai Municipality/ ; 32170643//National Natural Science Foundation of China/ ; 2023YFF1001600//National key R&D program/ ; 24JS2840300, 23JS1400800//Computational Biology Program of Science and Technology Commission of Shanghai Municipality/ ; },
abstract = {Horizontal gene transfer (HGT) is the transfer of genetic material between distantly related organisms. Although HGT is a pervasive mechanism of genetic exchange among prokaryotes, gene transfer events involving eukaryotes are generally considered rare and restricted to a small number of lineages. Here we report genome-wide identification of HGT regions (HGTs) in 10 eukaryotes, including human, mouse, cow, lizard, frog, zebrafish, fruit fly, nematode, Arabidopsis and yeast. By comparing their genomes with thousands of eukaryote, bacteria and virus genomes, we found between 10 and 237 non-redundant HGTs per eukaryote species. Third-generation sequencing across most of the 10 analyzed genomes, combined with targeted PCR in Arabidopsis thaliana, was applied to validate the result HGTs and exclude contamination. Genes impacted by HGTs are enriched in transmembrane transport. Some HGTs have duplicated extensively within the host genome, affecting hundreds, even thousands of genes. Our findings reveal that HGT is ubiquitous in all diverse eukaryotes analyzed here, and it is a non-negligible, previously underappreciated contributor to genome evolution for eukaryotes.},
}

@article {pmid42252973,
year = {2026},
author = {Lee, ES and Kyung, SM and Lee, JH and Xiang, XR and Yoo, HS},
title = {Revealing genetic variation of Actinobacillus pleuropneumoniae Korean isolates using whole genome sequence analysis.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {64},
number = {5},
pages = {e2512010},
doi = {10.71150/jm.2512010},
pmid = {42252973},
issn = {1976-3794},
support = {RS-2024-00392205//National Research Foundation of Korea/ ; //Seoul National University/ ; },
abstract = {Actinobacillus pleuropneumoniae (APP) is the etiological agent of porcine pleuropneumoniae (PP), a high contagious respiratory disease with significant impact on the swine industry in both clinically and economically. Despite of the several attempts to control APP, the emergence of novel serotypes and antimicrobial resistance (AMR) strains highlights the importance of monitoring the genetic characteristics of APP at single nucleotide level. Despite the importance of genomic surveillance of APP to develop effective control strategies, genetic information on the recent Korean isolates of APP is not available at whole genome level. Therefore, in this study, six APP strains were isolated from porcine lungs with characteristic lesions of PP from 2022 to 2024. And their whole genomic sequences, serotypes, virulence factors, and AMR traits were investigated using combined short- and long-read sequencing methods. In silico PCR serotyping identified the isolates as serotype 1, 7, and 15, while one isolate was non-typeable. Multiple AMR genes including Hinf_PBP3_BLA, Ecol_EFTu_PLV, tet(B), tet(O), tetR, sul2, aph(3'')-Ib, aph(6)-Id, and aph(3')-Ia were detected. Also, these genes were located with adjacent to mobile genetic elements, suggesting the possibility of horizontal gene transfer. Phylogenetic comparison with 40 global APP complete genomes, presented that Korean isolates were closely related with China and Switzerland strains. This study provides the whole genome sequences based genetic characterization on the recent Korean isolates of APP, and this study emphasizes that continuous monitoring of APP genomic variation to support effective control of porcine pleuropneumoniae.},
}

@article {pmid42254514,
year = {2026},
author = {Tian, Y and Zou, L and Ji, Y},
title = {Comprehensive genomic analyses revealed the adaptation strategies of Exiguobacterium and its phage genomic diversity.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1841508},
pmid = {42254514},
issn = {1664-302X},
abstract = {Exiguobacterium exhibits high species diversity and complex evolutionary patterns, with members widely distributed across diverse habitats. To elucidate the mechanisms enabling its high adaptability to various environments, 187 genomes of Exiguobacterium strains were analyzed using the phylogenomic and comparative genomics methods. Our analysis revealed that nearly all Exiguobacterium strains harbor genes encoding the utilization of diverse complex polysaccharides and proteinaceous, as well as intact glycolysis and tricarboxylic acid cycle pathways. These abilities suggest that the strains of this genus can easily obtain carbon and nitrogen from the environment. Furthermore, Exiguobacterium strains encode heat- and cold-shock proteins for temperature adaptation, accumulate potassium and compatible solutes such as mannitol, betaine, glutamate, and proline for osmotic balance, and synthesize antioxidant enzymes including superoxide dismutase, catalase, peroxidase, disulfide isomerase, and methionine sulfoxide reductase to mitigate oxidative stress. Each Exiguobacterium strain also contains many genes for resistance to antibiotics and heavy metals, many of which are identified within genomic islands, indicating that horizontal gene transfer has substantially contributed to the rapid acquisition and spread of these adaptive traits. In addition, the presence of diverse phages further enhances genomic variability, and the identification of three auxiliary metabolic genes indicates a potential role for these phages in modulating specific host metabolic processes during infection. This study enhances our understanding of the adaptive mechanisms and key genomic traits of Exiguobacterium that enable its cosmopolitan distribution.},
}

@article {pmid42249988,
year = {2026},
author = {Patil, KS and Gathalkar, GB and Pathan, EK},
title = {Endophytic entomopathogenic fungi: The next frontier in mycological biocontrol.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {7},
pages = {},
pmid = {42249988},
issn = {1573-0972},
abstract = {Entomopathogenic fungi (EPF) are eco-friendly alternatives to chemical pesticides. However, high costs, the instability of the formulations, sensitivity to environmental factors and variability in virulence limit adoption by farmers. We argue that these problems can be overcome by using EPF strains established as endophytes. The ability of endophytic entomopathogenic fungi (EEPF) to modulate the release of volatiles to attract the predators of insect pests positions them as dual-purpose biocontrol agents in agriculture. As endophytes, these fungi are persistent, lowering the costs for pest control. Endophytic entomopathogenic fungi can also promote plant growth and improve tolerance to abiotic stress. Research on the molecular mechanisms underlying plant tissue colonization by EEPF, their persistence in plants and virulence towards insects suggests that EEPF acquire virulence factors and metabolic versatility through horizontal gene transfer from plants. Therefore, establishing and maintaining EPF as endophytes within plants may compensate for the loss of virulence associated with repeated in vitro subculturing of EPF on artificial media. However, despite these potential advantages of EEPF, challenges still remain, such as variability in endophytic colonization under field conditions, host specificity, ecological risks, and scalability. This review critically evaluates these limitations, focusing on well-studied genera, such as Metarhizium, Beauveria, and Lecanicillium, and outlines future directions for improving the reliability of the application of EEPF. By integrating ecological, molecular, and applied perspectives, we provide a comprehensive and updated framework that positions EEPF as next-generation biocontrol agents in sustainable agriculture.},
}

