@article {pmid42466126,
year = {2026},
author = {Bhure, M and Shukla, N and Purohit, H and Patel, N and Chavda, P and Mistry, M and Shingala, H and Solanki, B and Shah, C and Joshi, M and Joshi, C and Bagatharia, S and Pandit, R},
title = {Genome-wide investigation of outbreak-associated Vibrio cholerae in Gujarat, India identifies antimicrobial resistance genes, virulence determinants, and mobile genetic elements.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1851551},
pmid = {42466126},
issn = {1664-302X},
abstract = {This study investigates the 2024 cholera outbreak in Gujarat, India, utilizing combined whole-genome analysis of clinical Vibrio cholerae isolates and wastewater surveillance. A total of, 69 V. cholerae isolates were recovered from affected patients, predominantly belonging to the O1 serogroup (51 isolates). Antimicrobial susceptibility test (AST) of 34 isolates revealed complete resistance to ampicillin and partial resistance to cotrimoxazole, whereas all isolates were susceptible to doxycycline, ciprofloxacin, chloramphenicol, tetracycline, and gentamicin. Whole-genome sequencing of 20 selected isolates revealed that the isolates belong to the seventh pandemic El Tor (7PET) lineage, sequence type ST69. Phylogenomic analyses using a multi-method approach, core genes, Composition Vector (CV) Tree, SNPs, and multilocus sequence typing (MLST) showed tight clustering with limited diversity among the isolates. All isolates contained 13-15 antimicrobial resistance genes, with high consistency between genotype-phenotype for most antibiotics, although discordance was observed for ciprofloxacin, cotrimoxazole, and chloramphenicol. Sixteen genes were identified as virulence factors, and 11 isolates also had ctxA/ctxB. All isolates also had two to four integrative conjugative elements (ICEs) containing antimicrobial resistance genes (ARGs) and important Vibrio cholerae pathogenicity islands (VPI-1, VPI-2) and Vibrio cholerae seventh pandemic islands (VSP-1, VSP-2). The pangenome analysis highlights extensive genomic flexibility within species, likely driven by horizontal gene transfer and ecological adaptation; however, further outbreak-specific investigations are required to determine their direct role in current outbreak. The detection of ctxA-positive signals in wastewater, 20% (28/140) of the samples, suggests a possible surveillance signal during the outbreak. These results highlight the presence of antimicrobial-resistant 7PET O1 El Tor strains in Gujarat outbreaks and support continued genomic monitoring to guide focused public health interventions in endemic areas. Furthermore, this study also underscores the importance of wastewater surveillance for monitoring V. cholerae.},
}

@article {pmid42454225,
year = {2026},
author = {Kafaie, S and Naseri, S and Mahoney, DBJ and Gagie, T and Beiko, RG and Maguire, F},
title = {Sarand: exploring antimicrobial resistance gene neighbourhoods in complex metagenomic assembly graphs.},
journal = {NAR genomics and bioinformatics},
volume = {8},
number = {3},
pages = {lqag066},
pmid = {42454225},
issn = {2631-9268},
mesh = {*Metagenomics/methods ; *Drug Resistance, Bacterial/genetics ; *Software ; Humans ; },
abstract = {Antimicrobial resistance (AMR) is a major global challenge to human and animal health. The genomic element (e.g. chromosome, plasmid, and genomic islands) and neighbouring genes associated with an AMR gene play a major role in its function, regulation, evolution, and propensity to undergo lateral gene transfer. Therefore, characterizing these genomic contexts is vital for effective AMR surveillance, risk assessment, and stewardship. Metagenomic sequencing is widely used to identify AMR genes in microbial communities but fragmentary short-read data do not directly provide this critical contextual information. Assembly of these reads provides some contextual information but fails to recover many mobile genetic elements. Here, we introduce Sarand, a method retaining some of the sensitivity of read-based methods while providing the genomic context of assembly by extracting AMR genes and their associated context directly from metagenomic assembly graphs. Sarand uses BLAST-based homology searches with coverage statistics to identify and visualize AMR gene contexts while filtering false chimeric contexts. Using both real and simulated metagenomic data, we show that Sarand outperforms metagenomic assembly and other recently developed graph-based tools in terms of precision and sensitivity for this problem. Sarand enables effective extraction of metagenomic AMR gene contexts to better characterize AMR evolutionary dynamics within complex microbial communities.},
}

*Metagenomics/methods
*Drug Resistance, Bacterial/genetics
*Software
Humans

@article {pmid42455014,
year = {2026},
author = {Wiltbank-Chau, LB and Cohen, JI and Burdett, DS and Larson, B and Khadka, P and Peterson, TR and Kehoe, DM},
title = {Multispectral regulation of chromatic acclimation by integration of the Rca system and the conserved dpx operon.},
journal = {Journal of bacteriology},
volume = {},
number = {},
pages = {e0002326},
doi = {10.1128/jb.00023-26},
pmid = {42455014},
issn = {1098-5530},
abstract = {Type III Chromatic Acclimation (CA3) in Fremyella diplosiphon has traditionally served as a model for cyanobacterial acclimation to red and green light. CA3 is controlled by the red-green responsive Rca phosphorelay system, including the cyanobacteriochrome RcaE. However, regulation of pigmentation persists in the absence of RcaE, which is attributed to the Cgi system. Nothing is known about how the Cgi regulatory system senses light color to differentially regulate pigment expression. DpxA is a teal/yellow-sensing cyanobacteriochrome that regulates cell pigmentation through an unknown regulatory pathway. Here, we show that DpxA and RcaE collectively control the vast majority of chromatic acclimation across the visible spectrum, implicating DpxA as the likely sensor for the Cgi system. The genetic context of DpxA is identified as part of a 3-gene operon alongside a response regulator (DpxB) and a hybrid histidine kinase (DpxC). The impact of the Dpx proteins is modulated by the RcaE-mediated genetic background, suggesting an integrated sensory response by the Dpx and Rca pathways. Beyond mechanistic insights, phylogenomic analysis reveals that the dpx operon is conserved across distantly related cyanobacterial species, including those incapable of CA3. These findings suggest the dpx operon was distributed via horizontal gene transfer, likely providing cell adaptation to diverse environmental niches through regulation of processes beyond color acclimation.IMPORTANCEThe ability to accurately sense and integrate multiple environmental cues is fundamental to bacterial behavior and survival. Type III Chromatic Acclimation (CA3) in Fremyella diplosiphon is an ideal model for signal integration because of its well-defined light cues, numerous predicted photoreceptors, and reliable physiological output. This study reveals that CA3 is governed by an interconnected, multispectral sensory network. We demonstrate that the conserved dpxABC operon-and its sensor DpxA-integrates with the Rca pathway into a coordinated acclimation response. Furthermore, the dpx operon is conserved across phylogenetically distant cyanobacteria, suggesting physiological benefits beyond CA3. These findings underscore the complexity of prokaryotic light signal integration, wherein multiple cues are synthesized into cohesive physiological responses.},
}

@article {pmid42456506,
year = {2026},
author = {Rincón-Gracia, M and Rosendal, T and João Silva, M and Lood, R and Woksepp, H and Bonnedahl, J},
title = {Bacterial SOS response as a potential driver of antibiotic resistance gene transfer in wastewater.},
journal = {Environmental research},
volume = {306},
number = {Pt 2},
pages = {125256},
doi = {10.1016/j.envres.2026.125256},
pmid = {42456506},
issn = {1096-0953},
abstract = {Wastewater treatment plants have been highlighted numerous times as hotspots for anthropogenic environmental pollution with antibiotic resistance genes and resistant bacteria. However, demonstrating horizontal gene transfer events in these environments has been challenging. The role of SOS response, that has been shown to promote horizontal gene transfer through other mechanisms such as transduction, is often overlooked. In the present study, we evaluated whether SOS response could be induced in influent and effluent samples from wastewater treatment plants and compared them to reference points and samples upstream and downstream of the wastewater treatment plants. Our results demonstrate that influent samples from three Swedish wastewater treatment plants could induce SOS response to a higher level than mitomycin C at 0.5 ng/ml in a reporter E. coli strain. While bacteriophage induction was not directly measured, SOS response induced at such concentrations of mitomycin C has been previously demonstrated to induce latent bacteriophages in E. coli. Bacteriophages can mobilize antibiotic resistance genes and facilitate genetic exchange between bacteria, serving as vehicles for horizontal gene transfer of antibiotic resistance genes in wastewater environments. These results suggest that SOS response could play an important role for the spread of antibiotic resistance genes in wastewater. Consequently, establishing pre-treatment strategies for wastewater may be beneficial to prevent genetic exchange between environmental bacteria and human and animal pathogens.},
}

@article {pmid42458587,
year = {2026},
author = {Shimasaki, T and Nose, Y and Masuda, S and Shibata, A and Shoji, T and Yabe, S and Furubayashi, M and Kikuchi, Y and Shirasu, K and Yazaki, K and Ichihashi, Y and Sugiyama, A and Nakano, RT},
title = {Horizontal acquisition of nicotine catabolism gene cluster enhances Arthrobacter fitness within tobacco root microbiota.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02466-x},
pmid = {42458587},
issn = {2049-2618},
support = {22KJ3147//Japan Society for the Promotion of Science/ ; 22K21367//Japan Society for the Promotion of Science/ ; },
abstract = {BACKGROUND: Plant roots are hotspots for interactions with soil microbes, where a characteristic bacterial community structure is formed. Plant specialized metabolites often play pivotal roles in this assembly process. However, the molecular basis underlying root microbiota responses to these bioactive compounds, and how such metabolic interactions shape the assembly of host-specific root microbiota, remain largely unknown. Nicotine is a toxic alkaloid predominantly produced by the genus Nicotiana, and the genus Arthrobacter is known as one of the nicotine-degrading bacteria in the tobacco root microbiota. In this study, we used the tobacco-Arthrobacter interaction system as a model and integrated comparative genomics and experimental genetic manipulation assays to uncover the role of bacterial catabolism capacity for host specialized metabolites in shaping host-specific root microbiota.

RESULTS: Nicotine catabolism genes are uniquely found in the Arthrobacter strains derived from nicotine-containing environments, and this restricted gene distribution is driven by a plasmid-mediated horizontal gene transfer. To assess the ecological consequences of this genomic adaptation in Arthrobacter fitness in tobacco roots, we characterized the nicotine utilization ability of Arthrobacter and conducted adaptation assays under in planta conditions using genetically manipulated Arthrobacter strains and tobacco mutants impaired in nicotine catabolism and biosynthesis, respectively. Nicotine improves Arthrobacter colonization of tobacco roots through a catabolism-dependent mechanism. Bacterial community analysis using a synthetic community approach further demonstrated that this metabolic adaptation enhances Arthrobacter fitness within tobacco root microbiota.

CONCLUSIONS: Our findings illustrated that bacterial catabolic capacity toward host-derived plant specialized metabolites is key for successful root colonization. This metabolic adaptation is driven by plasmid-mediated horizontal gene transfer and ultimately shapes the structure of the root microbiota community. Video Abstract.},
}

@article {pmid42461028,
year = {2026},
author = {Kathol, M and Barton, Q and Immethun, C and Saha, R},
title = {Performance of the pBHR1 mobilization protein MobV and its role in stable plasmid expression in Rhodopseudomonas palustris CGA009.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0381925},
doi = {10.1128/spectrum.03819-25},
pmid = {42461028},
issn = {2165-0497},
abstract = {UNLABELLED: Mobilizable plasmids are typically used in metabolic engineering studies, especially for their small size, to express heterologous proteins in new host organisms to manipulate their metabolism. Rhodopseudomonas palustris is a non-model soil bacterium of interest that is well-known for its extensive metabolic versatility, being able to accumulate a wide range of industrially relevant bioproducts, such as polyhydroxybutyrate, n-butanol, hydrogen, and other lignin-derived compounds. However, many of these non-model organisms are more genetically recalcitrant, and the rules of genetic stability, or even plasmid stability, can change drastically from organism to organism. This study investigates the effects of pBHR1's native mobilization protein, MobV, on the retention of pBBR1 origin plasmids in R. palustris, and the effects of supercoil regulation on both plasmid stability, as well as plasmid-based gene expression. Mobilization proteins participate in horizontal gene transfer between bacterial species. Through two functional assays, a relaxation and a conjugation assay, we determine that the relaxation mechanism is similar to a previously annotated mobilization protein, MobM, and confirm that R. palustris is able to participate in conjugation using its two native type IV secretion systems, respectively. Using flow cytometry, we determine that mutations to various homologous active sites deleteriously impact plasmid expression. Finally, through RT-qPCR, we also determine that the presence of the mobilization protein confers a large positive effect on copy number, where its absence reduces the copy number from 44.27 ± 2.00 copies per cell to 22.86 ± 0.63.

IMPORTANCE: Plasmid instability remains a major barrier to genetic engineering in non-model gram-negative bacteria, such as Rhodopseudomonas palustris. During previous efforts to optimize plasmid vectors for this species, we observed rapid post-transformation unstable plasmid-based expression when using a minimized pBHR1 backbone lacking the native mobilization protein MobV. Restoring MobV eliminated this instability, suggesting an uncharacterized role in plasmid maintenance. In this study, we systematically dissect the contribution of MobV to plasmid expression in R. palustris by performing site-directed mutagenesis for several histidine residues. By comparing MobV to the well-characterized relaxase MobM, and generating active-site mutants, we link specific catalytic residues to plasmid persistence, stable genetic expression, and MobV activity. These findings clarify a previously overlooked mechanism of plasmid maintenance in R. palustris and provide design principles for constructing stable, high-performing vectors in non-model gram-negative hosts. This work therefore supports more reliable metabolic engineering strategies in organisms of growing biotechnological interest.},
}

@article {pmid42462268,
year = {2026},
author = {Ajose, DJ and Adetoyinbo, II and Tchatchouang, CK},
title = {Genomic mining of Bacillus safensis and Enterococcus lactis from food sources.},
journal = {Letters in applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/lambio/ovag061},
pmid = {42462268},
issn = {1472-765X},
abstract = {The growing complexity of food-safety systems and the increasing emergence of multidrug-resistant (MDR) foodborne pathogens demonstrate the importance of enhanced genomic surveillance. This study employed whole genome sequencing (WGS) to characterise the genomes of Bacillus safensis NWU MK_WT, Enterococcus lactis ENT7_CNKT_NWU, and ENT3_CNKT_NWU, isolated from food sources. Phenotypic antibiotic susceptibility testing revealed that all strains displayed MDR phenotypes, with resistance to erythromycin, ampicillin, and meropenem. Genome assemblies ranged from 2.6 to 3.7 Mb, exhibiting high completeness (100%) and diverse functional gene profiles. Furthermore, antibiotic resistance genes (ARGs), including vanT and aac(6'), mediating antibiotic inactivation, efflux, and target modification, were identified. Virulence factors, including adhesion, invasion, and biofilm formation, were detected across genomes, indicating pathogenic potential. Mobile genetic element profiling revealed the presence of insertion sequences, plasmids, and an intact prophage in B. safensis NWU MK_WT, demonstrating genomic plasticity and the potential for horizontal gene transfer (HGT). Phylogenomic comparison showed close relatedness between the isolates and strains from Asia, suggesting possible transboundary movement of genetic material. These findings highlight the growing relevance of WGS for monitoring opportunistic foodborne bacteria that harbour and disseminate resistance and virulence determinants, provide foundational data for improving food safety surveillance, and support antimicrobial resistance mitigation strategies.},
}

@article {pmid42462719,
year = {2026},
author = {Michoud, G and Geers, A and Peter, H and Thorpe, AC and Zhong, ZP and Rich, V and Battin, TJ},
title = {Evolutionary radiation of Polaromonas from mountain glaciers downstream.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2026.06.070},
pmid = {42462719},
issn = {1879-0445},
abstract = {Habitat transitions are central to microbial ecology and evolution and have been extensively studied across vastly different environments, such as between saline and non-saline environments. However, microbial habitat transitions along other large-scale environmental gradients remain poorly studied. This is particularly true for transitions involving the cryosphere, despite building evidence suggesting the Cryogenian as important for evolutionary radiation. Here, we investigated ecosystem transitions and the related genomic adaptations of the cosmopolitan cryospheric Polaromonas bacterium. We constructed a pangenome from 282 high-quality genomes, sourced from glaciers, glacier-fed streams (GFSs), lakes, wetlands, groundwater, rivers, and soils. Phylogenetic reconciliation suggested that the ancestral Polaromonas genome radiated from glacier ecosystems into various downstream environments through multiple independent transitions. These transitions were likely marked by extensive horizontal gene transfer and gene loss, with mobile genetic elements such as plasmids and prophages playing key roles in genomic diversification. Predicted ancestral genomes encoded versatile metabolic and stress-response capacities, which support adaptation to fluctuating and extreme conditions in the various cryospheric habitats. Compared to the ancestral Polaromonas genome, distinct genomic signatures were associated with specific habitats: GFS lineages possess expanded stress-tolerance repertoires, glacier lineages gained chemolithotrophic and anaerobic pathways, lake and wetland genomes acquired phototrophic functions, and soil lineages expanded substrate transport and stress tolerance. Together, our findings highlight the role of genomic plasticity in the ecological success of Polaromonas and also underscore the cryosphere as a potential evolutionary cradle from which lineages dispersed and adapted to downstream aquatic and terrestrial environments.},
}

@article {pmid42464129,
year = {2026},
author = {Yalçın, S and Ünlü Çelebi, S and Yıldız, SRO and Kurt Azap, Ö and Şahintürk, H and Üsküdar Güçlü, A},
title = {Genomic analysis reveals multi-lineage carbapenem-resistant Pseudomonas aeruginosa mimicking a hospital outbreak.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05421-w},
pmid = {42464129},
issn = {1471-2180},
support = {KA24/445//Baskent Üniversitesi/ ; },
abstract = {BACKGROUND: Pseudomonas aeruginosa is a major cause of nosocomial infections, often exhibiting multidrug resistance (MDR) and high genetic adaptability. This study investigated temporal cluster of MDR P. aeruginosa isolates obtained from five different hospitalized patients within a single healthcare facility. The isolates shared similar antimicrobial resistance patterns, suggesting a common source or transmission event. However, pulsed-field gel electrophoresis (PFGE) genotyping identified four distinct clones, indicating clonal heterogeneity rather than a single-strain outbreak. To further elucidate the genetic basis of resistance, virulence, and genomic diversity, whole-genome sequencing (WGS) was performed.

RESULTS: All the isolates were resistant to cefepime, ceftazidime, meropenem, ciprofloxaxin, levofloxaxin, piperacillin-tazobactam; three of them were susceptible to amikacin, and all were susceptible to colistin. Resistome analysis revealed a diverse array of antimicrobial resistance genes, including chromosomal class C (blaPDC-16/37/374) and D (blaOXA-50 family:395/847/848/906) and blaVIM-2 type β-lactamases, and a wide variety of efflux pumps (such as MexAB-OprM, MexCD-OprJ MexGHI-OpmD, MexJK-OprM, MexMN-OprM, MexPQ-OpmE, MuxABC-OpmB). Virulome analysis identified key pathogenicity determinants related to biofilm formation, adherence, motility, immune evasion, toxin and other virulence traits. Multiple mobile genetic elements were determined, suggesting horizontal gene transfer (HGT) as a significant factor in the dissemination of resistance traits.