@article {pmid42250117,
year = {2026},
author = {Zainal Fithri, HH and Samsulrizal, NH and Mansor, NN and Hamzah, N and Abu Halim, NH and Ridzuan, MSM and Abdullah, A and Abdul Rahim, NAS and Abdul Hamid, AA},
title = {Unveiling Complete Genome of Streptococcus agalactiae from Malaysian Aquaculture: A Closer Look at Molecular Characteristics and Phylogenomic.},
journal = {Marine biotechnology (New York, N.Y.)},
volume = {28},
number = {3},
pages = {},
pmid = {42250117},
issn = {1436-2236},
support = {P21300040170502//12th Malaysia Plan budget: R&D of Fish Health Programs in Aquaculture/ ; },
abstract = {Streptococcus agalactiae (Group B Streptococcus, GBS) is a significant pathogen in aquaculture worldwide and is responsible for high mortality in farmed fish. Despite its regional impact, complete genome data from Malaysian isolates remain scarce. In this study, we report the first complete genome of a Malaysian S. agalactiae isolate, SA2BKE, derived from infected tilapia. Using Oxford Nanopore long-read sequencing, we assembled a 2.03 Mb circular complete genome of S. agalactiae. The functional annotation revealed 1,970 protein-coding genes and 108 RNA genes. Several antimicrobial resistance genes, including tet(M), mreA, and mprF, are associated with resistance to tetracyclines, macrolides, and peptides, respectively. Notably, there are 15 virulence-associated proteins involved in cell wall/membrane/envelope biogenesis. Multilocus sequence typing (MLST) identified SA2BKE as sequence type ST283, which has the potential to infect both fish and humans. Comparative phylogenomic analysis revealed 215 global strains positioned SA2BKE within a clade of other ST283 isolates from Asia and South America, suggesting potential transregional transmission. Pan-genome analysis identified 555 core genes shared among the analysed genomes, highlighting substantial genomic diversity within the species. Additionally, 14 mobile genetic element-associated regions were detected in SA2BKE, indicating potential genome plasticity and horizontal gene transfer events. These findings expand the genomic reference data for S. agalactiae isolates from Malaysia, contributing to regional surveillance efforts across Southeast Asia and supporting integrated disease management strategies in aquaculture.},
}

@article {pmid41634036,
year = {2026},
author = {Huang, L and Pu, YT and Zhao, YH and Sun, XY and Zhu, Y and Lu, YP and Leng, HX and Feng, J and Jin, LR and Sun, KP},
title = {Diet and environmental factors jointly drive the gut microbiome, resistome, and virulome of urban bats.},
journal = {NPJ biofilms and microbiomes},
volume = {12},
number = {1},
pages = {},
pmid = {41634036},
issn = {2055-5008},
support = {32430066//National Natural Science Foundation of China/ ; 32171525//National Natural Science Foundation of China,China/ ; },
mesh = {Animals ; *Chiroptera/microbiology ; *Diet ; *Gastrointestinal Microbiome ; Feces/microbiology ; *Bacteria/genetics/classification/drug effects/isolation & purification ; *Virulence Factors/genetics ; Anti-Bacterial Agents/pharmacology ; Environment ; Gene Transfer, Horizontal ; Female ; Genes, Bacterial ; Multiomics ; Drug Resistance, Bacterial ; },
abstract = {The coexistence and horizontal transfer of antibiotic resistance genes (ARGs) and virulence factor genes (VFGs) carried by urban wildlife represent an emerging form of biological pollution, constituting a significant threat to public health. We employed meta-omic approaches to evaluate the effects of host traits (sex, age, etc.), environmental factors (including geographical location and time), and diet (including food composition and antibiotic residues) on the bacterial, ARG, and VFG profiles of Vespertilio sinensis, an urban-dwelling bat. Our results demonstrate that the feces of V. sinensis harbor diverse ARGs and VFGs, but their genomic evidence for horizontal mobility in bacterial communities is limited. Notably, environmental changes over time and across geographical locations are associated with the ARG and VFG profiles, potentially due to the influence of pollutants in specific habitats. Dietary factors are associated with their dynamics through the microbiome, with antibiotic residues exerting selective pressure on ARG profiles. No significant impacts of sex, age, body size, and reproductive status on the gut microbiota, resistome, or virulome were observed. This study provides valuable insights into the ecological drivers of the gut microbiome, resistome, and virulome in bats, thereby contributing to our understanding of the public health risks associated with urban wildlife.},
}

Animals
*Chiroptera/microbiology
*Diet
*Gastrointestinal Microbiome
Feces/microbiology
*Bacteria/genetics/classification/drug effects/isolation & purification
*Virulence Factors/genetics
Anti-Bacterial Agents/pharmacology
Environment
Gene Transfer, Horizontal
Female
Genes, Bacterial
Multiomics
Drug Resistance, Bacterial

@article {pmid42248925,
year = {2026},
author = {Rodrigues, DLN and Sodrzeieski, PA and Parise, D and Benko-Iseppon, AM and Azevedo, V and de Castro Soares, S and Aburjaile, FF},
title = {GIPSy2: high-performance and scalable genomic island prediction software.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-53034-0},
pmid = {42248925},
issn = {2045-2322},
abstract = {Dealing with genomic mobility is a complex task for current predictors. With an increasing number of sequencing genomes, there is a constant demand for software that can handle multiple inputs. Considering this, we present the Genomic Island Prediction Software 2 (GIPSy2), a new version of well-established software for predicting bacterial genomic islands and mobilome. Statistical methods were used to provide the values associated with each prediction, such as Fisher's exact test, Support vector machine, and Logistic regression. The new version also improves scalability, allowing the simultaneous analysis of multiple genomes, and provides structured outputs to facilitate interpretation and reproducibility. Comparative analyses show that GIPSy2 achieves performance comparable to the original version under default settings, while offering increased flexibility through user-defined parameterization. These improvements make GIPSy2 a versatile tool for genomic island prediction across diverse bacterial datasets. GIPSy2 is currently available on Zenodo repository at https://zenodo.org/doi/10.5281/zenodo.10222587.},
}

@article {pmid42249169,
year = {2026},
author = {Dayrit, GB and Harun, AB and Karim, MR and Pambid, CPT},
title = {Phylogenetic Analysis of blaCTX-M and blaTEM Genes in E. coli from Hospital Wastewater.},
journal = {EcoHealth},
volume = {},
number = {},
pages = {},
pmid = {42249169},
issn = {1612-9210},
abstract = {Molecular surveillance of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli in environmental reservoirs is essential for understanding antimicrobial resistance (AMR) transmission within the One Health framework. This study aimed to characterize the genetic diversity and phylogenetic relationships of blaCTX-M and blaTEM genes in ESBL-producing E. coli isolated from hospital wastewater in Manila and Quezon City, Philippines. Seventeen isolates carrying blaCTX-M-1, blaCTX-M-9, and blaTEM-1 genes, confirmed by multiplex PCR, were subjected to DNA sequencing and phylogenetic analysis alongside global reference strains. Phylogenetic analysis of the blaCTX-M gene sequences revealed two distinct clusters: six blaCTX-M-15 variants clustered within the CTX-M-1 clade, showing close relatedness to strains from Thailand, Iran, and neighboring Southeast Asian clinical and environmental samples, while two blaCTX-M-27 clustered within the CTX-M-9 group, closely related to isolates from India, Australia, and Spain. All blaTEM-1 gene sequences aligned with globally disseminated TEM-1 references. The co-occurrence of multiple ESBL gene variants in individual effluent samples underscores active horizontal gene transfer facilitated by mobile genetic elements in wastewater environments. These findings reveal substantial genetic diversity of ESBL determinants and demonstrate the convergence of clinical and environmental AMR reservoirs through hospital effluents. Incorporating genetic surveillance of hospital wastewater into national AMR action plans can enhance detection of emerging resistance variants, inform risk assessment, and guide targeted interventions to mitigate environmental dissemination. Future work should integrate whole-genome sequencing to elucidate plasmid dynamics and resistance gene mobilization mechanisms, advancing One Health strategies to curb the AMR threat.},
}

@article {pmid42249518,
year = {2026},
author = {Alkemade, JA and Buddie, AG and Kermode, A and Barraclough, TG},
title = {Accessory regions and horizontal gene transfer shape the evolution of clonal Colletotrichum nymphaeae infecting strawberry.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.71314},
pmid = {42249518},
issn = {1469-8137},
support = {//Calleva Research Centre, Magdalen College, Oxford/ ; //John Fell Fund, University of Oxford/ ; },
abstract = {Rapid adaptation in fungal plant pathogens is often attributed to sexual recombination, yet many important pathogens are largely clonal. We investigated how genetic and phenotypic diversity arises in the predominantly asexual fungus Colletotrichum nymphaeae, the main cause of strawberry anthracnose in Europe and North America. We performed comparative genomics on 36 C. nymphaeae genomes and 45 other Colletotrichum genomes sampled from strawberry or from closely related species, assessing population structure, transposable element (TE) content, genome compartmentalisation and signatures of horizontal transfer, and linked these features to phenotypic variation and virulence. Colletotrichum nymphaeae consists of three major lineages, with a globally distributed clonal lineage showing high variability in morphology and virulence. Extensive variation in TE content was detected among and within lineages. Genomes are compartmentalised into core regions and TE-rich accessory regions (ARs) that cluster by lineage and are enriched for gene duplications, genes under relaxed selection and genes linked to stress, virulence and fungicide resistance. We identified a Starship element and a 2 kb region containing two effector genes that were horizontally acquired. TE-rich ARs and horizontal gene transfer drive diversification in this largely asexual pathogen, shaping its evolution and posing challenges for durable strawberry anthracnose management.},
}

@article {pmid42249519,
year = {2026},
author = {Hambücken, L and Baurain, D and Cornet, L},
title = {Exploring thylakoid emergence: evolution of membrane biogenesis and photosystem II assembly in early-diverging cyanobacteria.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.71284},
pmid = {42249519},
issn = {1469-8137},
support = {PDR T.0018.24 OR-OX-PHOT-IN-CYN//Belgian National Fund for Scientific Research (F.R.S.-FNRS)/ ; FRIAGrant: 2.5020.11//Belgian National Fund for Scientific Research (F.R.S.-FNRS)/ ; },
abstract = {Thylakoid membranes (TM) in cyanobacteria and chloroplasts host the light-dependent reactions of oxygenic photosynthesis. Gloeobacterales, the earliest-diverging cyanobacterial lineage, lack TM and perform photosynthesis in the cytoplasmic membrane (CM), representing an ancestral state relative to other cyanobacteria (Phycobacteria). This study investigates the evolutionary origin of TM. Phylogenomic analyses were performed across a phylogenetically diverse set of cyanobacteria, including extensive representation of basal lineages (Gloeobacterales, Thermostichales, Gloeomargaritales, and Pseudanabaenales), as well as micro- and macrocyanobacteria, using orthologous proteins involved in membrane dynamics and photosystem II (PSII) assembly, together with structural modeling using AlphaFold3. We identified two candidate proteins associated with membrane trafficking that may contribute to TM biogenesis, including the SPFH (Stomatin, Prohibitin, Flotillin, en HflK/C) family member Slr1106, proposed to have been acquired by lateral gene transfer. Analysis of 36 PSII assembly factors revealed modifications in late-stage assembly, notably in manganese homeostasis. Structural changes in the YidC translocase may have facilitated the relocation of linear electron transfer components from the CM to TM. Altogether, these phylogenetic and functional prediction analyses provide new insight into the molecular innovations that led to TM emergence, including membrane trafficking systems, PSII assembly changes, and protein targeting adaptations.},
}