CONCLUSION: These findings demonstrate that nosocomial outbreak-like event of MDR P. aeruginosa can involve multiple unrelated clones co-circulating within the same hospital environment, challenging traditional epidemiological assumptions. Despite a high degree of core genome synteny and similar resistance profiles, the identification of four distinct clones among simultaneous patient cases indicates that the outbreak was not caused by a single strain. These results further emphasize the potential for multiple co-circulating clones in MDR P. aeruginosa outbreaks and challenge assumptions of single-source transmission. Whole-genome sequencing plays a critical role in understanding transmission dynamics and guiding infection control strategies.},
}

@article {pmid42465056,
year = {2026},
author = {Li, Q and Chen, M and Lu, Y and Xu, C and Zheng, Y and Zeng, Z and Xu, D and Qin, W and Zhang, Y},
title = {Close spatial and metabolic association between heterotrophic and ammonia-oxidizing marine Nitrososphaerota.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag173},
pmid = {42465056},
issn = {2730-6151},
abstract = {Following the ubiquitous autotrophic ammonia-oxidizing archaea (AOA), heterotrophic representatives of the marine Nitrososphaerota (HMN) form the second most abundant group within this archaeal phylum. However, their eco-evolutionary strategies remain poorly understood. Previous studies have reported a consistent co-occurrence of HMN with marine AOA (MAOA), prompting a detailed investigation into their potential interaction. Through large-scale (meta)genomic and metatranscriptomic analyses, we reveal that HMN possess ultra-streamlined genomes and globally co-occur with marine AOA. The absence of most B vitamin biosynthesis pathways, incomplete citrate cycle and glycolysis, along with the essential requirement for exogenous amino acids, suggest their potential metabolic dependency on AOA. Meanwhile, catalyzed reporter deposition fluorescence in situ hybridization supports a close physical association between HMN and AOA. The nearly synchronous origins of HMN and AOA after oxygen rise, coupled with HMN's dispersive microhabitats (evidenced by dense, shallow subclades) and extensive horizontal gene transfer between these groups, further support their close relationship-although HMN likely acquired heterotrophic capabilities from bacteria. This study reveals a previously unrecognized association between HMN and AOA, implying a tight coupling between autotrophic and heterotrophic processes in deep-sea habitats.},
}

@article {pmid42465062,
year = {2026},
author = {Firrincieli, A and Broglia, G and Rizzo, G and Greggio, N and Ghezzi, D and Barosa, B and Sauro, F and Cappelletti, M},
title = {Genomic evidence for aerotrophy as a defining trait of Ktedonobacteria inhabiting silica-rich oligotrophic caves.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag175},
pmid = {42465062},
issn = {2730-6151},
abstract = {Members of the class Ktedonobacteria (phylum Chloroflexota) are widespread across various terrestrial environments, including oligotrophic caves, although the genomic basis underlying this distribution remains unclear. Here, we present a systematic genomic analysis of Ktedonobacteria across ecosystems, with a focus on oligotrophic caves. Cave Ktedonobacteria belong to novel genera within the Ktedonobacteraceae and harbour genes associated with a mixotrophic metabolism combining the use of organic and inorganic substrates as energy and carbon sources. Comparative analyses of all available Ktedonobacteria genomes from diverse environments showed that most metabolic traits, including those associated with atmospheric gas oxidation, are primarily conserved among members of the same family. In contrast, genes involved in CO2 fixation are enriched in Ktedonobacteria inhabiting caves. Phylogenetic analysis indicated that the RuBisCO of Ktedonobacteria likely represents a novel Form I subtype (named group IG) encompassing thermophilic and acidophilic bacteria from six different phyla that often inhabit similar extreme environments. The presence of this subtype across distinct lineages in comparable habitats suggests that it may confer a selective advantage in nutrient-poor settings (like caves) and that its distribution may be influenced by horizontal gene transfer. This inferred autotrophic capacity is associated with a transaldolase variant of the Calvin-Benson-Bassham cycle that was previously described only in a single Firmicutes species. Overall, this study provides genetic evidence for the potential coupling of atmospheric gas oxidation with dark CO2 fixation in Ktedonobacteria, highlighting their possible role in sustaining primary production in oligotrophic ecosystems, including caves.},
}

@article {pmid42465308,
year = {2026},
author = {Maier, JL and Callahan, B and Duerkop, BA and Kleiner, M},
title = {Perturbations shift the composition of bacterial DNA carried by virus-like particles in the murine gut microbiome.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.07.08.737213},
pmid = {42465308},
issn = {2692-8205},
abstract = {Horizontal gene transfer (HGT) is a driving force in microbial evolution that allows community members to rapidly evolve to cope with environmental stressors and competition. Despite the importance of HGT for the generation of genetic diversity, little is known about the specific mechanisms or dynamics of transfer in complex communities. Transductomics is a sequencing based technique which identifies potential HGT by bacteriophages (transduction) through sequencing of the transductome - the DNA carried by bacteriophages and other virus-like particles in a sample. We analyzed the murine gut transductome before and after perturbations with antibiotics and Clostridioides difficile infection (CDI). We found that several bacterial families - the Oscillospiraceae, Butyricoccaceae, and Turicibactericeae - disproportionally contributed to the transductome. Some families, like the Butyricicoccaceae, were frequent transducers in both the baseline and perturbed murine gut microbiome while other taxa displayed condition-specific transduction indicating that there may be specific transducing subpopulations or regulatory mechanisms controlling transduction frequency. Additionally, we found a diversity of highly abundant and enriched mobile genetic elements (MGEs) in the transductome including plasmids, integrative conjugative elements, phage satellites and transposons. The detection of MGEs containing conjugative elements suggest that some MGEs may spread through both transduction and conjugation. Overall, our work reveals a complex network of gene exchange occurring through transduction in the gut microbiome.},
}

@article {pmid42465457,
year = {2026},
author = {Maier, J and Deshmukh, N and Kleiner, M},
title = {High throughput chromatographic ultra-purification of virus-like particles for downstream viromics.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.07.09.737491},
pmid = {42465457},
issn = {2692-8205},
abstract = {Virus-like particles (VLPs) are an abundant component of microbiomes with critical ecological roles such as population control through viral predation and horizontal gene transfer. Studying the collection of viruses in microbiomes (the virome) through metagenomics has provided important insights into the composition and functions of VLPs in different environments. However, the current gold-standard method for VLP purification, CsCl density gradient ultracentrifugation (CsCl), is low throughput, time consuming and suffers from biases which limits the ability to study viromes in larger sample sets and can interfere with data interpretation. Here we present an anion exchange (AEX) chromatography-based approach for the purification of VLPs from microbiome samples that allows for significant increases in throughput and reproducibility while achieving VLP purity levels similar to or higher than CsCl. We used microbiome samples of known composition to first establish and evaluate the AEX approaches and compare them to CsCl. We implemented the AEX approach both for fast performance liquid chromatography (FPLC) and in multi-well plates. We compared the VLPs purified with CsCl and AEX using shotgun metagenomic sequencing and found that AEX performs similarly to or better than CsCl for purification of VLPs. AEX purified VLP-fractions captured significantly more viral DNA compared to CsCl. We also found that both AEX and CsCl were capable of capturing viruses present at extremely low relative abundances (<0.001%). Additionally, we found that DNase digestion and CsCl may bias against filamentous phage morphologies. Finally, we purified VLPs from conventional murine feces using AEX and CsCl. AEX purified murine fecal VLPs had a much higher viral DNA content (85%) than CsCl (41%). While there were some differences in viral contigs assembled from AEX and CsCl VLP metagenomes, these method unique viral contigs made up only small proportions (<8%) of the relative abundance in the VLP metagenomes. AEX, particularly in the multi-well format, enables the ultrapurification of VLPs from tens to hundreds of samples in a single day thus facilitating virome studies with the large sample numbers needed for translational and clinical research.},
}

@article {pmid42465717,
year = {2026},
author = {Kerek, Á and Husz, LH and Szarka, E and Tornyos, GÁ and Barnácz, F and Csirmaz, B and Kovács, L and Jerzsele, Á},
title = {Regional phenotypic surveillance of antimicrobial susceptibility in chicken-associated commensal Staphylococcus, Enterococcus, and Escherichia coli from Southern Transdanubia, Hungary.},
journal = {Frontiers in veterinary science},
volume = {13},
number = {},
pages = {1873052},
pmid = {42465717},
issn = {2297-1769},
abstract = {BACKGROUND: Antimicrobial resistance in commensal bacteria from poultry is an important indicator of selection pressure within food-animal production systems and may contribute to the broader One Health burden of antimicrobial resistance. Region-specific phenotypic surveillance is therefore needed to characterize antimicrobial susceptibility patterns in bacterial populations associated with intensive poultry production. The objective of this study was to characterize region-specific phenotypic antimicrobial susceptibility and co-resistance patterns in chicken-associated commensal Staphylococcus, Enterococcus, and Escherichia coli isolates from large-scale poultry flocks in Southern Transdanubia, Hungary.

METHODS: This study assessed the antimicrobial susceptibility profiles of chicken-associated commensal Staphylococcus, Enterococcus, and Escherichia coli isolates collected from large-scale flocks in Southern Transdanubia, Hungary. In total, 198 isolates, comprising Staphylococcus spp. (n = 40), Enterococcus spp. (n = 84), and E. coli (n = 74), were examined by broth microdilution to determine minimum inhibitory concentrations against a panel of antimicrobial agents relevant to veterinary and public health surveillance. Interpretive classifications were applied only where appropriate clinical breakpoints or epidemiological cut-off values were available; otherwise, MIC distributions were reported descriptively.

RESULTS: Multidrug-resistant phenotypes were frequent, occurring in 65.0% of Staphylococcus, 73.8% of Enterococcus, and 82.4% of E. coli isolates, with the highest proportions observed among E. coli and Enterococcus. Exploratory correlation, clustering, and network-based analyses indicated structured phenotypic co-resistance patterns, suggesting repeated co-occurrence of reduced susceptibility to selected antimicrobial classes within the tested isolate collection.

CONCLUSION: These associations should not be interpreted as direct evidence of genetic linkage, horizontal gene transfer, or shared resistance determinants, but they may indicate possible co-selection requiring confirmation by future genomic studies. Overall, this study provides region-specific baseline data on antimicrobial susceptibility among chicken-associated commensal bacteria from Hungary and supports the need for harmonized phenotypic surveillance, prudent antimicrobial use, and genotype-informed follow-up investigations within a One Health framework.},
}

@article {pmid42465973,
year = {2026},
author = {Wen, M and Mettouchi, E and López Sánchez, A and Yamaichi, Y},
title = {Selective elimination of donor bacteria to analyze plasmid reactions during conjugative transfer.},
journal = {Biology methods & protocols},
volume = {11},
number = {1},
pages = {bpag038},
pmid = {42465973},
issn = {2396-8923},
abstract = {Bacterial conjugation is an important means of horizontal gene transfer in which DNA is transferred from a donor to a recipient cell by direct cell-to-cell contact. Dissemination of antibiotic resistance in bacteria is very often driven by conjugative plasmids harboring antibiotic resistance genes. Recent research highlighted the temporal cascade of DNA reactions that are critical for the establishment of a plasmid in the new host, which include prompt and robust induction of anti-defense genes as well as re-formation of double-stranded circular form of the plasmid after transfer as single-stranded linear DNA. The nature of conjugation which occurs in a mixture of cell populations, constrained the research on plasmid establishment. Since plasmid molecules before and after transfer are indistinguishable, distinction between donor and recipient/transconjugant cells is required, and physical separation is particularly necessary for the genomic approaches. We established a novel method exploiting a mutant donor which can be expeditiously eliminated from the conjugation, mixture with simple manipulation. This method, dubbed ED-TA for elimination of donor cells for transconjugant analysis, was shown to be a powerful tool to unveil plasmid gene expression profile at the early stages of conjugation (Wen et al. 2025, Nucleic Acids Res, doi: 10.1093/nar/gkaf1299). Here we present an optimized protocol for the ED-TA method which will help our study on plasmid actions during establishment in new host cell, including emerging interests between host defense and plasmid anti-defense systems.},
}

@article {pmid42450606,
year = {2026},
author = {Jia, L and Hou, Y and Zhang, M and Li, L and Zhang, Y and Wang, J and Yuan, Z and Fan, G and Shi, C and Zhao, H},
title = {Distribution and Evolutionary Implications of Flagellum-Associated Gene Families in Representative Algal Genomes.},
journal = {Biology},
volume = {15},
number = {13},
pages = {},
doi = {10.3390/biology15131058},
pmid = {42450606},
issn = {2079-7737},
support = {2021YFD2201000//National Key Research and Development Program of China/ ; //Research and Demonstration of Key Technologies for "Bamboo as Substitutes for Plastic" in Pilot Member States of the International Bamboo and Rattan Organization/ ; },
abstract = {Eukaryotic flagella are evolutionarily conserved organelles that mediate motility, sensory transduction, and environmental adaptation, yet their presence and gene composition vary considerably across algal lineages. Dinoflagellates, a lineage within the superphylum Alveolata, derived from secondary endosymbiosis, exhibit larger and more reorganized genomes than their red-algal relatives and possess a distinctive biflagellate morphology, making them an informative group for studying flagellar evolution. To systematically investigate flagellar gene distribution in this lineage, we performed comparative genomic analyses on 102 genomes spanning four algal groups-Chlorophyta, Rhodophyta, Alveolata (represented by dinoflagellates), and Bacillariophyta. Genomes were selected based on assembly completeness, retaining only those with BUSCO completeness > 50% to balance data quality with taxonomic coverage. Orthologous groups were identified using a reciprocal best BLAST v2.11.0(rBH) strategy, from which we curated 94 conserved flagellar gene families. Quantitative comparisons revealed significant lineage-specific expansions of flagellar gene families within dinoflagellates, including WDR35, TTLL5, and STK36, with fold enrichment values ranging from 3.6 to 5.8 (adjusted p < 0.01). Phylogenetic analyses further identified two axonemal components, BBS9 and C1A-18, as candidates acquired via horizontal gene transfer, with bootstrap support exceeding 80% and Alien Index values > 45. Collectively, these phylogenomic analyses suggest that lineage-specific expansion and horizontal gene transfer have jointly contributed to the evolution of flagellar systems in dinoflagellates, providing a framework for future functional studies.},
}

@article {pmid42450707,
year = {2026},
author = {Dai, Y and Qiao, Y and Xie, N and Zhu, J and Lin, Q and Xu, B and Dai, Y},
title = {Contrasting Roles of Mobile Genetic Elements and Metal Resistance Genes in Shaping the Gut Resistome of Wild Fish from the Qiantang River.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {13},
pages = {},
doi = {10.3390/ani16132000},
pmid = {42450707},
issn = {2076-2615},
support = {LHZY24C190001//Zhejiang Provincial Natural Science Foundation/ ; },
abstract = {The dissemination of antibiotic resistance genes (ARGs) in riverine ecosystems poses a pressing public health threat, while the mechanisms governing the assembly of the gut resistome in wild fish remain poorly elucidated. This study aimed to elucidate the distributional patterns of ARGs across multiple environmental compartments and to identify factors associated with their variation, particularly the contributions of mobile genetic elements (MGEs) and metal resistance genes (MRGs) to gut resistome variation. Metagenomic sequencing was conducted on 60 samples, comprising water, sediment, and gut contents from three wild fish species (Megalobrama terminalis, Aristichthys nobilis, and Coilia nasus) with distinct feeding habits, collected from four reaches of the Qiantang River basin. A total of 305 ARG subtypes belonging to 23 classes were identified. ARG composition differed significantly across environmental media and host species (permutational multivariate analysis of variance, PERMANOVA; p < 0.01), with host species identity as the primary structuring factor. Variance partitioning analysis (VPA) revealed that MGEs independently explained the largest fraction of ARG variation in A. nobilis (33.8%, p = 0.006), whereas MRGs dominated in C. nasus (33.3%, p = 0.005); in M. terminalis, MGEs and MRGs together accounted for 47.9% of the variation. Metagenomic assembly recovered 2622 ARG-carrying contigs, of which 28.3% (743) were predicted as plasmid sequences; physical co-localization among ARGs, MGEs, and MRGs was detected on both chromosomes and plasmids. Metagenomic binning validated the physical co-localization of ARG-MGE-MRG modules in genera such as Morganella and Burkholderia at the genome level, while plasmid-borne high-risk ARGs were identified in Aeromonas. Risk ranking further revealed significant enrichment of Rank II potentially high-risk ARGs (e.g., mcr-7.1, blaZ) in fish guts, carried by potential pathogens. These findings suggest that horizontal gene transfer involving MGEs and co-selection related to MRGs are closely associated with the fish gut resistome composition in a manner dependent on host ecology, providing a scientific basis for shifting riverine resistance management from concentration-based control toward the interruption of dissemination pathways.},
}

@article {pmid42453110,
year = {2026},
author = {Guo, J and Song, H and Xi, Z and Geng, W and Wang, F},
title = {The role of gut microbiome in antimicrobial resistance transmission between companion animals and livestock: mechanisms, drivers, and One Health implications.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1872946},
pmid = {42453110},
issn = {1664-302X},
abstract = {Antimicrobial resistance (AMR) poses a critical global public health challenge, with animal gut microbiomes serving as significant reservoirs and transmission hubs for antimicrobial resistance genes (ARGs). This review synthesizes current knowledge on the central role of gut microbiomes in companion animals and livestock in facilitating AMR dissemination. It examines key mechanisms that enable horizontal gene transfer within intestinal ecosystems: conjugation, transduction, and transformation. It also highlights how co-selection by heavy metals, disinfectants, and other non-antibiotic agents sustains resistance even without direct antibiotic use. The review analyzes major drivers of AMR, including antimicrobial usage, husbandry practices, and environmental pressures. It critically evaluates microbiome-based interventions such as probiotics, postbiotics, and fecal microbiota transplantation. A distinctive contribution is the integration of these elements into a network-centric One Health framework that explicitly maps cross-species transmission pathways from livestock and companion animals to humans via direct contact, food chains, and environmental dissemination. By moving beyond descriptive cataloging to provide a mechanistic and ecological synthesis, this review aims to guide the development of targeted, microbiome-informed intervention and surveillance strategies.},
}