@article {pmid41570365,
year = {2026},
author = {Zhu, S and Yu, F and Yang, B and Zhang, M and Zhang, H and Wang, Z and Liu, Y},
title = {Deciphering the roles of AcrAB-TolC efflux pump in promoting the transmission of antibiotic resistance.},
journal = {Drug resistance updates : reviews and commentaries in antimicrobial and anticancer chemotherapy},
volume = {85},
number = {},
pages = {101358},
doi = {10.1016/j.drup.2026.101358},
pmid = {41570365},
issn = {1532-2084},
mesh = {*Anti-Bacterial Agents/pharmacology ; Plasmids/genetics/metabolism ; *Membrane Transport Proteins/genetics/metabolism ; *Escherichia coli Proteins/genetics/metabolism ; Quorum Sensing/drug effects/genetics ; *Escherichia coli/genetics/drug effects/metabolism ; Chlorpromazine/pharmacology ; Gene Transfer, Horizontal ; *Drug Resistance, Multiple, Bacterial/genetics ; *Drug Resistance, Bacterial/genetics ; Conjugation, Genetic ; *Carrier Proteins/genetics/metabolism ; *Bacterial Outer Membrane Proteins/genetics/metabolism ; Gene Expression Regulation, Bacterial ; Lipoproteins ; ATP-Binding Cassette, Sub-Family C Proteins ; },
abstract = {Plasmid-mediated conjugative transfer drives the global dissemination of antimicrobial resistance, posing a global threat to public health. Besides extruding antibiotics, bacterial multidrug efflux pumps modulate virulence, yet their influence on resistance plasmid spread in antibiotic-free settings remains undefined. Herein, we demonstrate that the AcrAB-TolC efflux pump is critical for the horizontal transfer of model plasmid RP4-7 and diverse clinical resistance plasmids. Single deletions of acrA, acrB or tolC significantly reduce plasmid transfer, and complementation fully restores conjugative frequencies to control levels. Mechanistic investigations reveal that acrB deficiency reduces interbacterial contact, diminishes energy metabolism, and impairs activity of the glutamate decarboxylase, quorum sensing and the conjugative systems. Furthermore, we identify chlorpromazine as a potential AcrB ligand, which blocks plasmid transfer both in vivo and in vitro. Collectively, our findings reveal the role of efflux pumps in plasmid transfer and underscore AcrB as a druggable target to curtail the spread of antibiotic resistance.},
}

*Anti-Bacterial Agents/pharmacology
Plasmids/genetics/metabolism
*Membrane Transport Proteins/genetics/metabolism
*Escherichia coli Proteins/genetics/metabolism
Quorum Sensing/drug effects/genetics
*Escherichia coli/genetics/drug effects/metabolism
Chlorpromazine/pharmacology
Gene Transfer, Horizontal
*Drug Resistance, Multiple, Bacterial/genetics
*Drug Resistance, Bacterial/genetics
Conjugation, Genetic
*Carrier Proteins/genetics/metabolism
*Bacterial Outer Membrane Proteins/genetics/metabolism
Gene Expression Regulation, Bacterial
Lipoproteins
ATP-Binding Cassette, Sub-Family C Proteins

@article {pmid42242469,
year = {2026},
author = {Ren, Q and Ji, G and Huang, Y and Li, H and Dai, X},
title = {Identification of three phage lysozymes and their function in innate immunity of Mercenaria mercenaria.},
journal = {Fish & shellfish immunology},
volume = {},
number = {},
pages = {111490},
doi = {10.1016/j.fsi.2026.111490},
pmid = {42242469},
issn = {1095-9947},
abstract = {Phage lysozyme, a protein traditionally associated with bacteriophages, has recently been identified in certain molluscs, which is thought to be acquired through horizontal gene transfer. However, the immune functions of phage lysozyme genes in Mercenaria mercenaria remain unclear. In this study, three phage lysozyme genes, designated as MmpLyso1, MmpLyso2, and MmpLyso3, were identified from M. mercenaria. MmpLyso1 encodes a 154-amino-acid protein, while MmpLyso2 and MmpLyso3 encode proteins of 171 and 225 amino acids, respectively. Genomic structure analysis showed that MmpLyso1 lacks introns and contains a single exon, whereas MmpLyso2 consists of two exons and one intron, and MmpLyso3 comprises three exons and two introns. Protein domain prediction revealed that MmpLyso1 and MmpLyso3 possess a conserved phage lysozyme domain, while MmpLyso2 contains a signal peptide and a 1LWK|A domain. Phylogenetic analysis classified MmpLyso1-3 into two distinct subgroups. Tissue distribution analysis demonstrated that these three genes are widely expressed in multiple tissues of M. mercenaria, with the highest expression levels detected in the marginal zone of the mantle. Expression pattern analysis indicated that the transcriptional levels of MmpLyso1-3 in the mantle were significantly upregulated to varying degrees after stimulation. Furthermore, in vivo knockdown of each phage lysozyme gene individually led to a significant decrease in the bacterial clearance ability of M. mercenaria. Collectively, these findings demonstrate that MmpLyso1-3 play crucial roles in the innate immune defense of M. mercenaria, thereby providing novel insights into the function and evolutionary origin of phage lysozyme genes in molluscs.},
}

@article {pmid42243268,
year = {2026},
author = {Desai, D and Sharma, T and Gandham, N and Khopkar-Kale, P and Bharti, N and Kasibhatla, SM and Sonavane, U and Banerjee, R},
title = {Genomic characterization of multidrug-resistant Klebsiella pneumoniae clinical isolates from India.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-54711-w},
pmid = {42243268},
issn = {2045-2322},
abstract = {Klebsiella pneumoniae is an emerging global threat driven by rising antimicrobial resistance and the spread of hypervirulent lineages. To investigate its evolving genomic landscape in India, we characterized two clinical K. pneumoniae isolates, NG_299 and NG_300, obtained from a tertiary care hospital in Pune and analyzed them in the context of Indian and global isolate collections. Comprehensive phenotypic and genomic analyses were performed using antimicrobial susceptibility testing, Illumina NovaSeq whole-genome sequencing and PCR-based confirmation of resistance and virulence markers. Both isolates exhibited multidrug resistance, remaining susceptible to only a limited subset of tested antibiotics. NG_299 (ST231) was susceptible to amikacin, colistin, and trimethoprim/sulfamethoxazole, whereas NG_300 (ST20) was found to be susceptible only to colistin and trimethoprim/sulfamethoxazole. Genomic profiling revealed thirty-two resistance determinants in NG_299 and fifty-two in NG_300, both of which produce extended-spectrum β-lactamases. Carbapenem resistance was linked to metallo-β-lactamase activity and the presence of AmpC was confirmed by antimicrobial susceptibility testing and PCR in NG_300. Pan-genome resistome analysis of global isolates identified conserved core genes (CRP, PhoP, rpoB) and a sparse occurrence of AMR genes (NDM, CTX-M, KPC, OXA, mcr) associated with horizontal gene transfer. Notably, NDM and CTX-M were present in both study isolates, with OXA variants detected in NG_299. Distinct missense mutations within shared resistance genes highlighted independent evolutionary trajectories. Both isolates carried virulence factors associated with adhesion, biofilm formation, iron acquisition, and secretion systems, including siderophores. Plasmid analysis identified IncF replicons in both isolates and blaNDM-5 on an IncFII plasmid in NG_299. These findings document the circulation of multidrug-resistant K. pneumoniae in Pune and underscore the urgent need for strengthened genomic surveillance.},
}

@article {pmid42243567,
year = {2026},
author = {Wang, Z and Wang, L and Zhu, C and Yan, D and Cheng, Y and Ma, F and Yan, K and He, S},
title = {Virulence and antibiotic resistance characteristics of Pasteurella multocida from sheep: integrated genomic and phenotype analysis.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {6},
pages = {},
pmid = {42243567},
issn = {1573-0972},
support = {no. 31702306//National Natural Science Foundation of China/ ; },
abstract = {Pasteurella multocida (Pm), a ubiquitous Gram-negative bacterium, causes respiratory diseases that pose a significant threat to the livestock industry. In this study, we performed whole genome sequencing, biological characteristics analysis, comparative genomics, antimicrobial susceptibility testing, and pathogenicity assessment to comprehensively characterize a clinical Pm isolate (designated YPm; GenBank accession number CM129929.1) from sheep. The genome of YPm comprises 2,304,730 base pairs with a GC content of 40.3% and encodes 2,140 protein-coding genes, including 126 virulence factors and 57 antimicrobial resistance genes. Genomic analysis identified the toxA gene within a genomic island and prophage region, suggesting its potential acquisition through horizontal gene transfer. The phenotypic characteristics of YPm were consistent with the genomic predictions, including high metabolic capacity and intermediate resistance to lincomycin. Concurrently, comparative genomics revealed the distinctive genomic structure and evolutionary distinctions of YPm. Antimicrobial susceptibility testing revealed intermediate resistance to lincomycin and clindamycin, while demonstrating sensitivity to all other tested antibiotics. Infection experiments in mice demonstrated significant bacterial colonization in the liver and lungs, accompanied by tissue damage and inflammatory reaction. This study characterizes the high virulence and multiple predicted antimicrobial resistance genes of an ovine-derived Pm capsular serotype D strain, providing molecular insights to inform clinical prevention and control.},
}

@article {pmid42243673,
year = {2026},
author = {Fenclova, D and Hrazdilova, K and Coufalova, M and Ter Beek, J and Berntsson, RP and Zurek, L and Cihalova, K},
title = {Prolonged zinc exposure modulates biofilm metabolic activity and conjugation in Enterococcus faecalis.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05250-x},
pmid = {42243673},
issn = {1471-2180},
support = {IGA24-AF-IP-032//Ministerstvo Školství, Mládeže a Tělovýchovy/ ; 2023-02423//Svenska Forskningsrådet Formas/ ; },
abstract = {BACKGROUND: Zinc oxide (ZnO), including its nanoparticulate form (ZnONPs), is widely used in agriculture and accumulates in the environment, where it may impose sustained selective pressure on microbial communities. However, the impact of prolonged zinc exposure on horizontal gene transfer and conjugation dynamics in Enterococcus faecalis remains poorly understood.

RESULTS: We exposed Enterococcus faecalis OG1RF:pCF10 (donor) and OG1SSp (recipient) to prolonged zinc exposure (20 serial passages) and analyzed phenotypic and transcriptional changes associated with conjugation and virulence-related traits. Chronic exposure to ZnO and ZnONPs was associated with pronounced aggregation in the plasmid-carrying donor strain, reduced optical density values, and significantly lower recoverable CFU/mL at 24 h, although extensive clumping likely affected CFU recovery. Zinc exposure was also associated with increased metabolic activity within established biofilms, while gelatinase production and antibiotic susceptibility remained unchanged. ZnONP-adapted recipient cells showed a significant increase in conjugation frequency, whereas ZnO-adapted recipients and zinc-adapted donors showed non-significant upward trends. Notably, transcription of genes within the plasmid-encoded prgQ conjugation operon was increased even in the absence of exogenous pheromone stimulation. In contrast, short-term zinc exposure did not enhance plasmid transfer, indicating that increased conjugation required long-term adaptation rather than acute stress.

CONCLUSIONS: These findings indicate that prolonged zinc exposure is associated with altered aggregation, biofilm-associated metabolic activity, and conjugation dynamics in E. faecalis. However, the underlying mechanisms remain unresolved and may involve a combination of physiological, regulatory, and genetic adaptations arising from long-term exposure.},
}

@article {pmid42245496,
year = {2026},
author = {Satharasinghe, DA and Pellissery, AJ and Kariyawasam, S and Bommineni, YR and Simon, DA and Zhou, L and Abramzon, Y and Stanek, D and Denagamage, T},
title = {Integrative phenotypic and functional genomic characterization of virulence and antimicrobial resistance in Salmonella enterica isolates from reptiles.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1841627},
pmid = {42245496},
issn = {1664-302X},
abstract = {The popularity of reptiles as exotic pets has increased over the years. Reptiles can harbor zoonotic pathogens, including Salmonella, posing a significant public health risk. This study evaluated the diversity of hosts affected by non-typhoidal Salmonella infections in reptiles, as well as the antimicrobial resistance (AMR), multidrug resistance (MDR), and virulence factor (VF) genes in whole-genome, plasmid DNA, and RNA in Salmonella isolated from reptiles in Florida, United States. Data on Salmonella culture testing from 2018 to 2025, available at the Bronson Animal Disease Diagnostic Laboratory, were analyzed for host diversity in Salmonella infections. Functional genomic analysis was conducted using whole-genome sequences (WGS), plasmid DNA, and RNA obtained from selected Salmonella isolates, targeting AMR and VF genes. The Salmonella culture case positivity rate in reptiles was 16.41% during the study period. The highest positivity percentage was observed in the order Squamata (35%), which includes lizards, dragons, iguanas, and snakes, followed by the orders Testudines and Crocodilia (12.2%). The antibiotic susceptibility testing of 24 Salmonella enterica isolates revealed that 58.3% were MDR and specifically resistant to beta-lactams (62.5%), aminoglycosides (62.5%), and tetracyclines (8.3%). Genomic analysis confirmed phenotypic AMR and revealed the presence of 55 AMR genes, with the majority showing resistance to fluoroquinolones (18.2%), carbapenems and quinolones (16.4%), tetracyclines and rifamycins (14.5%), amphenicols (12.7%), and other classes. The presence of the tetA gene in both the genomic and plasmid DNA of a tetracycline-resistant isolate highlighted reptiles' role as stable zoonotic reservoirs for highly mobile genetic elements that can facilitate rapid horizontal gene transfer among pathogens. Transcriptomic analysis of isolates with MDR revealed differential expression patterns largely consistent with WGS analysis and identified additional AMR-related genes associated with MDR, efflux pumps, and membrane transport systems. A total of 239 VF genes were identified in isolates. Despite the health status of reptiles, the largest number of genes was associated with the Type III secretory system, invasion, motility, iron uptake, siderophore, fimbrial adherence, endotoxin, and lipopolysaccharides. Findings from this study underscore the importance of ongoing surveillance and improved hygiene practices when handling reptiles to reduce the risk of reptile-associated salmonellosis in humans.},
}