@article {pmid42453402,
year = {2026},
author = {Zhang, M and Yang, B and Sun, J and Wang, Z and Liu, Y},
title = {Targeting bacterial phosphotransferase system to prevent the dissemination of antibiotic resistance genes.},
journal = {Acta pharmaceutica Sinica. B},
volume = {16},
number = {7},
pages = {4575-4591},
pmid = {42453402},
issn = {2211-3835},
abstract = {Antimicrobial resistance (AMR) poses a significant challenge to public health and human security, with plasmid-mediated horizontal gene transfer (HGT) being a primary driver for its dissemination. Here, we identify indole analogs containing electron-withdrawing groups as a new category of HGT inhibitors. Using indole-3-acetic acid (IAA) as a representative scaffold, we demonstrate that IAA targets glycolytic enolase to deplete phosphoenolpyruvate (PEP) in donor bacteria; this suppresses phosphotransferase system (PTS) activity, blocks PtsI phosphorylation, reduces cAMP synthesis and prevents catabolite repressor protein (CRP) activation, ultimately limiting intracellular ATP availability. Concurrently, IAA attenuates reactive oxygen species (ROS) generation by inhibiting FADH2 oxidation and riboflavin biosynthesis. The concerted reduction in ATP and ROS arrests conjugative plasmid transfer. Overall, our work suggests the potential of indole analogs as a new class of conjugative transfer inhibitors and highlights that bacterial phosphotransferase system represents a promising target to prevent the propagation of AMR.},
}

@article {pmid42444166,
year = {2026},
author = {Mishra, S and Weit, K and Lercher, MJ},
title = {The Fate of Horizontally Acquired Genes: Rapid Initial Turnover Followed by Long-Term Persistence.},
journal = {Molecular biology and evolution},
volume = {43},
number = {7},
pages = {},
pmid = {42444166},
issn = {1537-1719},
support = {//Deutsche Forschungsgemeinschaft/ ; },
mesh = {*Gene Transfer, Horizontal ; Evolution, Molecular ; Genome, Bacterial ; *Bacteria/genetics ; Phylogeny ; },
abstract = {A major driver of bacterial evolution is horizontal gene transfer (HGT), the acquisition of genes from other strains or species. Transfers between closely related taxa are more likely to succeed, while the pervasive deletion bias of bacterial genomes drives frequent turnover of horizontally acquired genes. However, whether the rate of gene loss after acquisition is constant across lineages or time remains unclear. Here, we analyze a comprehensive dataset of bacterial genomes to infer the frequency, distribution, and retention of inter-phylum HGT events. The retention of inter-phylum gene transfers is highly skewed, with only a small subset of bacterial genomes accounting for the majority of such events. Most transferred genes are lost rapidly. Those genes that survive the initial purging are retained over long periods, are biased toward functions such as transport and metabolism, and have larger numbers of protein-protein interactions.},
}

*Gene Transfer, Horizontal
Evolution, Molecular
Genome, Bacterial
*Bacteria/genetics
Phylogeny

@article {pmid42445489,
year = {2026},
author = {Zhu, J and Knoll, W and Wang, B and Pelosi, P},
title = {New potential antimicrobial peptides with mirror-symmetrical structure in fungi and insects.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1843407},
pmid = {42445489},
issn = {1664-302X},
abstract = {A new family of genes encoding potential antimicrobial peptides with compact and elegant structure has been found in the genomes of several Fungi and some arthropod species. Their expression products are constituted of about 85 amino acids, including a signal peptide, and are folded into two α-helical segments connected by a short unstructured coil. Three conserved disulphide bridges between cysteines located in symmetrically mirrored positions connect the two helical domains. These peptides, here named as Hairpin Loop Peptides (HLPs), have been found in the genomes of many Fungi species but only in selected clades. Orthologues have also been discovered in the genomes of some insects, notably Hemiptera, a few other arthropods and other organisms. They are not found in plants, that however express smaller peptides of similar topology with HLPs, but different amino acidic composition and physicochemical properties. They appear to have originated in Fungi and then migrated to insects through horizontal gene transfer. The antimicrobial activity of HLPs is predicted by several software programmes, but this aspect needs to be supported by experimental evidence. The occurrence of HLPs in several edible mushrooms may suggest potential uses of these peptides in food preservation and possibly also in medical applications. Their simple and nearly rigid structure can be easily modified to improve specificity, stability and solubility, thus making these peptides suitable for a variety of different applications.},
}

@article {pmid42445684,
year = {2026},
author = {Cao, Y and Yu, W},
title = {The Integrative and Conjugative Element ICEPmiW2 in Proteus mirabilis W2 Facilitates the Dissemination of Antibiotic-Resistance Genes.},
journal = {The Canadian journal of infectious diseases & medical microbiology = Journal canadien des maladies infectieuses et de la microbiologie medicale},
volume = {2026},
number = {},
pages = {5112699},
pmid = {42445684},
issn = {1712-9532},
abstract = {BACKGROUND: The extensive use of antibiotics for treating infectious diseases leads to their release into the environment, which in turn results in antibiotic pollution and thereby facilitates the dissemination of antibiotic-resistance genes (ARGs). Recently, despite the implementation of strict antibiotic usage restrictions, the accumulation of ARGs and multidrug-resistant bacteria in the aquaculture environment continues to show a trend of persistent spread.

METHODS: The W2 strain was isolated in the presence of 32 μg/mL doxycycline. A broth microdilution assay was employed to determine the minimum inhibitory concentrations. Whole-genome sequencing was conducted to characterize ARGs and their mobility through bioinformatics analysis. The spread of ARGs was detected by conjugation assays.

RESULTS: W2 strain was isolated from the wastewater of a crucian carp aquaculture plant in Jinan, China, and identified as Proteus mirabilis. W2 genome contained a 190,320 bp antibiotic-resistance-conferring integrative and conjugative element (ICE), named ICEPmiW2. ICEPmiW2 contains 21 ARGs, 14 conjugative transposon protein-encoding genes, and one complex type I integron. No transconjugants were obtained using W2 as the donor strain and Escherichia coli 25DN as the recipient strain. However, evolutionary analysis revealed that ICEPmiW2 likely evolved from ICEs of other P. mirabilis strains.

CONCLUSIONS: The multiple-antibiotic-resistant P. mirabilis W2 strain with potential pathogenicity to aquatic animals was isolated, and the antibiotic-resistance-conferring ICEPmiW2 was identified in P. mirabilis W2. Our findings suggest that ICEPmiW2 of P. mirabilis W2 can potentially spread ARGs among environmental P. mirabilis strains.},
}

@article {pmid42445792,
year = {2026},
author = {Medoro, A and Castagnetti, A and Intrieri, M and Scapagnini, G and Davinelli, S},
title = {Diet, mycobiome and virome: from mucosal immunity to gut-brain axis regulation.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1873950},
pmid = {42445792},
issn = {2296-861X},
abstract = {The gut microbiota plays a central role in regulating host metabolism, immune function and gut-brain axis signaling. Although bacterial communities have dominated microbiome research, the intestinal ecosystem also encompasses fungal communities and bacteriophages that can influence microbial functions and host physiology. This review examines how interactions among the mycobiome, virome (principally bacteriophages), and the bacterial microbiota shape metabolic signaling pathways relevant to gut-brain axis regulation. Fungal-bacterial and phage-bacterial interactions can remodel bacterial community function through ecological competition, biofilm formation, prophage induction and horizontal gene transfer. These multi-kingdom interactions modulate key microbial metabolites, including short-chain fatty acids, tryptophan-derived indole metabolites and bile acid intermediates, which act as major regulators of intestinal barrier integrity, immune responses and neuroimmune signaling. Disruption of these metabolic pathways may contribute to altered host signaling through receptors such as the aryl hydrocarbon receptor (AhR) and bile acid receptors, with downstream effects on intestinal inflammation and neuroimmune regulation. Diet is among the most influential determinants of this ecosystem, directly shaping microbiota bacterial metabolism, fungal growth and phage-bacteria interactions. Dietary patterns rich in fermentable fibers and bioactive compounds may promote beneficial microbial metabolic outputs, whereas Western-type diets and high sugar intake may favor ecological imbalances that disrupt microbial signaling pathways relevant to gut-brain axis regulation.},
}

@article {pmid42447304,
year = {2026},
author = {Cao, J and Ye, Z and Pan, J},
title = {Metagenomics for antimicrobial resistance: from resistome surveillance to mechanistic inference.},
journal = {Journal of bacteriology},
volume = {},
number = {},
pages = {e0009026},
doi = {10.1128/jb.00090-26},
pmid = {42447304},
issn = {1098-5530},
abstract = {Antimicrobial resistance (AMR) is a global health crisis shaped by complex ecological and evolutionary processes that often occur in polymicrobial communities. Metagenomics enables culture-independent profiling of microbial DNA directly from clinical or environmental samples, providing an unparalleled view of community composition, resistome content, and the mobile genetic elements that drive horizontal gene transfer (HGT). Yet, a recurring challenge is that metagenomic detection of antibiotic-resistance genes does not automatically translate into a mechanistic understanding of resistance phenotypes, nor does it replace culture-based functional validation. Here, we synthesize how modern metagenomics supports AMR research across three linked questions: (i) what resistance determinants are present and how do they change across time and space, (ii) which hosts and mobile genetic elements carry these determinants, and how gene flow can be inferred, and (iii) what evidence is required to move from "resistance potential" to robust mechanistic claims. We emphasize practical design principles (sampling, controls, and contamination management), analytical choices (database and parameter effects), and recent advances, including long-read sequencing for resolving antibiotic-resistance genes context, and rapid clinical metagenomic sequencing for time-sensitive decision support. We propose an evidence ladder for mechanistic inference that integrates metagenomics with targeted assays and culture-dependent experiments. Beyond synthesizing recent advances, this review provides operational tools for critical appraisal and study design: an evidence ladder for mechanistic inference, a decision-gated workflow that ties metagenomic outputs to allowable claim language, a minimum reporting checklist aligned to evidence strength, and a "pitfall → consequence → fix" guide to reduce over-interpretation. To support a more comprehensive, forward-looking view, we also summarize emerging directions that are rapidly reshaping AMR metagenomics-multi-omics integration, single-cell, and epigenetic linkage strategies, CRISPR-enabled enrichment/depletion, and AI-assisted discovery/mining-and clarify where these advances strengthen (or do not strengthen) mechanistic claims within the same evidence ladder.},
}

@article {pmid42447506,
year = {2026},
author = {Liu, KD and Wang, FY and Hao, WH and Fang, LX and Sun, J and Liao, XP and Wang, MG},
title = {EnvZ/OmpR-dependent OmpF induction contributes to colistin-enhanced plasmid conjugation.},
journal = {Microbiological research},
volume = {312},
number = {},
pages = {128634},
doi = {10.1016/j.micres.2026.128634},
pmid = {42447506},
issn = {1618-0623},
abstract = {Plasmid-mediated horizontal gene transfer plays a pivotal role in accelerating the dissemination of antimicrobial resistance. However, the molecular mechanisms linking antibiotic-induced envelope stress to conjugation remain incompletely understood. Here, we demonstrate that sub-inhibitory colistin significantly enhances conjugative transfer of the RP4 and multiple clinically relevant resistance plasmids in E. coli without affecting bacterial growth. This enhancement was also observed under biofilm-forming conditions. Mechanistically, colistin induces envelope perturbation characterized by increased membrane permeability, elevated lipopolysaccharide release, and structural damage to the membrane. This remodeling is accompanied by selective upregulation of the outer membrane porin OmpF, whereas OmpC remains unchanged. Genetic analyses showed that OmpF is important for the enhancement of plasmid transfer observed under colistin exposure in both donor and recipient strains. Upstream regulatory analysis identified the EnvZ/OmpR two-component system as the principal pathway mediating OmpF induction. Colistin exposure increased envZ and ompR transcription and promoted OmpR phosphorylation, while electrophoretic mobility shift assays confirmed that OmpR binds to the ompF promoter with enhanced activity. Further analyses showed that this activation is not attributable to classical osmotic stress, as neither NaCl nor sucrose induced comparable responses, whereas supplementation with Mg[2 +] or Ca[2+] attenuated colistin-induced gene expression. Collectively, this study uncovers a potential molecular link between colistin-induced envelope stress and horizontal gene transfer in bacteria, providing mechanistic insight into antibiotic-induced horizontal gene transfer.},
}

@article {pmid42447582,
year = {2026},
author = {Lin, H and Li, X and Wang, X and Yuan, Q and Yang, F and Hu, W and Li, X and Lei, L and Luo, Y},
title = {The antibiotic resistome in oysters across the Chinese coastline: Enrichment, microbial drivers, and implications for health risk.},
journal = {Journal of hazardous materials},
volume = {515},
number = {},
pages = {142811},
doi = {10.1016/j.jhazmat.2026.142811},
pmid = {42447582},
issn = {1873-3336},
abstract = {Oysters extensively farmed in China represent a critical but under-investigated pathway for human exposure to antibiotic resistance genes (ARGs). This study employed metagenomic analysis of 75 samples from representative Chinese oyster farms to explore ARGs distribution in oysters and their surrounding environments, alongside assessing their health risk. Results exhibited significant spatial heterogeneity and marked ARG enrichment in oyster compared to surrounding seawater along the Chinese coastline, with an enrichment factor 2.60 ± 2.43 folds higher. This enrichment is primarily driven by selective retention of specific microbes, particularly the opportunistic pathogen Vibrio, which emerged as a dominant ARG host. Furthermore, the co-occurrence of mobile genetic elements and diverse ARGs, particularly IS91 and tnpA, suggests a high potential for horizontal gene transfer within oyster bacteriome, potentially exacerbating the dissemination of antibiotic resistance. From a public health perspective, the mean estimated daily intake (EDI) of ARGs via oyster consumption was calculated at 1.7E-1 ± 1.7E-1 copies/16S/g/individual. Given that oyster can be consumed raw and harbor pathogenic Vibrio, this ARG exposure may underscores potential health risk for consumers. Integrating the EDI with a resistome scoring system, the Risk Index (RI) demonstrated site-specific health threats that necessitate differentiated management priorities. Collectively, these results provide critical evidence of how marine aquaculture serves as a reservoir for ARGs and highlight the urgent need for integrated surveillance under the One Health approach to mitigate the transmission of antibiotic resistance from marine environments to the human food chain.},
}

@article {pmid42449969,
year = {2026},
author = {Chen, TA and Chuang, YT and Lin, HY and Chang, YF and Hsieh, YH and Chen, CH and Lin, CS and Wang, YJ},
title = {Serratia marcescens in Intensive Care Units: Molecular Epidemiology, Biofilm-Mediated Persistence, Antimicrobial Resistance, and Genomic Surveillance.},
journal = {International journal of molecular sciences},
volume = {27},
number = {13},
pages = {},
doi = {10.3390/ijms27135697},
pmid = {42449969},
issn = {1422-0067},
mesh = {*Serratia marcescens/genetics/drug effects/physiology ; *Biofilms/drug effects/growth & development ; Humans ; *Intensive Care Units ; *Serratia Infections/epidemiology/microbiology/drug therapy ; Molecular Epidemiology ; *Cross Infection/microbiology/epidemiology ; *Drug Resistance, Bacterial ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Genome, Bacterial ; },
abstract = {Serratia marcescens has emerged as an important opportunistic pathogen in intensive care units (ICUs), where critically ill patients, invasive devices, antimicrobial exposure, and complex environmental reservoirs create favorable conditions for colonization, infection, and recurrent outbreaks. This narrative review synthesizes evidence from the past decade regarding the clinical and molecular epidemiology, environmental persistence, device-associated transmission, biofilm-mediated resistance, and infection-control strategies of S. marcescens in ICU settings. The literature was reviewed using an integrative approach informed by Ferrari's narrative review framework, with thematic synthesis across clinical, microbiological, environmental, and genomic domains. Recent evidence indicates that ICU-associated S. marcescens infections frequently involve respiratory tract colonization, ventilator-associated pneumonia, bloodstream infection, urinary tract infection, and device-related transmission. Hospital water systems, sink drains, wet surfaces, ventilator circuits, reusable equipment, and contaminated antiseptic or liquid products may serve as persistent reservoirs, particularly when biofilm formation supports long-term survival and recurrent dissemination. At the molecular level, S. marcescens demonstrates substantial genomic diversity, intrinsic and acquired antimicrobial resistance, inducible AmpC β-lactamase activity, efflux-mediated tolerance, and plasmid-associated resistance gene transfer. This review particularly emphasizes the molecular determinants that enable S. marcescens to persist in ICU ecosystems, including AmpC-mediated β-lactam resistance, efflux-associated tolerance, quorum-sensing-regulated biofilm formation, plasmid-mediated horizontal gene transfer, and WGS-defined clonal transmission. Whole-genome sequencing, rapid molecular diagnostics, active surveillance, environmental sampling, and integrated infection-control bundles have become increasingly important for distinguishing clonal outbreaks from endemic transmission and guiding timely interventions. Emerging perspectives emphasize the need to combine antimicrobial stewardship, environmental engineering, respiratory-care auditing, anti-biofilm strategies, and AI-assisted real-time surveillance into adaptive ICU infection-control frameworks. Overall, S. marcescens should be regarded not merely as an episodic outbreak organism, but as a highly adaptable ICU-associated pathogen requiring multidisciplinary prevention strategies.},
}

*Serratia marcescens/genetics/drug effects/physiology
*Biofilms/drug effects/growth & development
Humans
*Intensive Care Units
*Serratia Infections/epidemiology/microbiology/drug therapy
Molecular Epidemiology
*Cross Infection/microbiology/epidemiology
*Drug Resistance, Bacterial
Anti-Bacterial Agents/pharmacology/therapeutic use
Genome, Bacterial

@article {pmid42450205,
year = {2026},
author = {Liu, Y and Han, Y},
title = {In Silico Genomic Analysis of Antibiotic Resistance Genes Carried by Mobile Genetic Elements in Pseudomonas aeruginosa.},
journal = {International journal of molecular sciences},
volume = {27},
number = {13},
pages = {},
doi = {10.3390/ijms27135938},
pmid = {42450205},
issn = {1422-0067},
support = {2025M783825//China Postdoctoral Science Foundation/ ; },
mesh = {*Pseudomonas aeruginosa/genetics/drug effects ; Gene Transfer, Horizontal ; *Genomics/methods ; Plasmids/genetics ; Genome, Bacterial ; *Interspersed Repetitive Sequences ; Anti-Bacterial Agents/pharmacology ; Computer Simulation ; Genes, Bacterial ; *Drug Resistance, Bacterial/genetics ; *Drug Resistance, Multiple, Bacterial/genetics ; },
abstract = {Pseudomonas aeruginosa is a notable opportunistic pathogen in the ESKAPE group due to its multidrug resistance (MDR) and its ability to cause severe healthcare-associated infections. Horizontal gene transfer (HGT) facilitates the dissemination of antibiotic resistance genes (ARGs) through mobile genetic elements (MGEs). A comprehensive genomic analysis of ARGs associated with these elements is essential to understand multidrug resistance in P. aeruginosa. Here, we analyzed 10,412 publicly available P. aeruginosa genome assemblies defined by the Genome Taxonomy Database (GTDB, release 226) species cluster, which provides standardized prokaryotic genome taxonomy. We identified plasmids, prophages, integrative and conjugative elements (ICEs), and integrative and mobilizable elements (IMEs) carrying ARGs. A group of highly prevalent ARG families was identified in P. aeruginosa, comprising mexD, fosA, catB7, blaPAO, and aph(3')-IIb, each of which was detected in over 96% of the genome assemblies. In contrast, 313 ARG families were found in fewer than 20% of the genomes. Many ARGs were located on plasmids, with certain pairs co-occurring frequently, such as aph(3″)-Ib and aph(6)-Id, CmlA9 and aadA6, or aac(6')-Ib3 and aph(3')-XV, which were associated with specific plasmids. Some of these plasmids closely resembled plasmids from E. coli and K. pneumoniae. Moreover, other MGEs displayed distinct ARG cargo enrichment: mexD on IMEs, aph(3')-IIb on prophages, and sul1, fosA, and catB7 on ICEs. Our study provides a high-resolution map of the P. aeruginosa MGE resistome and highlights the potential roles of MGEs in disseminating different resistance genes. Our results emphasize the significance of ICE- and plasmid-associated ARG dissemination, particularly sul1, which may be linked to class 1 integrons. They also suggest that interspecies plasmid exchange may contribute to the evolution of MDR in P. aeruginosa.},
}