@article {pmid42245501,
year = {2026},
author = {Zhang, M and Yang, X and Li, R and Qian, J and Hao, R and Xu, L and He, Q and Shen, Z and Wang, J and Zhu, Y and Qiu, Z},
title = {A newly discovered Aerococcus urinae mediates transfer of the pCF10 plasmid via SPI-WT regulation.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1817926},
pmid = {42245501},
issn = {1664-302X},
abstract = {INTRODUCTION: Pheromone-regulated horizontal transfer serves as the core mechanism for horizontal gene transfer of antibiotic resistance genes, playing a pivotal role in driving the spread of resistance. Given the strict species-specific constraints of this regulatory system, it is imperative to determine whether novel regulatory signal peptides and cross-genus receptors responsive to these signals exist, thereby elucidating its potential for disseminating resistance across broader microbial communities.

METHODS: This study isolated and screened a Gram-positive coccus, Aerococcus urinae Ae1, from the gut microbiota, and confirmed that Ae1 can undergo intergeneric plasmid transfer with Enterococcus faecalis (E. faecalis), challenging the conventional understanding that the pCF10 plasmid spreads only within the same species.

RESULTS AND DISCUSSION: Results showed an intergeneric plasmid transfer frequency of (3.41 ± 0.26) × 10[-3] in Ae1, which increased to (7.97 ± 1.77) × 10[-3] upon exogenous addition of the cCF10 signal peptide, indicating cCF10's regulatory role in this process. Furthermore, the Ae1 signal peptide SPI-WT appeared to functionally resemble the cCF10 mechanism, possibly by acting on the prgZ/prgX pathway to promote pCF10 intergeneric transfer. This study suggests that Aerococcus urinae can acquire the pCF10 plasmid via intergeneric transfer and provides preliminary evidence that its endogenous signal peptide SPI-WT may play a regulatory role via the prgZ/prgX pathway. However, direct proof of natural secretion, physical binding, intracellular uptake, and relief of transcriptional repression is lacking; these remain important questions for future investigation. Nonetheless, our findings provide new insights into the dissemination pathways of intestinal antibiotic resistance genes.},
}

@article {pmid42246191,
year = {2026},
author = {Das, D and Dixit, R and Pandey, M},
title = {The Biliary Multi-Omics Landscape: Integrating Microbiome and Metabolomics in Gallbladder Carcinogenesis.},
journal = {Journal of gastroenterology and hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jgh.70462},
pmid = {42246191},
issn = {1440-1746},
abstract = {BACKGROUND: Gallbladder cancer (GBC) is a highly aggressive malignancy with a dismal prognosis, frequently diagnosed at advanced stages. While cholelithiasis is a primary risk factor, the role of the biliary microbiome and its metabolic products in driving carcinogenesis is increasingly recognized. This review synthesizes multi-omics data to elucidate the interplay between microbial dysbiosis and metabolomic shifts in GBC.

METHODS: A systematic literature search was conducted on PubMed (up to January 2026) focusing on biliary bacteria, the gut-bile axis, and multi-omics markers. A narrative synthesis integrated findings from metagenomic, metaproteomic, and metabolomic studies involving human cohorts and experimental models.

RESULTS: GBC is characterized by profound biliary dysbiosis, specifically the enrichment of Enterobacteriaceae, Streptococcus, and Helicobacter species. This taxonomic shift triggers a pro-carcinogenic metabolomic flux, where microbial 7α-dehydroxylation converts primary bile acids into secondary bile acids, such as deoxycholic acid (DCA), which induce DNA damage and promote tumor growth. Metaproteomic signatures identify bacterial proteins (e.g., QDR3, ompA) that facilitate biofilm formation and oxidative stress evasion. Furthermore, emerging paradigms like cross-species horizontal gene transfer (HGT) suggest that microbial genetic material can directly modulate host oncogenic pathways.

CONCLUSION: The GBC multi-omics landscape reveals a complex gut-bile axis where microbial and chemical factors converge. These integrated signatures offer potential as noninvasive biomarkers for early diagnosis and precision therapy.},
}

@article {pmid42247751,
year = {2026},
author = {Nabiabad, HS and Amini, M},
title = {Gene expression profiling of antibiotic resistance genes in multidrug-resistant bacteria in Northeast Syria: Evolving challenges in a conflict-affected region.},
journal = {Diagnostic microbiology and infectious disease},
volume = {116},
number = {3},
pages = {117498},
doi = {10.1016/j.diagmicrobio.2026.117498},
pmid = {42247751},
issn = {1879-0070},
abstract = {BACKGROUND: Conflict-affected regions represent under-characterized reservoirs for antimicrobial resistance (AMR), where healthcare disruption, population displacement, limited diagnostic capacity, and sustained antibiotic exposure may accelerate the emergence and dissemination of multidrug-resistant (MDR) pathogens. However, the molecular mechanisms underlying resistance gene regulation in Syria remain poorly characterized.

METHODS: We conducted a cross-sectional quantitative study in hospitals across Northeast Syria between June 2023 and September 2025. A total of 910 patients were screened for bacterial isolation and antimicrobial susceptibility testing. Representative multidrug-resistant isolates were subsequently analyzed using RT-qPCR to investigate transcriptional profiles of 273 resistance-associated genes across seven clinically important bacterial pathogens: Acinetobacter baumannii, Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, Enterococcus faecalis, Citrobacter freundii, and Staphylococcus aureus. Promoter regions of resistance determinants were sequenced to identify regulatory mutations.

RESULTS: Multiple resistance genes, including blaOXA-23, blaVEB-1, blaVIM, rmpA, blaSHV-1, GIM, and strB, demonstrated significantly elevated transcription in resistant isolates, whereas integron-associated genes, cfxA, and fosA showed no significant differences, potentially reflecting local antibiotic prescribing practices. Promoter analyses revealed recurrent base substitutions, notably a triple TG (TGTGTG) motif within the -18 region, consistent with enhanced transcriptional activity.

CONCLUSION: These findings indicate that sustained antibiotic pressure in conflict settings promotes promoter-level regulatory adaptations that enhance resistance gene expression. Such mechanisms may enable the persistence of multidrug resistance independent of ongoing horizontal gene transfer, highlighting the urgent need for context-specific antimicrobial stewardship in fragile healthcare systems.},
}

@article {pmid42247893,
year = {2026},
author = {Li, Z and Huang, J and Li, Y and Cao, F and Gao, X and Lin, Y and Li, Y},
title = {Type VI secretion system: Central regulator of antimicrobial resistance dynamics via indirect mechanisms.},
journal = {Microbiological research},
volume = {311},
number = {},
pages = {128574},
doi = {10.1016/j.micres.2026.128574},
pmid = {42247893},
issn = {1618-0623},
abstract = {Multidrug resistance (MDR) in bacteria poses a significant global threat to public health. Elucidating the core molecular regulatory mechanisms underlying MDR is crucial for developing novel intervention strategies. In Gram-negative bacteria, the phage-derived Type VI Secretion System (T6SS) functions as a versatile "molecular weapon". Beyond its classical role in interbacterial antagonism, T6SS acts as a key indirect regulatory hub for modulating bacterial antimicrobial resistance (AMR) in a strain-specific and environment-dependent manner. Although T6SS does not directly participate in the expression of antibiotic resistance genes (ARGs) or the catalytic activity of AMR-related enzymes, it profoundly influences the development and dissemination of AMR across strains and species through multiple indirect mechanisms. This review systematically analyzes four core T6SS-mediated mechanisms: (1) secretion of AMR-associated effectors and biofilm modulation to establish resistant phenotypes; (2) formation of synergistic regulatory networks with biofilm development, oxidative stress response, efflux pumps, and other secretion systems, which specifically enhances bacterial antibiotic tolerance (distinct from antibiotic resistance phenotypes); (3) acceleration of horizontal gene transfer (HGT) of ARGs through natural transformation, plasmid conjugation, and outer membrane vesicle (OMV)-mediated transport; (4) targeted interbacterial killing enabling antimicrobial-resistant strains to overcome colonization resistance, gain ecological advantages, and exacerbate clinical infections. Building on this framework, novel anti-AMR strategies targeting T6SS are outlined, including direct disruption of T6SS assembly and function, interference with upstream regulators (e.g., quorum sensing), optimization of CRISPR-Cas gene editing, and engineered T6SS-targeted delivery platforms. By dissecting the T6SS-driven AMR network and its clinical translational potential, this review provides a foundation for designing next-generation therapies to reverse AMR and block ARG transmission and also discusses existing bottlenecks limiting the clinical translation of T6SS-targeted therapies, while identifying critical future research directions such as deciphering species-specific mechanisms and enhancing targeted delivery efficiency.},
}

@article {pmid42248075,
year = {2026},
author = {Wang, Q and Wu, Q and Song, H and Liu, Q and Zou, L and Zhou, Q and Qiu, D and Wu, Z and Xiao, E},
title = {Cracking the trade-off in waste activated sludge valorization: A synergistic engineering framework integrating alkali-activated ammonium persulfate pretreatment for concurrent carbon recovery and antibiotic resistance risk control.},
journal = {Water research},
volume = {303},
number = {},
pages = {126226},
doi = {10.1016/j.watres.2026.126226},
pmid = {42248075},
issn = {1879-2448},
abstract = {Anaerobic fermentation (AF) of waste activated sludge (WAS) for short-chain fatty acid (SCFA) recovery holds significant resource potential. However, the pretreatment-driven enhancement of acidogenesis may inadvertently alter the occurrence and dissemination risks of antibiotic resistance genes (ARGs), whose net effects and dominant mechanisms remain poorly understood. Therefore, an alkali-activated ammonium persulfate (AP/Alk) pretreatment-AF system was constructed to elucidate ARG fate alongside SCFA promotion. Results showed that AP/Alk achieved a maximal SCFA yield of 5001.8 mg COD/L and increased total ARG abundance by 57.2%, while simultaneously curbing the horizontal gene transfer (HGT) risk of ARGs. Mechanistically, AP/Alk synergy shifted dissolved organic matter (DOM) from lignin-like toward more bioavailable protein/amino-sugar, carbohydrates and lipids. This restructuring favored hydrolytic and acidogenic bacteria, specific lineages of which served as ARG hosts. Crucially, mobile genetic elements (MGEs) decreased by 26.9% alongside widespread downregulation of type IV secretion systems (T4SS), effectively decoupling ARG enrichment from HGT potential. Network analysis and partial least squares path modeling confirmed that DOM restructuring reshaped the microbial community and activated metabolism, creating a cascade effect that promoted SCFA accumulation while driving ARG enrichment primarily via vertical gene transfer (VGT) during host proliferation. Accordingly, a retrofittable engineering route integrating pretreatment, AF, and solid-liquid separation is proposed. Beyond this specific configuration, future system design should shift its objective from maximizing product yield under acceptable risk to achieving the greatest net risk reduction and net resource recovery per unit of carbon footprint or cost, a life-cycle perspective essential for advancing circular and low-carbon wastewater infrastructure.},
}