*Pseudomonas aeruginosa/genetics/drug effects
Gene Transfer, Horizontal
*Genomics/methods
Plasmids/genetics
Genome, Bacterial
*Interspersed Repetitive Sequences
Anti-Bacterial Agents/pharmacology
Computer Simulation
Genes, Bacterial
*Drug Resistance, Bacterial/genetics
*Drug Resistance, Multiple, Bacterial/genetics

@article {pmid42436619,
year = {2026},
author = {Zheng, C and Song, J and Shan, M and Zhang, H and Qiu, M and Zhang, L and Yu, Y and Wang, X and Fang, H},
title = {Bridging ecological processes to elevated antibiotic resistance risk in tomato microbiome under fungicide stress.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag182},
pmid = {42436619},
issn = {1751-7370},
abstract = {From a "One Health" perspective, antibiotic resistance genes (ARGs) harbored by the plant microbiome pose a significant threat to public health, yet their ecological mechanisms under fungicide stress remain largely unexplored. Here, a comprehensive framework integrating selection, dispersal, antagonistic interactions, and horizontal gene transfer (HGT) is established to elucidate the ecological risks and assembly mechanisms of the tomato resistome under fungicide stress, using multi-omics and several validation experiments. The indirect/direct ecological risks of ARGs in aboveground tomato tissues increase by 1.69-93.81-fold and 1.29-123.49-fold under fungicide exposure, respectively, compared to the control. Dispersal and selection emerge as the dominant ecological processes shaping the resistome under fungicide stress, driven by antibiotic-resistant bacteria (ARB) with streamlined and multifunctional metabolic traits, respectively. A fluorescently labeled ARB migration model and an indigenous ARB-based conjugation model demonstrate that fungicides promote the upward dispersal of native ESKAPE pathogens and intensify HGT among them, facilitating the emergence of multidrug-resistant bacteria. Validation experiments confirm that fungicides induce metabolic reprogramming of flavonoid biosynthesis in roots, which enhances HGT by modulating various physiological phenotypes. These findings underscore the ecological risks posed by fungicides in promoting ARG dissemination within the plant microbiome through multiple ecological mechanisms.},
}

@article {pmid42438306,
year = {2026},
author = {Adler, C and Segal, G},
title = {A Nutrient-Responsive LuxR Regulator Orchestrates Effector Gene Expression Across the Legionella Genus.},
journal = {Molecular microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/mmi.70095},
pmid = {42438306},
issn = {1365-2958},
support = {1469/24//Israel Science Foundation/ ; },
abstract = {Legionella pneumophila utilizes the Icm/Dot secretion system to translocate > 330 effectors into host cells, yet the regulatory mechanisms controlling the expression of many effector-encoding genes (EEGs) remain unknown. Here, we identify and characterize LexR1 (lpg2524), a LuxR-type transcriptional regulator that controls EEG expression in L. pneumophila and other Legionella species. In L. pneumophila, LexR1 directly activates the expression of four EEGs (lem26, lem16, ravW, and legC1) by binding a conserved inverted repeat located upstream of these genes. We demonstrate that LexR1 activity is stimulated by a nutrient-derived ligand present in casamino acids, and orthologs from other Legionella species exhibit similar casamino acid dependent activation of their target genes. Genomic analyses identified 29 genes containing the LexR1 regulatory element in the seven Legionella species containing LexR1, most of which encode validated effectors or proteins harboring common effector domains. Many of these genes are shared among the species and appear to have co-transferred with their regulatory regions via horizontal gene transfer. LexR1 expression is positively regulated by RpoS and repressed by Fis, linking it to the broader effector regulatory network. Together, these findings identify LexR1 as a regulator of EEGs that coordinates nutrient sensing with effector gene expression across the Legionella genus.},
}

@article {pmid42440204,
year = {2026},
author = {Roy, MK and Bhattacharjee, A and Borah, B and Singh, AK},
title = {Soil to host environmental determinants fueling horizontal gene transfer and global AMR dissemination.},
journal = {Folia microbiologica},
volume = {},
number = {},
pages = {},
pmid = {42440204},
issn = {1874-9356},
support = {OLP-2403 and OLP-2503A//Council of Scientific and Industrial Research, India/ ; GPP-0423//Anusandhan National Research Foundation/ ; },
abstract = {Antimicrobial resistance poses a critical and escalating threat to global health, with horizontal gene transfer serving as a primary driver of resistance dissemination among microbial communities across diverse ecological niches. The three classical horizontal gene transfer mechanisms, including transformation, transduction, and conjugation, are complemented by supplementary routes involving outer membrane vesicles, gene transfer agents, and nanotubes. Both internal and external drivers synergistically influence horizontal gene transfer. Factors influencing the within-host microbiome include gut metabolites, antibiotic exposure, temperature fluctuations, and microplastic ingestion, while external environmental drivers such as antibiotic residues, heavy metals, agrochemicals, and micro/nano-plastics similarly enhance the mobility of antimicrobial resistance genes. The main mechanisms contributing to increased antimicrobial resistance gene transfer include elevated oxidative stress markers, altered membrane permeability, and stimulation of conjugation-related gene expression. The synergistic effects of these biotic and abiotic pressures have accelerated the co-selection of antimicrobial resistance genes and mobile genetic elements, intensifying the proliferation of antimicrobial resistance in both clinical and environmental reservoirs. Novel mitigation strategies such as conjugation inhibitors, bacteriophage-based interventions, and biochar amendments show promise in curbing horizontal gene transfer-mediated antimicrobial resistance; however, these approaches still lack insight into the intricate molecular mechanisms underlying horizontal gene transfer and often act non-specifically against different pathogens. Moreover, strategies utilizing biochar remain time-consuming and require further optimization. Overall, understanding the mechanistic interplay between environmental stressors and genetic exchange pathways is essential for developing sustainable interventions to counteract antimicrobial resistance. This review highlights the pressing need for integrated surveillance and ecological risk assessment to effectively manage the environmental aspects of antimicrobial resistance.},
}

@article {pmid42440971,
year = {2026},
author = {Gahlot, KD},
title = {Dietary modulation of the gut resistome: ecological and metabolic pathways driving antimicrobial resistance.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1868638},
pmid = {42440971},
issn = {2296-861X},
abstract = {Antimicrobial resistance (AMR) is traditionally viewed as a consequence of antibiotic exposure and genetic adaptation; however, resistance also emerges from the ecological and metabolic context of microbial communities. The human gut microbiome represents a major reservoir of antibiotic resistance genes (ARGs), and diet is increasingly recognised as a dominant regulator of its structure and function. Here, I synthesise current evidence and propose a conceptual framework in which diet shapes resistome dynamics through three interrelated pathways: ecological selection, metabolic regulation, and physicochemical modulation of horizontal gene transfer. Dietary components influence microbial composition, metabolic activity, and the spatial organisation of fermentation along the colon. Diverse fibre types differentially regulate short-chain fatty acid production and microbial competition, whereas high-fat, low-diversity diets destabilise communities and favour opportunistic taxa. Beyond macronutrients, food additives and the physical structure of food alter gut barrier function, microbial stress responses, and spatial ecology, thereby influencing resistome stability. Diet-induced metabolic states further determine antibiotic susceptibility, including transitions between tolerance and resistance. Taken together, this integrated ecological perspective positions diet as a modifiable driver of AMR and highlights nutritional strategies as complementary approaches to mitigating resistome expansion.},
}

@article {pmid42441853,
year = {2026},
author = {Kapoor, RR and Schwager, EE and Phuangphong, S and Rivard, EL and Kuyyamudi, C and Ghosh, S and Ronai, I and Extavour, CG},
title = {Evolutionary innovation through fusion of sequences from across the tree of life.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {29},
pages = {e2602557123},
doi = {10.1073/pnas.2602557123},
pmid = {42441853},
issn = {1091-6490},
support = {2023356057//NSF | NSF Graduate Research Fellowship Program (GRFP)/ ; DMS-1764269//NSF (NSF)/ ; n/a//Herchel Smith Graduate Fellowship/ ; RGP0041/2022//Human Frontier Science Program (HFSP)/ ; n/a//HHMI (HHMI)/ ; n/a//Harvard University (Harvard)/ ; n/a//Life Sciences Research Foundation (LSRF)/ ; },
mesh = {Animals ; *Evolution, Molecular ; *Phylogeny ; *Gene Transfer, Horizontal/genetics ; *Arthropods/genetics/classification ; *Gene Fusion ; Genome ; Gene Duplication ; },
abstract = {Novel genes arise through multiple mechanisms, including gene duplication, gene fusion, and horizontal gene transfer (HGT). While HGT has increasingly been documented in animals, the posttransfer evolutionary fate of horizontally acquired genes is less well understood. We hypothesized that fusion with endogenous sequences in animal genomes might generate what we call "HGT-chimeras": genes with regions of nonmetazoan and metazoan descent in the same open reading frame. To test this hypothesis, we developed a molecular phylogenetics pipeline that enables the identification of HGT-chimeras. We applied our pipeline to 319 high-quality annotated arthropod genomes and uncovered a high-confidence set of 274 HGT-chimeras corresponding to 104 independent origination events across diverse arthropods. HGT-chimeras contain intervals acquired from across the tree of life, and many likely originated via a gene duplication-based mechanism. To assess whether HGT-chimeras might be functionally important, we performed RT-PCR and Sanger sequencing of tissues from 20 arthropod species predicted to harbor HGT-chimeras in their genome. We found evidence for the expression of contiguous chimeric messenger RNA transcripts (mRNAs) for 36 of 41 tested HGT-chimeras across 18 of 20 different tested species. We also found evidence that HGT-chimeras evolve under purifying selection and have acquired potentially functional domain architectures, consistent with the hypothesis that these genes are in active use and may participate in diverse biological processes. These results illuminate an underappreciated combinatorial mechanism underlying the origin of novel genes across the largest animal phylum, and suggest that interdomain sequence fusion can play important roles in animal biology and evolution.},
}

Animals
*Evolution, Molecular
*Phylogeny
*Gene Transfer, Horizontal/genetics
*Arthropods/genetics/classification
*Gene Fusion
Genome
Gene Duplication

@article {pmid42443210,
year = {2026},
author = {Wang, YF and Xu, JY and Liu, Y and Ni, B and Zhang, TL and Cui, HL and Qi, FY and Qiao, M and Li, HZ and Gillings, MR and Zhu, YG and Zhu, D},
title = {Divergent mechanisms of active antibiotic resistance gene enrichment in soil driven by pesticide diversity.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-75445-3},
pmid = {42443210},
issn = {2041-1723},
support = {22193062//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Antimicrobial resistance is an escalating global threat, with soils serving as reservoirs and conduits for the dissemination of antibiotic resistance genes (ARGs). Pesticide use in agriculture contributes to ARG proliferation, and ~60% of agricultural soils contain multiple pesticide residues. However, how pesticide diversity influences ARG dynamics in active microbial populations (active ARGs) remains unclear. Here, we evaluate the effects of pesticide diversity on active soil ARGs through a long-term field experiment integrating bioorthogonal non-canonical amino acid tagging (BONCAT), fluorescence-activated cell sorting (FACS), and metagenomics. We show that both low and high pesticide diversity significantly increase active ARG abundance relative to untreated control, whereas total ARG levels remain largely unchanged. The underlying mechanisms differ with pesticide diversity. At low diversity, active ARG co-selection via efflux pumps in Acinetobacter baumannii is a prominent mechanism. At high diversity, elevated reactive oxygen species and SOS responses promote horizontal gene transfer of active ARGs, as validated by culture experiments. These findings demonstrate that increasing pesticide diversity accelerates the emergence and dissemination of active ARGs, highlighting the need for integrated pesticide management strategies that consider both application intensity and diversity to mitigate resistance risks under the One Health framework.},
}

@article {pmid42429623,
year = {2026},
author = {Lill, Z and Thongchol, J and Solis, D and Zhang, J},
title = {The cryo-EM structure of bacteriophage PRR1 and its role in conjugation inhibition.},
journal = {Journal of virology},
volume = {},
number = {},
pages = {e0051526},
doi = {10.1128/jvi.00515-26},
pmid = {42429623},
issn = {1098-5514},
abstract = {The global rise of antimicrobial resistance (AMR) demands innovative strategies to limit the spread of multidrug-resistant bacteria. Conjugative plasmids, particularly those in the incompatibility group P (IncP), play a central role in disseminating resistance genes across bacterial species via their encoded type IV secretion system (T4SS). Here, we characterize the single-stranded RNA (ssRNA) bacteriophage (ssRNA phage) PRR1, which selectively targets bacteria carrying the IncP plasmid RP4, including many Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter species, and Escherichia coli (ESKAPEE) pathogens, and assess its ability to inhibit conjugation. Using cryo-electron microscopy, we resolved the mature PRR1 virion at 3.45 Å resolution, revealing two phage maturation protein (Mat)-RNA interactions within the 3' untranslated region: a conserved interaction (Mat-U1) and a novel interaction (Mat-V1) for ssRNA phages. To characterize the PRR1-RP4 pilus interaction, we performed alanine-scanning mutagenesis and pinpointed four critical TrbC pilin residues (S12, W13, S72, and R77) for infection. Computational modeling revealed that these residues are located near the termini of the pilin at the phage-pilus interface. Notably, native and non-infectious, UV-cross-linked PRR1 was sufficient to block RP4 transfer, indicating conjugation inhibition does not require a complete infection cycle. Finally, combining PRR1 and antibiotic treatment yielded nine unique phage-resistant mutants within T4SS-associated genes on the RP4 plasmid. Eight of these mutants nearly abolished conjugation, while the trbE frameshift mutant retained ~30% of wild-type efficiency, which is pivotal to clarifying the relationship between phage infection and pilus function. Collectively, these results establish ssRNA phages as specific T4SS plasmid-targeting agents and underscore their potential to limit horizontal gene transfer in AMR pathogens.IMPORTANCEAntimicrobial resistance (AMR) spreads rapidly through horizontal gene transfer, largely driven by conjugative plasmids. Despite their central role, few strategies exist to directly block plasmid transfer. Here, we show that the IncP plasmid-dependent ssRNA phage PRR1 can inhibit the spread of antibiotic resistance genes by targeting the RP4 T4SS pilus. Structural and mutational analyses reveal previously unrecognized RNA packaging interactions and identify four pilin residues critical for infection. Remarkably, non-infectious PRR1 particles alone are sufficient to block conjugation, offering inhibition without the selective pressure from phage replication. Almost all PRR1-resistant RP4 mutants lost or had severely reduced plasmid transfer, while the remaining mutant is critical for studying the link between T4SS function and phage infection. These results highlight ssRNA phages as precise agents for limiting AMR gene dissemination.},
}

@article {pmid42429760,
year = {2026},
author = {Nguyen, NHA and Bohmova, A and Novotna, J and Wiener, J and Riha, J and Hoang, TC and Sevcu, A},
title = {Antibiotic resistance genes are more abundant in microplastic textile biofilms than natural cotton biofilms in freshwater.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0071926},
doi = {10.1128/aem.00719-26},
pmid = {42429760},
issn = {1098-5336},
abstract = {UNLABELLED: Microplastic fibers (MPFs) are widespread pollutants in freshwater systems, providing artificial surfaces that facilitate microbial attachment and the potential spread of antibiotic resistance genes (ARGs). We compared bacterial colonization on natural cotton fibers with that on synthetic MPFs (Kevlar, acrylonitrile, polyester, and nylon) incubated in river and lake water. Bacterial biomass and community composition were analyzed using epifluorescence microscopy, scanning electron microscopy, and 16S rRNA sequencing, while the presence and relative abundance of key ARGs (blaNDM-1, blaKPC, and blaOXA-48) were quantified using qPCR. Cotton fibers developed substantially higher biofilm loads than any synthetic MPF, supporting dense and taxonomically diverse microbial communities. In contrast, synthetic MPFs supported lower levels of bacterial colonization but exhibited significantly higher levels of ARG enrichment, with blaOXA-48 showing the highest relative abundance. Several taxa, including Fluviicola, Sphingobium, Nitrospira, Schlesneria, and TRA3-20 (Burkholderiaceae), harbored ARGs across all synthetic MPF types. Overall, the findings highlight a clear difference in biofilm quantity and ARG prevalence, with cotton accumulating the most biofilm but having the lowest ARG burden, whereas synthetic MPFs supported ARG-associated bacteria despite lower colonization. These results suggest that synthetic MPFs may play a disproportionately large role in the environmental dissemination of antibiotic resistance due to their mobility and affinity for ARG-harboring microbial communities in freshwater ecosystems.