@article {pmid42248101,
year = {2026},
author = {Xu, Z and Zhang, L and Zhu, D and Zhi, S and Ashbolt, NJ and Li, G and Luo, W and Nghiem, LD},
title = {Optimising composting to reduce plasmid and integrative conjugative element conjugation to minimise antibiotic resistomes in livestock manure for safe organic fertilisation.},
journal = {Journal of hazardous materials},
volume = {514},
number = {},
pages = {142573},
doi = {10.1016/j.jhazmat.2026.142573},
pmid = {42248101},
issn = {1873-3336},
abstract = {Antimicrobial resistance is a critical threat to organic fertilizer production from livestock manure by composting. This study provides new insights to the dynamics of antimicrobial resistance genes (ARGs) during composting to propose strategies for their elimination. Results from genome-resolved metagenomics, meta-analysis, and quantitative assessment showed temperature and moisture content as key factors governing ARG dynamics during composting. Although integrative conjugative elements (ICE) could be transferable by some thermophilic bacteria, composting temperature to above 60 °C reduces mobile ARGs driven by plasmid conjugation for elimination. Further controlling moisture content to low than 60% inhibits the secretion of extracellular polymeric substances to restrain ARG rebound by ICE conjugation, particularly at the maturation stage of composting. These results are significantly useful for China, where swine manure accounted for most of livestock manure-derived ARGs (91.5%). Applying findings from this study to optimise the composting of livestock manure could reduce ARG proliferation by up to 59.3% in China.},
}

@article {pmid42248139,
year = {2026},
author = {Yuan, J and Zhang, X and Li, S and Wang, K and Sun, Y and Luo, M and Su, Y and Kou, Q and Liu, C and Yu, Y and Li, R and Wang, L and Li, X and Chu, K and Xiang, J and Li, F},
title = {Deep-sea megafauna co-opts microbial energy metabolism genes to withstand ultra-long starvation.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2026.05.012},
pmid = {42248139},
issn = {1097-4172},
abstract = {The deep-sea supergiant isopod is renowned for surviving over 5 years without food, which is a crucial adaptive trait for megafauna inhabiting extreme environments. Here, morphological, physiological, and genomic comparisons of deep-sea isopods reveal a dual adaptive strategy underlying this trait: a distended, food-retentive stomach that enables episodic hyperphagia and a markedly reduced basal metabolic rate (BMR). Notably, central to this adaptation is the ancient horizontal acquisition of the microbial energy metabolism-related gene ND1, which thereafter achieved significant dosage enhancement via post-transfer duplication and ultra-high expression that is specifically regulated by histone acetylation at its promoter. Functional assays in transgenic zebrafish, nematodes, and cell lines demonstrate that ND1 reduces BMR by downregulating endogenous energy-production genes and thus extends starvation survival under cold-induced metabolic suppression. These findings uncover an exceptional evolutionary strategy whereby deep-sea megafauna co-opts and epigenetically optimizes exogenous microbial genes to reconcile the metabolic conflict between energy-demanding gigantism and extreme energy limitation.},
}

@article {pmid42248261,
year = {2026},
author = {Qi, H and Ruan, C and Yuan, MM and Byeon, H and Liao, J and Zhu, L and Yu, P},
title = {Longitudinal transcriptomic insights into microbial aggregation, trophic cooperation, and genomic adaptation during algal-bacterial granular sludge formation.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135082},
doi = {10.1016/j.biortech.2026.135082},
pmid = {42248261},
issn = {1873-2976},
abstract = {Microbial aggregates such as algal-bacterial granular sludge (ABGS) rely on tightly coordinated microbial interactions to maintain structural stability and functional performance. Despite the significance of co-assembly of phototrophs and heterotrophs in ABGS systems, the ecological and genomic succession during their formation remains poorly understood. Here, time-series multi-omics analysis was conducted to track the dynamic shifts in microbial interactions during ABGS maturation. The granulation process entailed the establishment of extensive cross-phylum nutrient exchange networks between Cyanobacteria and core heterotrophs (e.g., Pseudomonadota and Bacteroidota). Concurrently, metatranscriptomic profiling revealed a significant upregulation of genes associated with biofilm formation (e.g., rpoS, glgC, and cysE) and quorum sensing processes (e.g., yidC and secG) in Cyanobacteria as ABGS stabilized. Furthermore, the spatial densification and metabolic stabilization were accompanied by distinct shifts in community evolutionary strategies: the enrichment of energetically costly antiviral defense systems (R[2] = 0.65, P < 0.05) but decreased frequency of horizontal gene transfer (HGT). Additionally, analyses of public datasets confirmed that these structural, metabolic, and genomic patterns were conserved across diverse structured algal-bacterial communities. Collectively, our findings demonstrate how physical aggregation, trophic cooperation, and genomic adaptation co-evolve during ABGS formation, providing new insights into the ecological principles governing engineered ecosystems.},
}

@article {pmid42248870,
year = {2026},
author = {Vasquez, YM and Romero, MF and Bowers, RM and Rohwer, RR and McMahon, KD and Woyke, T and Schulz, F},
title = {Vicennial metagenomic time series unveils evolutionary dynamics of giant viruses in a freshwater ecosystem.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-73437-x},
pmid = {42248870},
issn = {2041-1723},
support = {DE-AC02-05CH11231//DOE | Office of Science (SC)/ ; },
abstract = {Giant viruses play crucial ecological roles in aquatic ecosystems, yet their evolutionary dynamics in response to environmental changes, particularly in freshwater environments, are not well understood. We analyzed a 20-year time series (2000-2019) of 471 co-assembled metagenomes from Lake Mendota (USA) to reconstruct 1512 giant virus metagenome-assembled genomes, providing insights into viral genome evolution. Viruses in the order Imitervirales dominate the virome, remaining consistent across seasons and years. Our findings reveal gene duplication (23% of genes) and horizontal gene transfer (29% of genes) as key drivers of genomic innovation. A co-occurrence network analysis indicates increased virus-host interactions following the introduction of an invasive predatory zooplankton in 2009, highlighting potential hosts in Bigyra, Perkinsea, and Euglenozoa. While single nucleotide polymorphism analysis shows predominantly purifying selection in viral genes, there is a significant increase in positively selected genes post-invasion, particularly those related to infection. Comparative evolutionary analyses reveal that giant viruses exhibit genome-wide substitution rates similar to co-occurring bacteria but significantly slower than smaller dsDNA phages, suggesting both stability and adaptability. Our study demonstrates that freshwater giant viruses employ various evolutionary strategies to respond to environmental change. These results underscore their significant yet often underappreciated role in freshwater ecosystem dynamics.},
}