IMPORTANCE: Microplastic fibers (MPFs) are widespread in freshwater systems but remain underexplored as reservoirs and vectors of antibiotic resistance. This study reveals that synthetic MPFs serve as enriched niches for bacteria harboring relevant antibiotic resistance genes (ARGs), in contrast to natural fibers like cotton. By combining high-resolution microscopy, 16S rRNA gene sequencing, and quantitative PCR, we demonstrate that MPFs selectively support ARG-bearing taxa, including Fluviicola and Sphingobium, across multiple fiber types. These findings suggest that MPFs in aquatic environments may facilitate horizontal gene transfer and contribute to the environmental dissemination of antibiotic resistance. Understanding microbial colonization patterns on MPFs is critical for assessing the ecological and public health risks posed by microplastic pollution.},
}

@article {pmid42430034,
year = {2026},
author = {Grassi, A and Rogo, U and Fambrini, M and Pugliesi, C and Agnolucci, M},
title = {Horizontal gene transfer in Saccharomyces cerevisiae and other Saccharomycotina yeasts: a review.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {8},
pages = {},
pmid = {42430034},
issn = {1573-0972},
mesh = {*Gene Transfer, Horizontal ; *Saccharomyces cerevisiae/genetics/classification ; Genome, Fungal ; Phylogeny ; Evolution, Molecular ; Fermentation ; High-Throughput Nucleotide Sequencing ; Genetic Variation ; },
abstract = {Species evolution has long been associated exclusively with vertical gene transfer, making genetic variability a result of recombination and spontaneous mutations. Although long considered exclusive to prokaryotes, horizontal gene transfer (HGT), plays an important evolutionary role even in complex eukaryotic lineages. This process can generate novel functions in the host, proving evolutionary paths not predicted by vertical inheritance. This review highlights how HGT has significantly shaped the genome evolution of Saccharomyces cerevisiae, providing key traits relevant to fermentation processes. HGT events from bacteria, alongside introgression from other yeasts, contribute to the genetic diversity and specific adaptations seen in domesticated strains of S. cerevisiae, distinguishing them from wild relatives and influencing their industrial utility. Here we report how the advent of next-generation sequencing (NGS), and the subsequent flood of genomic data, have fundamentally accelerated the discovery and analysis of HGT events across all domains of life. The sheer volume of NGS data has driven the development of sophisticated bioinformatics tools and algorithms specifically designed to detect the phylogenetic and compositional signatures of HGT. We also discuss how detecting HGT events helps to understand yeast genome plasticity and to identify useful "foreign" DNA, which can then be manipulated to create novel yeast strains with enhanced fermentation performance, flavour profiles, or stress tolerance.},
}

*Gene Transfer, Horizontal
*Saccharomyces cerevisiae/genetics/classification
Genome, Fungal
Phylogeny
Evolution, Molecular
Fermentation
High-Throughput Nucleotide Sequencing
Genetic Variation

@article {pmid42430049,
year = {2026},
author = {Genevieve, KK and S, HKK and Paul, D and P, N and Arafath, Y and Bareh, E and Kiran, GS and Selvin, J},
title = {Phenotypic and genomic insights into Stenotrophomonas sepilia SMBL8: metabolic versatility, antibiotic resistance and pathogenic potential.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {8},
pages = {},
pmid = {42430049},
issn = {1573-0972},
mesh = {Anti-Bacterial Agents/pharmacology ; Genome, Bacterial/genetics ; *Stenotrophomonas/genetics/metabolism/drug effects/pathogenicity/isolation & purification/classification ; Microbial Sensitivity Tests ; Phenotype ; Whole Genome Sequencing ; *Drug Resistance, Bacterial/genetics ; Base Composition ; Lakes/microbiology ; Genomics ; Carbohydrate Metabolism/genetics ; Genomic Islands ; Virulence/genetics ; },
abstract = {Stenotrophomonas sepilia SMBL8 is a motile, hemolytic, Gram-negative environmental bacterium isolated from a polluted lake. S. sepilia, a recently identified member of the Stenotrophomonas maltophilia complex, has been reported in both clinical and environmental settings; however, it remains understudied. In this study, we comprehensively investigated the phenotypic and genomic characteristics, emphasising metabolic versatility, antibiotic resistance profile, and pathogenic potential. Antibiotic susceptibility testing revealed sensitivity to trimethoprim/sulphamethoxazole, levofloxacin, and minocycline; resistance and intermediate resistance to β-lactams, aminoglycosides, and chloramphenicol. Whole-genome sequencing revealed a genome length of 4,510,692 bp and a G + C content of 66.56%. Functional annotation revealed enrichment and abundant gene distribution in carbohydrate metabolism and binding activity essential for carbohydrate-active metabolism. Subsequent analysis identified a diverse carbohydrate-active enzyme repertoire with potential biotechnological applications as a biocatalyst for substrates such as xylan and chitin. Conversely, further genomic analysis revealed siderophore-encoding genes, multiple putative resistance genes, and mobile genetic elements, including prophages and genomic islands, that encode cascades of putative virulence-associated genes with G + C content distinct from the core genome, suggesting acquisition through horizontal gene transfer. In conclusion, our findings address an existing knowledge gap and highlight the potential dualistic nature of S. sepilia SMBL8, both as a beneficial industrial bacterium and an opportunistic pathogen, facilitated by metabolic versatility and genomic plasticity. Our study also emphasises the critical need for environmental surveillance in anthropogenically disturbed habitats to monitor and mitigate the potential emergence of resistant opportunistic pathogens.},
}

Anti-Bacterial Agents/pharmacology
Genome, Bacterial/genetics
*Stenotrophomonas/genetics/metabolism/drug effects/pathogenicity/isolation & purification/classification
Microbial Sensitivity Tests
Phenotype
Whole Genome Sequencing
*Drug Resistance, Bacterial/genetics
Base Composition
Lakes/microbiology
Genomics
Carbohydrate Metabolism/genetics
Genomic Islands
Virulence/genetics

@article {pmid42430196,
year = {2026},
author = {Marquiegui-Alvaro, A and Kottara, A and Thomas, MJN and Scarampi, A and Chacón, M and Brockhurst, M and Dixon, N},
title = {Using auxotrophic donor strains to explore pQBR57 plasmid host range among environmental soil bacterial isolates.},
journal = {Microbiology (Reading, England)},
volume = {172},
number = {7},
pages = {},
doi = {10.1099/mic.0.001737},
pmid = {42430196},
issn = {1465-2080},
mesh = {*Plasmids/genetics ; *Soil Microbiology ; Conjugation, Genetic ; *Pseudomonas fluorescens/genetics/isolation & purification ; *Host Specificity ; *Pseudomonas putida/genetics/isolation & purification ; Phylogeny ; },
abstract = {Plasmid host range (PHR) plays a key role in the spread of ecologically important genes, alongside applications in microbiome engineering and environmental biotechnology. PHR is a complex trait arising from the combination of plasmid, donor and recipient properties. Most studies of PHR use a single donor strain, leaving the role of the donor unexplored and often require genetically tagged recipient strains for counter-selection, which limits the use of non-genetically tractable strains. Here, we applied auxotrophic donor counter-selection in a relatively high-throughput and accessible screening format to characterize PHR across a diverse collection of environmental isolates without the need for recipient engineering. Specifically, we used two auxotrophic donors (Pseudomonas fluorescens and Pseudomonas putida) and plasmid pQBR57-tphKAB, an environmental plasmid engineered for terephthalic acid bioremediation. We screened a library of 101 soil isolates as potential recipients, including genera such as Pseudomonas, Bacillus and Xanthomonas. We only observed conjugation into other Pseudomonas, but donor identity was found to affect PHR, with P. fluorescens conjugating the plasmid into more recipient strains than P. putida. Phylogenomic analysis revealed that transconjugants clustered primarily with the Pseudomonas citronellolis lineage, previously isolated from soil. In strains that were close relatives of transconjugants but unable to acquire the plasmid, we observed five defence systems not present in transconjugants that may act as barriers to plasmid acquisition. Our approach demonstrates how auxotrophic donor counter-selection can be deployed at scale to screen PHR in environmental isolates and to investigate the influence of donor identity on plasmid conjugation.},
}

*Plasmids/genetics
*Soil Microbiology
Conjugation, Genetic
*Pseudomonas fluorescens/genetics/isolation & purification
*Host Specificity
*Pseudomonas putida/genetics/isolation & purification
Phylogeny

@article {pmid42429479,
year = {2026},
author = {Warkentin, KM and Falk, JJ and Casper, AMA},
title = {Evolution, Development, and the Incoherence of Sex: A Framework for Multiple Sex Concepts.},
journal = {Integrative and comparative biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/icb/icag113},
pmid = {42429479},
issn = {1557-7023},
abstract = {The word sex can refer to at least seven distinct, evolutionarily related biological phenomena (0-6 below). Bacteria and archaea use mechanisms for horizontal gene transfer (0) broadly and promiscuously, even without cell contact. Their endosymbiotic merger led to eukaryotes and a new form of gene exchange, using syngamy and meiosis (1) to mix and recombine similar genomes. This innovation altered the course of evolution. The requirement for chromosome homology in meiosis separated evolving lineages. Mating types evolved within them, differentiating roles of the cells pairing in syngamy, and gamete size dimorphisms (2) evolved many times. Organisms evolved diverse gamete-production strategies (3) and a plethora of traits associated with those strategies (4). They also evolved many ways to facilitate gamete encounters (5). Some of these were expressed in other contexts and gained new functions (6). These phenomena include cellular genetic processes (0, 1), alternative states of cells and organisms (2-4), and things organisms do (5, 6) that have diversified over billions of years. Sex is neither biologically simple nor conceptually singular, but the word is often used without qualifiers, assuming shared understanding that may not exist. We present a framework for multiple sex concepts that serve as anchor points to discuss the relationships among these phenomena and the diversity and complexity of each, including the biologically fuzzy edges generated by developmental variation and evolutionary change. We highlight several communication challenges that may limit biological understanding and/or facilitate the deployment of biology to justify social harms. For instance, sex is used for three alternative-state concepts (2-4 above) whose distinctions are sometimes collapsed, fostering overgeneralization based on the supposed simplicity of anisogamy, but even gamete sex is evolutionarily complex and subject to shifting definitional criteria. Attempts to narrowly bound "biological sex" minimize this complexity and what we can learn from it, while facilitating the misuse of biology in anti-diversity social projects. Another challenge is that using accessible language that works for organisms like ourselves may misrepresent or obscure the biology of other life forms, but specialized language can create information silos; these limit the broad comparisons that are necessary both for perspective on our own biology and a more expansive understanding of life. The multiple sex concepts framework is a way to acknowledge the scope and discuss the complexity of sex in biology, offering a scaffold to facilitate broader thinking, better communication, and discovery.},
}

@article {pmid42419617,
year = {2026},
author = {Zhang, J and Su, P and Li, L},
title = {Pressure-induced occurrence and distribution of antibiotic resistance genes in extracellular and intracellular polymeric substances.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125196},
doi = {10.1016/j.envres.2026.125196},
pmid = {42419617},
issn = {1096-0953},
abstract = {Extracellular polymeric substances (EPS) form a multilayered matrix that governs the retention, transformation, and propagation of antibiotic resistance genes (ARGs) in activated sludge. This study systematically examined the stratified distribution of tetracycline resistance genes (tet) across slime EPS (SEPS), loosely bound EPS (LB), tightly bound EPS (TB), and intracellular polymeric substances (IPS) in sequencing batch reactors (SBR) and membrane bioreactors (MBR). Tetracycline accumulated predominantly in SEPS and LB, where elevated selective pressure promoted tet gene enrichment. ARG profiles shifted over time from efflux-pump genes [tet A, tet C, tet G] to ribosomal-protection [tet M] and enzymatic-deactivation [tet X] mechanisms. Protein secondary structure analysis revealed more compact EPS in MBR, which enhanced DNA retention and reduced ARG release into effluent. Correlation analysis showed that tetracycline concentration, rather than biomass abundance, was the dominant driver of ARG proliferation, highlighting the likely role of eDNA and horizontal gene transfer. These findings underscore the mechanistic role of EPS microenvironments in ARG dissemination and provide actionable strategies for mitigating antibiotic resistance in wastewater treatment systems.},
}

@article {pmid42421846,
year = {2026},
author = {Cuteri, V and Storoni, C and Cao, S and Li, Y},
title = {Artificial intelligence-driven phage therapy in veterinary medicine: an adaptive One Health strategy to mitigate antimicrobial resistance in livestock systems.},
journal = {Frontiers in veterinary science},
volume = {13},
number = {},
pages = {1829777},
pmid = {42421846},
issn = {2297-1769},
abstract = {Antimicrobial resistance (AMR) in animal production systems is a major structural driver of the global resistance crisis. Food-producing animals account for the majority of global antimicrobial consumption, generating sustained selective pressure across livestock, environmental, and zoonotic bacterial reservoirs. Intensive poultry, swine, cattle, and aquaculture systems amplify pathogen transmission and accelerate resistance emergence. Bacteriophage therapy offers a species-specific, microbiome-preserving alternative to conventional antibiotics; however, large-scale veterinary implementation has historically been constrained by challenges including strain-level host prediction, resistance evolution, biosafety considerations, manufacturing scalability, economic feasibility, and regulatory adaptation. Recent advances in artificial intelligence (AI) show promise for enabling precision veterinary phage therapy, though most applications remain at the computational proof-of-concept or preclinical stage. Deep learning and graph-based genomic models have demonstrated high accuracy on benchmark datasets, reinforcement learning has been explored in computational models for cocktail optimization, and AI-assisted genomic screening can enhance biosafety assessment. Integration with real-time AMR surveillance could potentially facilitate adaptive deployment strategies, subject to field validation. Economic modeling suggests that moderate reductions in metaphylactic antibiotic use could yield production and public health benefits, though these estimates remain illustrative. This review synthesizes current evidence on AI-guided phage discovery, epidemiological modeling, microbiome modulation, horizontal gene transfer risk assessment, economic evaluation, and regulatory innovation. Within a One Health framework, adaptive AI-guided phage platforms represent a high-leverage strategy for reducing antimicrobial dependence, provided that critical knowledge gaps are addressed.},
}

@article {pmid42423304,
year = {2026},
author = {Rehman, M and Sajjad, W and Kang, S and Rafiq, M and Zhao, Y},
title = {Mobilization of the ancient resistome from thawing permafrost.},
journal = {Critical reviews in microbiology},
volume = {},
number = {},
pages = {1-21},
doi = {10.1080/1040841X.2026.2698958},
pmid = {42423304},
issn = {1549-7828},
abstract = {Permafrost, ground frozen for at least two consecutive years, covers nearly one-quarter of the Northern Hemisphere and hosts diverse microbial communities. Climate-driven thaw is releasing preserved microorganisms and genetic material into contemporary ecosystems, where ancient genetic elements may be reintroduced into modern microbes and participate in gene exchange processes. Among these, antibiotic resistance genes (ARGs), which confer resistance to antibiotics, represent a critical yet underrecognized threat. Many originate from ancient microbial ecosystems shaped by natural antibiotic production and resistance, encode mechanisms not yet observed in clinical settings, and are associated with mobile genetic elements (MGEs) that facilitate horizontal gene transfer across microbial domains. Here, we synthesize evolutionary, molecular, and ecological perspectives on the preservation, release, and mobilization of permafrost-derived ARGs. We highlight mineral-DNA interactions that enhance the long-term stability of extracellular DNA containing ARGs and review the roles of MGEs in redistributing resistance determinants following thaw. We discuss conceptual models of rare cross-domain gene transfer and consider ecological and evolutionary implications under thawing conditions. ARG release from permafrost represents a neglected environmental factor that may contribute to antimicrobial resistance (AMR) dynamics and warrants investigation. Finally, identify key knowledge gaps and propose interdisciplinary frameworks for surveillance, risk assessment, and mitigation.},
}

@article {pmid42424608,
year = {2026},
author = {Solís-Lemus, C},
title = {Evolving view on phylogenetic networks.},
journal = {Systematic biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/sysbio/syag045},
pmid = {42424608},
issn = {1076-836X},
abstract = {Reticulate processes such as hybridization, introgression, and horizontal gene transfer cannot be fully represented by a bifurcating tree. Enter phylogenetic networks: first as split graphs to visualize tree discordance, then as explicit probabilistic models that capture biological phenomena. Here, we describe the broad taxonomy of network representations, distinguishing the principal classes of explicit networks, their biological interpretability and our ability to accurately estimate them from empirical data. We also trace the evolution of the main network inferential methods from hybrid detection tests, distance- and subgraph-based amalgamation methods, probabilistic approaches under the multispecies network coalescent, composite-likelihood and divide-and-conquer frameworks, while highlighting the selective pressures of statistical identifiability and computational scalability that have shaped this evolution. As we move towards a network thinking paradigm, previously isolated methodological lineages from population genetics, phylogenomics, and mathematical network theory are now introgressing, uniting diverse network models into a shared framework that can integrate sequence- and species-level reticulate processes, increase robustness to systematic errors, and refine algorithms for genome-scale data, expanding the tree of life into a richer, more entangled yet clearer picture of evolution.},
}

@article {pmid42424815,
year = {2026},
author = {Tang, Q and Zhang, Y and Garza, DR and Ruan, C and Liu, B and Rocha, U and Shen, P and Wei, Y and Deng, Y and Zhang, J and Richnow, HH},
title = {Virus-mediated fate of antimicrobial resistance genes in livestock manure anaerobic digestion.},
journal = {Water research},
volume = {305},
number = {},
pages = {126401},
doi = {10.1016/j.watres.2026.126401},
pmid = {42424815},
issn = {1879-2448},
abstract = {Antimicrobial resistance (AMR) poses a critical global health challenge, with livestock manure acting as a significant environmental reservoir for antimicrobial resistance genes (ARGs). Anaerobic digestion (AD) is a pivotal process for mitigating ARG dissemination at the livestock-environment-human interface. This study aims to elucidate the global dynamics of ARGs in AD systems, focusing on virus-host interactions and arms race, to identify actionable strategies for AMR control. We analyzed 205 metagenomic (4.5 Tb) and 36 meta-transcriptomic (640 Gb) datasets, including 15 newly generated datasets, revealing that pig manure AD harbors the highest ARG abundance (0.668 ARGs/16S rRNA), while AD systems generally exhibit limited transcriptional activation of ARGs. We constructed a viral dataset for livestock manure AD (GVD_LMAD), comprising 59,316 DNA and 727 RNA viral operational taxonomic units (vOTUs). Virus-host interactions established by CRISPR-Cas spacer, tRNA and homology matches revealed 889 lytic infections of antimicrobial-resistant bacteria (ARB) compared to only 18 ARG transduction events. Further analysis showed that the relative abundance of vOTUs assigned to the reduction role (4.11% ± 3.19%) was substantially higher than that of reproduction (0.72% ± 0.64%) and transduction (0.19% ± 0.30%), demonstrating that, among viral processes, lysis outweighs transduction in contributing to ARG abundance reduction in AD. Furthermore, an antiviral defense system (ADS) catalogue (GADSC_LMAD), derived from 2760 high-quality metagenome-assembled genomes (MAGs) containing 39,307 ADS, with ADS prevalence in ARB (7.8 ± 6.0 per MAG), indicating an intensified virus-host arms race in AD that may shield ARB from phage lysis. The resulting CRISPR-Cas immune network with expressed spacers targets foreign ARG-carrying sequences (primarily plasmids and ICEs), suggesting a mechanism that restricts horizontal gene transfer (HGT) via conjugation and transformation, despite shielding ARB from phage lysis. Collectively, these findings highlight that viral communities significantly contribute to ARG reduction through phage lysis relative to transduction, while the ADS-mediated arms race, despite protecting ARB, constructs a biological firewall that potentially limits HGT of ARGs. This study provides novel insights into virus-host dynamics as a key mechanism for controlling ARG dissemination in AD systems.},
}

@article {pmid42425460,
year = {2026},
author = {Feng, B and Chen, J and Wang, C and Fu, J and Wang, R and Zhang, J and Zhang, B and Cheng, C},
title = {Fate of antibiotic resistance genes during rural domestic wastewater treatment: Anaerobic unit as enrichment hotspot versus aerobic unit as attenuation zone.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135356},
doi = {10.1016/j.biortech.2026.135356},
pmid = {42425460},
issn = {1873-2976},
abstract = {Rural domestic wastewater treatment systems are important but understudied reservoirs for antibiotic resistance genes (ARGs), whose full-process migration mechanisms remain unclear. Herein, the contribution of each treatment unit of ARGs was investigated using metagenomic methods across two seasons in typical rural domestic wastewater treatment systems. Although a removal efficiency (69 % in winter and 22 % in summer) was observed for ARGs, higher antibiotic residues and temperature dramatically induced ARG occurrence in wastewater and horizontal gene transfer (HGT) risk during wastewater treatment. The ARG abundances in the anaerobic unit increased by 1.6-2.1 fold compared to the regulating pool, primarily driven by elevated mobile genetic element (MGE) activity. In sharp contrast, ARG reduction was achieved through ARG host removal and suppressed HGT potential in the aerobic unit. Notably, mobile ARGs were dominated by tetracycline resistance genes in winter and co-dominated by tetracycline and sulfonamide genes in summer, with most flanked by transposases. Key pathogenic hosts, including Klebsiella pneumoniae, Escherichia coli, and Pseudomonas aeruginosa carrying ARG-MGE complexes, were primarily concentrated in the regulating pool and the influent, forming high-risk upstream sources of dissemination. Partial least-squares path model highlighted MGEs as the primary drivers, and variance partitioning analysis indicated that MGEs account for 31 % of the explained variation in ARGs during wastewater treatment. In summary, the anaerobic unit was an ARG enrichment hotspot, while the aerobic unit as ARG attenuation zone during wastewater treatment. These findings provide crucial evidence to optimize rural wastewater treatment processes and to target the control of antibiotic resistance.},
}

@article {pmid42427100,
year = {2026},
author = {Weis, KS and Kaur, A and Ghosh, P and Potnis, N},
title = {Genome evolution in plant pathogenic bacteria.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evag174},
pmid = {42427100},
issn = {1759-6653},
abstract = {Bacterial plant pathogens have ravaged crops since the dawn of agriculture and continue to pose a serious threat today. Bacteria and their plant hosts have co-evolved in an evolutionary arms race, with artificial selection due to agriculture tipping the scale in favor of the pathogen. This review gives an overview of plant pathogenic bacterial diversity, showing that pathogenicity has independently evolved numerous times, and that there is not one unifying trait determining plant pathogenicity. Instead, these bacteria represent repeated, independent evolutionary transitions driven by life in complex ecological networks, that include plant hosts, insect vectors, microbial competitors, and highly heterogenous abiotic environments. Their genomes reflect this interplay through a dynamic balance of architecture and flux. These structural features, along with highly variable pangenomes, capture the balance between genome stability and flux imposed by ecological constraints and epidemiological dynamics. Horizontal gene transfer via conjugative plasmids, prophages, integrative and conjugative elements, transposons, and in some lineages, natural competence, remains the major source of adaptive novelty, enabling rapid remodeling of virulence repertoires, metabolic capabilities, and antibiotic or heavy metal resistance genes. These changes create distinct selective landscapes. Agricultural practices such as chemical use, host resistance deployment, or seed trade, can drive recurrent bottlenecks, expansions, and admixture events that leave strong genomic signatures in pathogens. Finally, this review explores the genomic differences enabling the divergence of lifestyles, while also acknowledging knowledge gaps and future directions of research on the evolution of bacterial plant pathogens.},
}

@article {pmid42429186,
year = {2026},
author = {Chen, J and Li, F and Wang, SY and Chen, TT},
title = {Crystal structure of Legionella pneumophila glycosidase effector LegY.},
journal = {Acta crystallographica. Section F, Structural biology communications},
volume = {},
number = {},
pages = {},
doi = {10.1107/S2053230X26006485},
pmid = {42429186},
issn = {2053-230X},
support = {2023QH1028//Fujian Medical University/ ; 2021-76//National Key Clinical Specialty Discipline Construction Program of China/ ; 2025J01639//Natural Science Foundation of Fujian Province/ ; 2020Y2006//Fujian Provincial Clinical Research Center for Hematological Malignancies/ ; 2025QNA018//Fujian Provincial Health Technology Project/ ; 2024Y9086//Joint Funds for the Innovation of Science and Technology, Fujian Province/ ; },
abstract = {Legionella pneumophila translocates approximately 330 effectors into host cells via its type IVB secretion system. These effectors mediate a diverse array of post-translational modifications, among which reversible glycosylation is closely associated with bacterial virulence. Although several glycosyltransferase effectors have been identified that glycosylate host proteins to subvert host cellular processes, no glycosidase effector has been reported to date. Here, we report the crystal structure of LegY, a putative glycosidase effector from L. pneumophila, determined to 1.46 Å resolution (PDB entry 27xj). LegY adopts a single-domain (α/α)6-barrel fold and is structurally assigned as a member of glycoside hydrolase family 15 (GH15). LegY structurally shows high similarity to fungal glucoamylases but shares lower homology with known prokaryotic counterparts. Phylogenetic analysis clusters LegY within the fungal clade, suggesting possible horizontal gene transfer or convergent evolution. This study provides structural insights into LegY, laying a foundation for future uncovering of its putative function during L. pneumophila infection.},
}

@article {pmid42415201,
year = {2026},
author = {Srithanasuwan, A and Zou, Y and Zadoks, RN and Suriyasathaporn, W and Schukken, YH},
title = {Recombination, mobile genetic elements, and genetic transfer contribute to the adaptation of Streptococcus uberis causing mastitis.},
journal = {Veterinary research},
volume = {57},
number = {1},
pages = {},
pmid = {42415201},
issn = {1297-9716},
mesh = {Animals ; *Streptococcus/genetics/physiology ; *Mastitis, Bovine/microbiology ; *Interspersed Repetitive Sequences ; *Streptococcal Infections/veterinary/microbiology ; *Recombination, Genetic ; Cattle ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Female ; Thailand ; Adaptation, Physiological/genetics ; },
abstract = {Streptococcus uberis is a major cause of bovine mastitis. However, the genomic mechanisms that facilitate adaptation of the pathogen within different host-associated environment or selection pressures remain poorly understood. This study analyzed whole-genome sequence data from three Thai dairy herds to investigate the contributions of recombination and mobile genetic elements (MGEs) to S. uberis evolution and adaptation. Among the 138 S. uberis genomes, 42 core genome sequence types (cgSTs) were identified, along with frequent detection of MGEs such as plasmid-associated genes (81.1% of isolates), prophages (67.4% of isolates), and insertion sequences (26.1% of isolates). The isolates from farm A exhibited the longest recombined fragment size, but with extremely low recombination frequency and recombination-to-mutation ratio. By contrast, the isolates from farm B, which had the highest prevalence of antimicrobial resistance (AMR) gene, showed a high recombination-to-mutation ratio (R/θ = 4.42) and more frequently contained MGEs associated with AMR genes. Finally, isolates from farm C shared a single core genome and AMR profile but harbored diverse prophages. Several prophages shared high sequence similarity (>99%) with phages infecting other bacterial genera, suggesting that ecological overlap between bacterial species may facilitate cross-genus genetic exchange, highlighting the influence of microbial ecology on the evolution of S. uberis. Collectively, our results illustrate the variety of mechanisms and genetic elements that contribute to the adaptive evolution of S. uberis in dairy farming environments.},
}

Animals
*Streptococcus/genetics/physiology
*Mastitis, Bovine/microbiology
*Interspersed Repetitive Sequences
*Streptococcal Infections/veterinary/microbiology
*Recombination, Genetic
Cattle
*Gene Transfer, Horizontal
Genome, Bacterial
Female
Thailand
Adaptation, Physiological/genetics

@article {pmid42415516,
year = {2026},
author = {Zhou, G and Liu, J and Liu, F and Xiao, Y and Graham, EB and Kuzyakov, Y and Ye, M and Xin, X and Chen, L and Zhang, C and Ma, D and Wu, Z and Zhou, Z and Zhou, J and Liang, Y and Zhang, J},
title = {Resource-Dependent Metabolic and Biogeochemical Consequences of Viruses in Agricultural Soils.},
journal = {Global change biology},
volume = {32},
number = {7},
pages = {e70994},
doi = {10.1111/gcb.70994},
pmid = {42415516},
issn = {1365-2486},
support = {42277336//National Natural Science Foundation of China/ ; 42425703//National Natural Science Foundation of China/ ; SKLSSA2501//Major Program of State Key Laboratory of Soil and Sustainable Agriculture/ ; BK20221561//Natural Science Foundation of Jiangsu Province/ ; CARS-03//China Agriculture Research System/ ; CARS-52//China Agriculture Research System/ ; CX(24)1003//Jiangsu Agricultural Science and Technology Innovation Fund/ ; NMKJXM202401-01//Key Special Projects of the "Science and Technology Revitalizing Inner Mongolia" Action Fund/ ; DE-AC05-76RL01830//Department of Energy, Office of Science, Biological and Environmental Research program and by Pacific Northwest National Laboratory/ ; },
mesh = {*Soil Microbiology ; Agriculture ; *Soil/chemistry ; Carbon/metabolism ; *Viruses/genetics/metabolism ; Metagenome ; Fertilizers ; },
abstract = {Soil viruses are crucial for microbial life, biogeochemical cycles of carbon and nutrients, and for microbial necromass formation. We hypothesized that the effects of viruses on these processes depend on organic matter and nutrient availability in soils. Here, we combined a 34-year long-term fertilization trial, 150 sequenced soil metagenomes, and microcosm experiments to explore how viruses modulate carbon and nutrient dynamics depending on resource availability. We uncovered 2789 viral populations (vOTUs) grouping into 301 viral clusters, 91% of which were previously unknown. Organically fertilized soils harbored most lytic viruses carrying diverse element cycling-related auxiliary viral genes (AVGs) acquired through co-evolution and horizontal gene transfer. Synthesis and heterologous expression assays further indicated that four AVGs (i.e., cbhA, pel, wbpD, GT2) had higher transcript levels in Escherichia coli under nutrient rich than nutrient poor conditions. Addition of virus particles to soils raised microbial carbon use efficiency (CUE; biomass production relative to carbon uptake) and accelerated microbial turnover leading to boosted microbial necromass formation by 14%. Conversely, in soils without organic fertilizers, viruses facilitate bacterial adaptation to stress (e.g., defense system and interference competition) and accelerate microbial decomposition of organic matter. 35 days after virus addition, CO2 and N2O emissions increased by 41% and 52%, respectively. Finally, we propose the Viral Entombing-Priming (VEP) framework to describe the contrasting roles of viruses in carbon and nutrient dynamics depending on soil fertility. This work reveals the viral "Matthew effect" (the rich get richer and the poor get poorer) in resource-rich and resource-poor soils and could unlock nature-based pathways to raise carbon and nutrient retention for sustainable agriculture.},
}

*Soil Microbiology
Agriculture
*Soil/chemistry
Carbon/metabolism
*Viruses/genetics/metabolism
Metagenome
Fertilizers

@article {pmid42415663,
year = {2026},
author = {Saati-Santamaría, Z and Flores, A and Canosa, I and García-Fraile, P},
title = {Horizontal Gene Transfer and Genome Rearrangements Shape Bacterial Adaptation for Bioremediation.},
journal = {Environmental microbiology},
volume = {28},
number = {7},
pages = {e70374},
pmid = {42415663},
issn = {1462-2920},
support = {CLU-2025-2-04//Escalera de Excelencia/ ; //Consejería de Educación de Castilla y León/ ; //FEDER Funds 2021-2027/ ; 101090267//Program EU Horizon Europe (HORIZON-TMA-MSCA-PF-EF)/ ; RYC2023-045204-I//MCIU/AEI/ ; CEX2020-001088-M//MCIN/AEI/ ; ProyExcel_00358//Programa de Excelencia de la Junta de Andalucía/ ; BIOD22_00033_20_PPCB. AGROREG//Plan Complementario de I+D+I, Plan de Recuperación, Transformación y Resiliencia/ ; PID2024-159973OB-I00//Programa Estatal Para la Investigación y el Desarrollo Experimental 2024-2027/ ; //University Pablo de Olavide/ ; },
mesh = {*Gene Transfer, Horizontal ; *Biodegradation, Environmental ; *Bacteria/genetics/metabolism ; *Genome, Bacterial ; *Adaptation, Physiological/genetics ; *Gene Rearrangement ; },
abstract = {Bacterial bioremediation involves bacterial strains and communities and their complex interactions with the environment, aiming to restore ecological balance by degrading contaminants in natural systems (soil, water, air). These processes rely on coordinated gene clusters encoding catabolic pathways. Many xenobiotic-catabolic gene clusters (XGCs) reside on mobile genetic elements (MGE), enabling horizontal gene transfer (HGT) and genome rearrangements that drive rapid microbial adaptation to anthropogenic contaminants. Here we review the evolutionary and ecological roles of HGT and genome restructuring in assembling and optimising biodegradative functions. We introduce the concept of metabolic HGT hubs-microbial taxa, mobile elements, and ecological features that serve as central nodes for gene exchange-facilitating metabolic innovation and cooperation within microbial consortia. These processes enhance ecosystem resilience and pollutant degradation efficiency by promoting functional redundancy and metabolic division of labour. Understanding these dynamics informs strategies for engineering microbial communities and genetic bioaugmentation to improve bioremediation outcomes. Our perspective highlights bioremediation as an extension of metabolic network evolution under anthropogenic selection, emphasising both its potential and the need to consider ecological and biosafety implications.},
}

*Gene Transfer, Horizontal
*Biodegradation, Environmental
*Bacteria/genetics/metabolism
*Genome, Bacterial
*Adaptation, Physiological/genetics
*Gene Rearrangement

@article {pmid42417524,
year = {2026},
author = {Tamura, N and Oda-Ishii, I and Satou, Y},
title = {Unique tunicate traits possibly encoded by horizontally transferred genes.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evag170},
pmid = {42417524},
issn = {1759-6653},
abstract = {While horizontal gene transfer (HGT) is common among prokaryotes, its prevalence and impact among metazoans are debatable. A clear example of HGT in animals is the cellulose synthase gene in tunicates, invertebrate chordates that possess the unique ability to produce a cellulose-containing tunic, despite sharing a conserved larval body plan with vertebrates. To investigate evolutionary roles of HGT in animals, we surveyed the genome of a tunicate and identified eight groups of candidate genes that are unlikely to have been vertically transferred. Notably, these candidates encode proteins potentially associated with physiological and structural features unique to tunicates, suggesting that integration of foreign genetic material has contributed to emergence of adaptive traits unique to the tunicate lineage.},
}

@article {pmid42419270,
year = {2026},
author = {Brown, EA and Brevi, A and Zong, DM and Zarrinpar, A},
title = {Engineering commensal microbes for host health.},
journal = {Cell host & microbe},
volume = {34},
number = {7},
pages = {1241-1261},
doi = {10.1016/j.chom.2026.05.025},
pmid = {42419270},
issn = {1934-6069},
mesh = {Humans ; Animals ; Synthetic Biology ; Bacteria/genetics/metabolism ; *Genetic Engineering ; *Microbiota ; *Biological Therapy/methods ; *Microorganisms, Genetically-Modified/genetics ; Neoplasms/therapy ; Metabolic Diseases/therapy ; },
abstract = {Engineered live biotherapeutic products (eLBPs) represent an emerging class of programmable microbial therapies capable of sensing and responding to host physiology. Advances in microbiome science and synthetic biology have driven the development of engineered bacteria that deliver therapeutic molecules, modulate host metabolism, or detect disease-associated signals. In this review, we summarize recent progress in the development of eLBPs across diverse disease indications, including inflammatory diseases, metabolic disorders, cancer, and infectious diseases. We highlight key factors that drive successful eLBP design, including chassis selection, methods for DNA delivery, approaches for tuning therapeutic expression, and genetic systems for biocontainment. Although early clinical studies demonstrate promising safety profiles, challenges remain in achieving predictable colonization, durable therapeutic activity, and robust biocontainment in vivo. By synthesizing advances across these areas, we propose a framework for the rational design of next-generation eLBPs that can more reliably translate from experimental systems to clinical application.},
}

Humans
Animals
Synthetic Biology
Bacteria/genetics/metabolism
*Genetic Engineering
*Microbiota
*Biological Therapy/methods
*Microorganisms, Genetically-Modified/genetics
Neoplasms/therapy
Metabolic Diseases/therapy

@article {pmid42340196,
year = {2026},
author = {Stuart, AJ and Du, Z and Hassan, NT and Adelson, DL},
title = {Ancient Persistence and Newfound Diversity of CR1-Group Retrotransposons Across Vertebrates.},
journal = {Genome biology and evolution},
volume = {18},
number = {7},
pages = {},
doi = {10.1093/gbe/evag155},
pmid = {42340196},
issn = {1759-6653},
mesh = {Animals ; *Retroelements/genetics ; *Vertebrates/genetics ; Phylogeny ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Variation ; Genome ; },
abstract = {Retrotransposons are mobile, repetitive DNA sequences that are ubiquitous across eukaryotes and widely recognized as key drivers of both gene and genome evolution. The CR1 group of retrotransposons is thought to have been present in the most recent common ancestor of vertebrates ∼560 Ma and is the dominant retrotransposon in the majority of vertebrate species. The advent of long-read sequencing technologies has enabled the assembly of high-quality genomes from representatives of almost all major vertebrate orders, enabling comparative analysis with deeply divergent species. To better understand the composition of CR1-group elements (CGEs) in vertebrates, we systematically characterized transposable elements across representative species from every available extant order of vertebrates. Our analysis uncovered previously unknown phylogenetic relationships of CGEs within and between species and has pushed back the origin of certain CR1-group subclades by tens of millions of years. Additionally, entirely novel elements with no close relatives in existing databases were uncovered within several of the species analyzed. We also detected numerous putative horizontal transfer events, many of which had not been previously documented. Overall, this investigation has provided the first vertebrate-wide analysis of an element that is historically understudied yet plays a pivotal role in genome biology and evolution.},
}

Animals
*Retroelements/genetics
*Vertebrates/genetics
Phylogeny
*Evolution, Molecular
Gene Transfer, Horizontal
Genetic Variation
Genome

@article {pmid42411838,
year = {2026},
author = {Furtado, KL and Gilbert, JA and Neal, M},
title = {Bioactive environments to combat antimicrobial resistance: artificial intelligence and model-driven microbial biocontrol for living materials.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxag161},
pmid = {42411838},
issn = {1365-2672},
abstract = {Antimicrobial resistance (AMR) continues to outpace development of new therapeutics. Many interventions focus on treating infection after it occurs, but resistant pathogens often emerge, persist, and spread within reservoirs, such as built environments. Microbial biocontrol offers a complementary, upstream strategy by reshaping ecological interactions to suppress the colonization, persistence, and transmission of AMR pathogens. Currently, biocontrol design relies upon the presumed functionality of probiotic genera across diverse environments despite limited experimental validation, alongside heuristic model predictions that prioritize efficiency over sensitivity. These approaches yield inconsistent outcomes, reflecting the context-dependent nature of microbial behavior. We review how advances in metabolic modeling and artificial intelligence (AI), in conjunction with experimental data, enable adaptable, context-aware biocontrol design with iterative design-test-learn cycles for optimization. We outline the ecological principles underlying microbial competition, highlighting Bacillus as a robust biocontrol chassis due to its biosynthetic capacity, stress tolerance, and genetic tractability. We then discuss how genome-scale, pan-genome-scale, and metabolism-and-expression models provide mechanistic insight into competitive fitness, metabolic trade-offs, and persistence. AI advances these approaches by extracting patterns from multi-omic datasets to build specific, yet versatile, foundation models (FMs) that guide strain and/or consortium selection for specific built environments. Moreover, these tools facilitate safe biocontrol deployment by enabling risk assessment of persistence, ecological displacement, and horizontal gene transfer (HGT), particularly for engineered living materials (ELMs) and bioactive building surfaces. Ultimately, AI-guided modeling and systems-level design provide scalable frameworks for developing durable, preventive strategies against AMR, shifting the focus from reactive treatment toward proactive control of pathogen ecology.},
}

@article {pmid42412049,
year = {2026},
author = {Maciszewski, K and Takahashi, K and Harada, R and Martinek, I and Nakayama, T and Iwataki, M and Inagaki, Y and Hehenberger, E},
title = {Recent plastid replacement in Karlodinium ballantinum (Kareniaceae, Dinoflagellata) challenges the paradigms of endosymbiotic gene transfer.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msag166},
pmid = {42412049},
issn = {1537-1719},
abstract = {Plastids, the photosynthetic organelles of eukaryotes, arose via endosymbiosis of cyanobacteria by a eukaryotic host and were subsequently spread across eukaryotic diversity by additional endosymbioses. The process of plastid endosymbiosis is poorly understood, as most endosymbiotic events happened long ago. One group of microbial eukaryotes, the dinoflagellates, are characterized by their highly convoluted plastid evolution, particularly the family Kareniaceae, who have replaced their ancestral dinoflagellate plastid in most members with haptophyte plastids. To further explore the evolutionary history of kareniacean plastids, we obtained transcriptomic data from two representatives: Gertia stigmatica and Karlodinium ballantinum. We determined that Gt. stigmatica retained its ancestral plastid and that it is nested deep within the Kareniaceae. Furthermore, the transcriptome shows no evidence of haptophyte plastid ancestry, indicating a haptophyte plastid was likely never present. Conversely, K. ballantinum has abundant gene transfers originating from haptophytes, shared with other Kareniaceae. Surprisingly, K. ballantinum's plastid genome is nearly identical to that of extant haptophyte Gephyrocapsa huxleyi, but we were unable to identify gene transfers from this current plastid across the transcriptome. We therefore conclude that i) the phylogenomic position of Gt. stigmatica and its retention of the ancestral plastid supports at least two independent plastid replacements in Kareniaceae, and ii) K. ballantinum has replaced its plastid organelle twice, with the second replacement being as yet unaccompanied by endosymbiotic gene transfer. Phylogenomics of plastid genomes suggests that the unusually high plastid replacement rate in Kareniaceae might be caused by accelerated mutation of the plastid genome within the host.},
}

@article {pmid42412807,
year = {2026},
author = {Willson, J and Warnow, T},
title = {CAMUS: scalable phylogenetic network estimation.},
journal = {Bioinformatics (Oxford, England)},
volume = {42},
number = {Supplement_1},
pages = {},
pmid = {42412807},
issn = {1367-4811},
support = {2316233//National Science Foundation/ ; },
mesh = {*Phylogeny ; *Algorithms ; *Computational Biology/methods ; *Software ; Evolution, Molecular ; Models, Genetic ; },
abstract = {MOTIVATION: Phylogenetic networks are models of evolution that go beyond trees, and so represent reticulate events such as horizontal gene transfer or hybridization, which are frequently found in many taxa. Yet, the estimation of phylogenetic networks is extremely computationally challenging, and nearly all methods are limited to very small datasets with perhaps 10-15 species (some limited to even smaller numbers).

RESULTS: We introduce Constrained Algorithm Maximizing qUartetS (CAMUS), a scalable method for phylogenetic network estimation. CAMUS takes an input rooted constraint tree T as well as a set Q of unrooted quartet trees and returns a level-1 phylogenetic network N that is built upon T through the addition of edges, in order to maximize the number of quartet trees in Q that are induced in N. We perform a simulation study under the Network Multi-Species Coalescent and show that a simple pipeline using CAMUS provides high accuracy and outstanding speed and scalability, in comparison to two leading methods, PhyloNet-MPL used with a fixed tree and SNaQ. CAMUS is slightly less accurate than PhyloNet-MPL used without a fixed tree, but is much faster (minutes instead of hours) and can complete on inputs with 201 species while PhyloNet-MPL fails to complete on the inputs with more than 51 species.

The source code is available at https://github.com/jsdoublel/camus.},
}

*Phylogeny
*Algorithms
*Computational Biology/methods
*Software
Evolution, Molecular
Models, Genetic

@article {pmid42413404,
year = {2026},
author = {Cao, Z and Gong, H and Qin, H and Wei, T and He, X and Yang, K and Li, X and Wang, Y and Jia, Y and Lan, X and He, W and Jing, X and Long, R and Li, B and Mi, J},
title = {Gut dysbiosis and Escherichia coli-associated enrichment of antibiotic resistance genes in diarrheal yak calves.},
journal = {Journal of hazardous materials},
volume = {514},
number = {},
pages = {142862},
doi = {10.1016/j.jhazmat.2026.142862},
pmid = {42413404},
issn = {1873-3336},
abstract = {Yak grazing systems are fundamental to pastoralist livelihoods on the Qinghai-Tibet Plateau (QTP), and their safe and sustainable development is essential for regional socioeconomic stability. Diarrhea is a multifactorial disease that severely impairs calf growth and may lead to mortality. In this study, we integrated second- and third-generation metagenomic sequencing with untargeted metabolomics to elucidate the underlying mechanisms and associated biosafety risks in yak calves with diarrhea. The results revealed significant gut microbiota dysbiosis in affected calves, characterized by reduced α-diversity and disrupted metabolism of arachidonic acid (AA) and its derivatives. Analysis of 1799 high-quality metagenome-assembled genomes (MAGs; ≥50% completeness and ≤5% contamination) showed a markedly increased relative abundance of Escherichia coli (16.4%) in diarrheal feces, far exceeding that observed in healthy controls. Eight assembled E. coli strains served as major reservoirs of antibiotic resistance genes (ARGs), contributing to high fecal abundances of resistance genes associated with MLS antibiotics (22.1%), bacitracin (21.7%), and β-lactams (19.9%), along with abundant mobile genetic elements (MGEs), including tnpA (21.1%) and IS91 (13.0%). Viral profiling identified E. coli as a key host for bacteriophages belonging to the families Chimeraviridae, Straboviridae, and Suoliviridae. These phages carried ARGs and MGEs that matched those detected in E. coli, potentially facilitating the dissemination of resistance through horizontal gene transfer. StrainPhlAn analysis further demonstrated that multidrug-resistant E. coli strains are widespread even among healthy calves, indicating the presence of a hidden resistome with potential for inter-individual transmission. These findings provide important theoretical guidance for managing yak calf diarrhea and offer valuable references for improving livestock production safety and mitigating antimicrobial resistance on the QTP.},
}

@article {pmid42414115,
year = {2026},
author = {Zhou, L and Chen, H and Wu, Y and Dolfing, J and Rittmann, BE},
title = {Periphytic biofilms entrap CO2 from industrial gas mixtures.},
journal = {Trends in biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tibtech.2026.06.015},
pmid = {42414115},
issn = {1879-3096},
abstract = {Industrial systems contribute approximately 30% of total anthropogenic CO2 emissions. Microalgal-based CO2 capture from industrial off-gases is a promising self-sustainable technology, but its efficacy is limited by the toxicity of high CO2, SOX, and NOX. Periphytic biofilms (PBs), composed of microalgae, bacteria, and abiotic components, can overcome these limitations through enhanced collective tolerance and CO2 fixation efficiency. This resilience arises from matrix-mediated physicochemical gradients and community-level adaptations, including metabolite exchange, horizontal gene transfer, and intercellular signaling. Translating PBs into a viable industrial technology requires a coordinated strategy encompassing advanced photobioreactor design, innovative material development, and microbial community regulation. Overcoming challenges related to biofilm stability, system scalability, and economic feasibility is crucial for advancing tailored PB systems for industrial carbon capture.},
}

@article {pmid42414947,
year = {2026},
author = {Kotb, DN and Zaki, S and Abdelrahim, SS},
title = {Assessment of genetic determinants of virulence and fluoroquinolone resistance in Proteus mirabilis isolates from urinary tract infections in Egypt.},
journal = {BMC infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12879-026-13838-x},
pmid = {42414947},
issn = {1471-2334},
abstract = {BACKGROUND: Proteus mirabilis (P. mirabilis) is a leading cause of urinary tract infections (UTIs) in both community and healthcare settings, especially in catheterized patients. Proteus species express various types of fimbriae that can serve as colonization-related virulence factors. The severity of infection escalates when these virulent strains acquire antibiotic resistance. The aim of this study was to investigate the prevalence, antimicrobial susceptibility, and genetic determinants of fluoroquinolone resistance in P. mirabilis isolates. Further, to screen for the presence of virulence genes encoding fimbriae and integrons.

METHODS: A total of 103 P. mirabilis isolates were recovered from urine samples collected from catheterized and non-catheterized UTI patients at Minia University Hospitals, Egypt. Antimicrobial susceptibility of fluoroquinolone-resistant (FQR) isolates was evaluated using the disc diffusion method. Phenotypic detection of extended-spectrum β-lactamase (ESBL) production was then performed, followed by molecular analysis for ESBL and plasmid-mediated quinolone resistance (PMQR) genes within the FQR isolates. All P. mirabilis isolates were screened by PCR for four virulence genes encoding fimbriae. Additionally, class 1, 2, and 3 integrons were investigated.

RESULTS: Among the 103 P. mirabilis isolates, 47 (45.6%) were non-susceptible to ciprofloxacin, of which 22 exhibited intermediate non-susceptibility and 25 were resistant. Multidrug resistance (MDR) was found in 70.2% (33/47) of FQR isolates, with significantly higher resistance to amoxicillin-clavulanic acid, sulfamethoxazole-trimethoprim, gentamicin, and amikacin compared to fluoroquinolone susceptible isolates. The virulence genes pmfA and mrpA were detected in 86.4% (89/103) and 78.6% (81/103) of isolates, respectively, while both atfA and ucaA were present in 70.9%. Isolates from catheterized patients showed significantly higher prevalence of virulence genes compared to those from non-catheterized individuals. PMQR genes were detected in 91.5% (43/47) of FQR isolates. The most prevalent were qnrS (74.5%), aac(6')-Ib-cr and qnrA (66% each), followed by qnrC (42.6%), qnrB (31.9%), and qepA (8.5%). Co-carriage of multiple PMQR genes was significantly more frequent in isolates with ciprofloxacin resistance than in those with intermediate non-susceptible (p = 0.0001). ESBL genes were detected in 36.8% of ESBL-producing FQR isolates, with blaTEM being the most prevalent (26.3%), followed by blaCTX-M-9 (21.1%), while blaSHV was not detected. Among the 103 P. mirabilis isolates, 99 (96.1%) carried class 1 and/or class 2 integrons, while none harbored class 3 integrons.

CONCLUSION: Our findings reveal a significantly high prevalence of fimbriae-associated virulence genes in P. mirabilis isolates from catheterized UTI inpatients, alongside notable dissemination of PMQR genes and class 1 integrons. The coexistence of these virulence and resistance determinants, particularly in hospital-derived strains, is concerning, as it may enhance horizontal gene transfer. This combination contributes significantly to MDR strain persistence and dissemination in the clinical settings.},
}

@article {pmid42373820,
year = {2026},
author = {Guo, J and Aroney, STN and Domínguez-Huerta, G and Smith, D and Vik, D and Owusu-Ansah, C and Pratama, AA and Solonenko, S and Tian, F and Howard-Varona, C and Zhong, ZP and Fofana, A and Smith, GJ and Hodgkins, SB and Cronin, D and , and , and Woodcroft, BJ and Tyson, GW and Rich, VI and Sullivan, MB and Roux, S and Bagby, SC},
title = {Mobile genetic elements shape microbial diversity and functions in thawing permafrost soils.},
journal = {Nature microbiology},
volume = {11},
number = {7},
pages = {1800-1814},
pmid = {42373820},
issn = {2058-5276},
support = {DE-SC0023307//DOE | SC | Biological and Environmental Research (BER)/ ; 10.46936/10.25585/60001148//DOE | SC | Biological and Environmental Research (BER)/ ; 2022070//NSF | Directorate for Biological Sciences (BIO)/ ; DE-AC02-05CH11231//DOE | Office of Science (SC)/ ; },
mesh = {*Interspersed Repetitive Sequences ; *Microbiota ; Biodiversity ; *Bacteria/classification/genetics/isolation & purification ; *Archaea/classification/genetics/isolation & purification ; *Permafrost/microbiology ; Gene Transfer, Horizontal ; Sweden ; *Soil Microbiology ; },
abstract = {Ecosystems are shaped by communities of microorganisms whose niches and impacts depend on functional profiles influenced by gene gains and losses. Culture-based experiments demonstrate that mobile genetic elements (MGEs) can mediate gene flux, but quantitative understanding of these dynamics in natural systems remains limited. Here we develop and apply a systematic, meta-omic framework to investigate MGEs in a complex natural system using an 8-year soil time series collected at Stordalen Mire, in Sweden's thawing permafrost margin. In this climate-critical peatland, we identify ~2.1 million MGE recombinases across 89 microbial phyla and assess ecological distributions, affected functions, past mobility and current activity. This revealed an active mobilome that shapes natural genetic diversity via differential impacts on major phyla and affects a wide range of functions, including metabolic genes involved in carbon flux and nutrient cycling. These findings and this analytic framework suggest avenues towards a better understanding of MGE diversity, activity, mobility and impacts across ecosystems.},
}

*Interspersed Repetitive Sequences
*Microbiota
Biodiversity
*Bacteria/classification/genetics/isolation & purification
*Archaea/classification/genetics/isolation & purification
*Permafrost/microbiology
Gene Transfer, Horizontal
Sweden
*Soil Microbiology

@article {pmid42405796,
year = {2026},
author = {Wang, N and Ma, H and Cheng, H and Yang, X and Liu, L and Zhu, D and Zhang, S and Zhou, X and Jia, R and Zou, Y and Li, L and Song, X and Yin, Z},
title = {Rhein reduces conjugation of IncFII-type plasmids in Escherichia coli and mitigates the spread of antibiotic resistance genes.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0339925},
doi = {10.1128/spectrum.03399-25},
pmid = {42405796},
issn = {2165-0497},
abstract = {UNLABELLED: Antibiotic resistance genes (ARGs) can be rapidly disseminated via bacterial conjugation, resulting in a substantial decline in the clinical efficacy of antibiotics. Novel therapeutic strategies independent of conventional antimicrobials are urgently needed. In this study, we identified rhein (RHE), a natural anthraquinone compound, as an effective IncFII plasmid transfer-reducing agent. At sub-inhibitory concentrations, RHE significantly reduced the conjugative transfer of IncFII plasmids in Escherichia coli. Importantly, the inhibitory effect of RHE extended to clinically relevant contexts, where it markedly impeded the transfer of the mcr-1 gene among clinical isolates and reduced plasmid dissemination in multiple organs in mouse models, demonstrating its in vivo potential. Mechanistic investigations revealed a dual mode of action that distinguishes RHE from traditional antimicrobials. Specifically, RHE compromises bacterial membrane integrity, leading to dissipation of the proton motive force and depletion of intracellular ATP, and concurrently disrupts the bacterial quorum-sensing system. Collectively, these findings establish RHE as a promising lead compound for the development of non-antibiotic therapeutics aimed at limiting the environmental and clinical spread of antimicrobial resistance. This study provides a novel and feasible strategy to address the escalating crisis of ARG transmission.

IMPORTANCE: Antimicrobial resistance in bacteria has become an increasingly severe global health challenge. The widespread dissemination of colistin resistance genes has markedly compromised the clinical efficacy of colistin, underscoring an urgent need for novel strategies to limit the spread of resistance determinants. In this study, we investigated the regulatory effects of rhein on IncFII-type plasmids and evaluated its intervention potential in the transmission of the colistin resistance gene mcr-1. Our results demonstrate that RHE effectively reduces mcr-1 transfer in both in vitro and in vivo models, highlighting its potential as a promising therapeutic candidate for the prevention and control of antimicrobial resistance gene dissemination.},
}

@article {pmid42405957,
year = {2026},
author = {Soto-Serrano, A and Vincze, T and Roberts, RJ and Krych, L and Mahony, J and Deptula, P},
title = {Comparative genomics and methylome profiling of Pseudolactococcus laudensis reveal signatures of niche adaptation and strain-level variation in mobile genetic elements and phage defence.},
journal = {Microbial genomics},
volume = {12},
number = {7},
pages = {},
doi = {10.1099/mgen.0.001779},
pmid = {42405957},
issn = {2057-5858},
mesh = {*Bacteriophages/genetics ; Genome, Bacterial ; Milk/microbiology ; *Interspersed Repetitive Sequences ; Genomics/methods ; Animals ; Gene Transfer, Horizontal ; DNA Methylation ; Adaptation, Physiological/genetics ; *Lactococcus/genetics/virology ; Phylogeny ; },
abstract = {Pseudolactococcus laudensis (formerly named Lactococcus laudensis) is an emerging lactic acid bacterium first isolated from raw milk in 2015 and subsequently detected in vegetables and dairy mesophilic starter cultures. Despite its recurrent isolation from diverse environments, the genetic basis of its niche adaptation, horizontal gene transfer and phage defence remains unexplored. Here, we perform the first comparative genomic and epigenomic analysis of P. laudensis using complete genomes of a plant-derived isolate (MCRI-603), a milk isolate (DSM 28961) and 20 strains from a Danish dairy mesophilic starter culture. Genomes were annotated and analysed using pangenomics, Clustering of Orthologous Genes and methylome profiling. Average nucleotide identity, pangenome and Clustering of Orthologous Genes analyses revealed niche-associated structure: dairy starter strains formed a tight cluster, while the plant isolate MCRI-603 and milk isolate DSM 28961 were more similar to each other than to the starter culture group. The pangenome comprised 4,946 genes, with 1,396 core genes. Dairy starter strains showed markedly elevated numbers of insertion sequences, pseudogenes, plasmids and genomic islands relative to MCRI-603, which was plasmid-free and carried very few insertion sequence elements or genomic islands. DSM 28961 displayed pseudogene count similar to the dairy starter strains but markedly fewer transposases. These patterns are consistent with a plant-associated origin of P. laudensis and progressive dairy specialization via mobile genetic element acquisition. The P. laudensis mobilome was found to carry key niche-related traits. Lactose utilization operons were plasmid-encoded, whereas exopolysaccharide-encoding loci, opp oligopeptide transport systems and several defence loci, including clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins (CRISPR-Cas), were consistently encoded within chromosomal integrative elements. All strains harboured prophage-like elements, including putatively intact prophages in 13 of them, and ~67% of 238 predicted antiphage systems resided on mobile genetic elements, underscoring their central role in phage defence. Restriction-modification systems dominated the defensome, and three strains encoded CRISPR-Cas systems (including type III-A and type I-C), indicating a higher prevalence than has been reported for Lactococcus lactis and Lactococcus cremoris, where CRISPR-Cas has rarely been observed. Methylome analysis identified 43 distinct motifs, of which 25 were novel. The P. laudensis methylome was overwhelmingly dominated by N[6]-methyladenine, and most motifs were short, non-palindromic and largely associated with type III restriction-modification systems and some type I and II subtypes. Nearly all strains exhibited distinct methylation profiles, including those isolated from the same dairy starter culture, highlighting extensive epigenetic diversification in dairy environments. Altogether, the data reveals a highly dynamic genomic and epigenomic landscape in P. laudensis, greatly shaped by mobile genetic elements, and provides a foundation for future work in this species and other Pseudolactococci.},
}

*Bacteriophages/genetics
Genome, Bacterial
Milk/microbiology
*Interspersed Repetitive Sequences
Genomics/methods
Animals
Gene Transfer, Horizontal
DNA Methylation
Adaptation, Physiological/genetics
*Lactococcus/genetics/virology
Phylogeny

@article {pmid42409099,
year = {2026},
author = {Jin, BJ and Chen, SC and Ji, BX and Wang, HB and Li, XY and Zhao, Y and Ding, K and Li, G},
title = {Manure-Free Organic Fertilization-Derived Lignin Alters the Dissemination of Antibiotic Resistance Genes from Soil to the Rhizosphere.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125194},
doi = {10.1016/j.envres.2026.125194},
pmid = {42409099},
issn = {1096-0953},
abstract = {Organic fertilizers significantly influence soil antibiotic resistance genes (ARGs); however, the impact of manure-free organic amendments on ARG dissemination from bulk soil to the rhizosphere remains unclear. This study investigated dissolved organic matter (DOM) composition and ARG profiles in bulk soil and the radish rhizosphere using three manure-free organic fertilizers with varying hydrochar contents (0%BC, 10%BC, and 30%BC). Under non-fertilized conditions, the rhizosphere harbored lower ARG abundances than bulk soil. Organic fertilization significantly elevated rhizospheric ARG enrichment, driven primarily by rhizosphere bacterial community shifts and antibiotic-resistant bacteria (ARB) accumulation rather than direct exogenous ARG inputs. Notably, the 10%BC treatment effectively mitigated this enrichment, maintaining absolute ARG abundances in the rhizosphere that were 69.5% and 72.5% lower than those in the 0%BC and 30%BC treatments, respectively. Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) revealed that 10%BC selectively enriched low-molecular-weight, highly oxidized lignin-like molecules with higher aromaticity. In contrast, 0%BC and 30%BC accumulated higher-molecular-weight, more bioavailable lignins. Network analysis and structural equation modeling (SEM) demonstrated that these chemically distinct lignins exerted contrasting effects: highly oxidized lignins under 10%BC potentially suppressed horizontal gene transfer (HGT) and ARB accumulation, whereas bioavailable lignins under 30%BC promoted them. Overall, fertilizer-derived lignins serve as crucial molecular mediators steering resistome dynamics across the soil-rhizosphere interface, with their oxidation states and molecular weights exhibiting contrasting roles in modulating HGT and ARG dissemination.},
}

@article {pmid42409253,
year = {2026},
author = {An, N and Wang, G and Wang, M},
title = {Screening of proteins interacting with the bacterial-origin horizontal transferred serine/threonine-protein kinase in Pacific white shrimp Litopenaeus vannamei.},
journal = {Developmental and comparative immunology},
volume = {181},
number = {},
pages = {105676},
doi = {10.1016/j.dci.2026.105676},
pmid = {42409253},
issn = {1879-0089},
abstract = {Litopenaeus vannamei is an economically important cultured shrimp worldwide, while frequent disease outbreaks restrict the development of its aquaculture. Pathogen-host horizontal gene transfer (HGT) provides new insights into improving shrimp disease resistance. The proto-oncogene serine/threonine-protein kinase mos-like (LvSTK) is a bacterial-derived horizontally transferred gene (HTG) identified in the L. vannamei genome. In the present study, yeast two-hybrid (Y2H) technology was employed to screen for proteins interacting with LvSTK in L. vannamei. A total of 28 independent positive interaction clones were ultimately identified. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed that these potential interacting proteins are involved in multiple biological processes, including immune response, disease regulation, cell growth and apoptosis, material transport and catabolism, as well as signal transduction. Ten potential interacting proteins were selected for pairwise validation and dot plate assay, and the results confirmed that 8 of them could all interact with LvSTK. Notably, peritrophin-1-like, β-actin, amylase, and other proteins are closely associated with immune regulation. These interacting proteins provide an important reference for elucidating the biological function of LvSTK and revealing the molecular mechanisms underlying the regulation of shrimp infection.},
}

@article {pmid42409359,
year = {2026},
author = {Al-Gallas, N},
title = {Genomic insights into the emergence, adaptation, and environmental dissemination of Enterococcus faecium as a multidrug-resistant pathogen: A One Health perspective.},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnag077},
pmid = {42409359},
issn = {1574-6968},
abstract = {Enterococcus faecium has become a prominent nosocomial pathogen, demonstrating significant multidrug resistance (MDR) and persistence in both hospital and environmental contexts. Genomic analyses indicate a highly adaptable genome characterized by a substantial accessory component enriched in antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs), including plasmids, transposons, integrative conjugative elements, and prophages. The acquisition and dissemination of resistance determinants, such as vancomycin (vanA, vanB), aminoglycoside, macrolide, tetracycline, and novel oxazolidinone resistance genes (optrA, poxtA), are predominantly facilitated by horizontal gene transfer mediated by these MGEs. Virulence factors, stress response regulators, and biofilm-associated genes augment E. faecium's survival in hospital settings and its colonization potential. Environmental reservoirs, such as wastewater, animal farms, and food products, facilitate interspecies gene exchange, underscoring the pathogen's significance within the broader One Health AMR network. This review brings together what we know about E. faecium's genome, focusing on its evolutionary adaptation, mobilome architecture, clinical and epidemiological importance, and spread in the environment. It gives us a complete picture of what we need to do to keep an eye on and control the disease in the future.},
}

@article {pmid42409569,
year = {2026},
author = {Cheng, P and Wang, Q and He, W and Zhu, X and Cheng, Y and Xiao, L and Dong, Q},
title = {Genomics-driven risk assessment of antimicrobial resistance: Current status, challenges, and future perspectives.},
journal = {Food research international (Ottawa, Ont.)},
volume = {240},
number = {},
pages = {119632},
doi = {10.1016/j.foodres.2026.119632},
pmid = {42409569},
issn = {1873-7145},
mesh = {Risk Assessment/methods ; *Genomics/methods ; *Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; *Food Microbiology ; Humans ; *Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/drug effects ; Phenotype ; },
abstract = {Antimicrobial resistance has become a major global public health challenge. However, conventional antimicrobial resistance risk assessment has largely focused on phenotypes while overlooking the dynamic dissemination of resistance genes and their mobility. This review systematically examines how genomics is reshaping microbial antimicrobial resistance risk assessment, with particular emphasis on the integration of key dimensions including clinically important antimicrobials, resistance gene mobility, evidence of ARG transmission along exposure pathways, and data quality and uncertainty. It discusses recent advances in qualitative, semi-quantitative, and quantitative assessment approaches, while also highlighting major challenges such as the parameterization of horizontal gene transfer, the integration of antimicrobial selection pressure, and the reliability of genomic-context evidence for resistance. Representative applications include WGS-based quantitative microbial risk assessment of foodborne pathogens, such as the Listeria monocytogenes case in which strain-level genomic heterogeneity was used to refine hazard characterization and exposure assumptions. Looking ahead, the integration of artificial intelligence is expected to further improve high-quality genome reconstruction, resistance phenotype inference, and transmission risk prediction, thereby facilitating more precise risk management.},
}

Risk Assessment/methods
*Genomics/methods
*Drug Resistance, Bacterial/genetics
Gene Transfer, Horizontal
*Food Microbiology
Humans
*Anti-Bacterial Agents/pharmacology
*Bacteria/genetics/drug effects
Phenotype

@article {pmid42398003,
year = {2026},
author = {Robinson, CRP and Dolezal, AG and Liachko, I and Newton, ILG},
title = {Host Range Breadth Correlates with Genic Diversity in Honeybee Phages.},
journal = {Genome biology and evolution},
volume = {18},
number = {7},
pages = {},
pmid = {42398003},
issn = {1759-6653},
support = {//Costco/Project Apis m/ ; 2005306//NSF IOS Collaborative Research/ ; 2022049//NSF DBI Biology Integration Institutes/ ; //Bill and Melinda Gates Foundation to Phase Genomics/ ; },
mesh = {Animals ; Bees/virology/microbiology ; *Bacteriophages/genetics ; *Host Specificity/genetics ; Genetic Variation ; Evolution, Molecular ; Genome, Viral ; Phylogeny ; Selection, Genetic ; Metagenome ; },
abstract = {Bacteriophages can evolve rapidly. Mutation and recombination via horizontal gene transfer allow them to counter adaptive responses by microbial hosts. However, little is known about the genomic processes underlying phage evolution within an ecological context-especially within natural microbial communities. This is due in part to the difficulty in resolving aspects of phage ecology, such as host range. To better understand the interplay of phage ecology and evolution within natural microbial communities, we combined measures of phage host range in vivo with measures of genome evolution in order to infer the evolutionary pressures acting on phage genomes within individual honeybee worker microbiomes. We show that near-identical phage genomes, cooccurring across multiple honeybee colonies, exhibit large variation with respect to gene modules, despite retaining a highly similar core genome. Estimates of genic diversity suggest deviations from neutral evolutionary models and identify loci under putative diversifying selection. We then use HiC-resolved metagenomics and show that the honeybee gut contains a dense phage community that exhibits a wide degree of host range variation. This variation differed across individual metagenomes in both the number and phylogenetic distance of potential hosts. We show that common measures of genetic variation positively correlate with host range in bee-associated phages and that functional targets of diversifying selection are partitioned differently between broad or narrow host range phages. Our work underscores the high host range variation associated with phages within host-associated microbial communities and provides evidence that this variation impacts rates of phage evolution.},
}

Animals
Bees/virology/microbiology
*Bacteriophages/genetics
*Host Specificity/genetics
Genetic Variation
Evolution, Molecular
Genome, Viral
Phylogeny
Selection, Genetic
Metagenome

@article {pmid42398478,
year = {2026},
author = {Gao, Q and Hou, J and Ding, W and Qi, C and Xu, D and Zhou, C and You, G},
title = {Carbon-to-nitrogen stoichiometry shapes divergent intracellular and extracellular antibiotic resistance gene fates through a dissolved organic matter-extracellular polymeric substance-mobile genetic element cascade in cyanobacteria-bacteria co-cultures.},
journal = {Water research},
volume = {304},
number = {},
pages = {126390},
doi = {10.1016/j.watres.2026.126390},
pmid = {42398478},
issn = {1879-2448},
abstract = {The carbon-to-nitrogen (C:N) ratio constrains microbial metabolism, yet whether nutrient stoichiometry controls the differential fates of intracellular (iARGs) versus extracellular antibiotic resistance genes (eARGs) remains unknown. This study aimed to test whether C:N ratios approaching the bacterial threshold elemental ratio (TER) would maximize iARG enrichment through a dissolved organic matter (DOM)-extracellular polymeric substance (EPS)-mobile genetic element (MGE) cascade, while eARG dynamics would be governed by physicochemical processes. Cyanobacteria-bacteria co-cultures at four C:N ratios (5:1, 10:1, 20:1, 40:1) were analyzed using shotgun metagenomics, FTICR-MS, 3D-EEM, untargeted metabolomics, and EPS fractionation. C:N = 10:1 produced the highest iARG abundance (65.1 ± 17.4 TPM, mean ± SD) and a 17-fold iARG/eARG ratio, while eARG showed no significant treatment effect (Kruskal-Wallis p = 0.082, treating triplicate subsamples as observations). FTICR-MS revealed the lowest intensity-weighted O/C (0.334), most negative NOSC (-0.67), and highest molecular diversity (8029 formulas) at C:N = 10:1, indicating a uniquely reduced, aliphatic-enriched DOM pool. (Note: FTICR-MS samples were pooled from triplicate subsamples per treatment, yielding one composite per C:N level; these results are therefore descriptive and unreplicated.) EPS polysaccharide/protein ratios peaked at 2.8, correlating with iARG across treatments (ρ=0.91, p < 0.001) but inversely with eARG (ρ=-0.59, p = 0.044). Guanosine (ppGpp precursor) peaked at C:N = 10:1 (ρ=0.75 with iARG) while UDP-glucose was depleted, confirming active EPS biosynthesis. Piecewise structural equation modeling identified a pathway from C:N through DOM, EPS, and MGE to iARG (R[2]=0.78, Fisher's C p = 0.31), whereas eARG depended on eDNA physicochemical trapping (R[2]=0.41). These findings provide evidence that nutrient stoichiometry acts as a selective control on ARG partitioning, suggesting that C:N monitoring could be incorporated into eutrophic water ARG risk assessment.},
}

@article {pmid42399985,
year = {2026},
author = {Ma, K and Zhang, Q and Jin, Z and Hao, R and Sun, X and Zhou, L and Li, M},
title = {Gut microbiota-derived extracellular vesicles: bridging microbial-host crosstalk in metabolic disorders.},
journal = {Cell communication and signaling : CCS},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12964-026-03034-4},
pmid = {42399985},
issn = {1478-811X},
support = {ZYZB-2022-798//National Administration of Traditional Chinese Medicine/ ; },
abstract = {Gut microbiota-derived extracellular vesicles have emerged as crucial mediators in microbe-host communication, not only facilitating intracellular communication, quorum sensing, and horizontal gene transfer among bacteria but also playing a central role in cross-kingdom dialogue. In recent years, bacterial extracellular vesicles (BEVs) have attracted widespread attention due to their ability to carry a diverse array of bioactive molecules-such as proteins, lipids, and nucleic acids-and deliver them to host cells, thereby precisely regulating host metabolic and immune homeostasis. This review systematically elaborates the entire biological process of BEVs, from their biogenesis to functional interactions with host cells, with a specific emphasis on revealing their roles in the pathogenesis of various metabolic diseases-including obesity, type 2 diabetes (T2DM), metabolic dysfunction-associated steatotic liver disease (MASLD), atherosclerosis, and hypertension-at both molecular and cellular levels. Furthermore, leveraging their inherent stability, biocompatibility, and targeting capabilities, we discuss the translational potential and challenges of BEVs in the diagnosis and treatment of metabolic disorders. Beyond summarizing the latest research advances on BEVs in metabolic disorders, this review provides a critical analysis of current mechanistic insights and clinical translation pathways, aiming to establish a theoretical framework for developing novel microbiome-based metabolic interventions. Deciphering the BEV-mediated microbiota-host interaction network holds promise for pioneering new strategies for the precision prevention and treatment of metabolic disease.},
}

@article {pmid42401055,
year = {2026},
author = {Li, BZ and Du, SH and Cui, HL and Gao, XX and Wu, JH and Li, BY and Gao, SH and Wang, AJ and Liang, B},
title = {Patterns and mechanisms of cross-media antimicrobial resistance development in a typical reclaimed water-receiving urban river.},
journal = {Water research},
volume = {304},
number = {},
pages = {126377},
doi = {10.1016/j.watres.2026.126377},
pmid = {42401055},
issn = {1879-2448},
abstract = {Reclaimed water (RW) from municipal wastewater treatment plants has raised environmental concern due to its complex mixtures of organic and inorganic pollutants, including emerging contaminants (ECs) occurring at trace levels. However, the extent to which ecological replenishment with RW promotes antimicrobial resistance (AMR) development in urban rivers, together with the underlying cross-media dissemination patterns, driving factors, and mechanisms across the water-sediment continuum, remains unclear. Here, we established a six-indicator framework to assess AMR risk and characterized its distinct spatial patterns in river water and sediment along a typical RW-receiving urban river. RW input rapidly reconfigured the resistome in the water column, whereas sediment exhibited a progressive, distance-dependent shift downstream. RW-associated selection pressures intensified AMR development in the water column by increasing antimicrobial resistance gene (ARG) abundance and horizontal gene transfer (HGT) potential, while strengthened cross-media exchange of antimicrobial-resistant bacteria (ARB) between water and sediment appeared to be an important process sustaining AMR development in sediment. By integrating structural equation modeling, machine learning, and correlation analyses, we identified several candidate factors of AMR dissemination (e.g., antimicrobials triclosan and sulfapyridine, along with four per- and polyfluoroalkyl substances) and quantified their contributions. Mantel analysis further supported triclosan and total nitrogen as influential RW-derived factors of sediment AMR dissemination. These findings clarify how RW reshapes AMR dissemination across the river water-sediment continuum and provide a mechanistic basis for managing AMR risks associated with urban RW reuse.},
}

@article {pmid42401059,
year = {2026},
author = {Ding, D and Xu, J and Fang, W and Zhu, G and Fan, Y and Chen, J and Ma, Y and Yang, M and Liang, Y and Liu, W and Qiu, X and Feng, H and Ding, Y},
title = {The overlooked risk of horizontal transfer of plasmid-borne antibiotic resistance genes induced by organophosphate esters in aquaculture environments.},
journal = {Water research},
volume = {304},
number = {},
pages = {126396},
doi = {10.1016/j.watres.2026.126396},
pmid = {42401059},
issn = {1879-2448},
abstract = {In recent years, the emergence of new environmental pollutants has drawn increasing attention to the plasmid-mediated conjugation transfer of antibiotic resistance genes (ARGs) induced by these contaminants. The widespread application of organophosphate esters (OPEs) has led to their frequent detection in aquaculture water, posing potential risks to the aquatic ecosystems and human health. In this study, we revealed that exposure to five types of OPEs (0.1-1000 µg/L) promoted the dissemination of RP4 plasmid from Escherichia coli to Pseudomonas alcaligenes, a multidrug-resistant bacterium isolated from actual aquaculture wastewater. Through the application of fluorescence detection, scanning electron microscopy, RT-qPCR, and RNA-seq techniques, we clarified at the cellular and molecular levels that OPEs promoted plasmid conjugation transfer by inducing reactive oxygen species (ROS) accumulation, activating the stress response (SOS), enhancing cell membrane permeability, improving intracellular energy supply, regulating the expression of conjugation-related genes, and activating the transfer apparatus encoded by RP4. Specifically, TBEP was selected as a representative OPE to systematically explore its impact on plasmid dissemination. Notably, a frequently overlooked aspect was that exposure to TBEP also enhanced the genetic stability and expression persistence of ARGs. Our findings emphasized that OPEs released from aquaculture facilities might act as driving factors to promote intergenus horizontal transfer of ARGs in actual aquaculture environments-a potential risk that has not yet been fully recognized.},
}

@article {pmid42402282,
year = {2026},
author = {Li, ZY and Cui, YW and Yang, RC and Mi, YN and Sui, Y},
title = {Dual roles of static magnetic field on enhancing sulfamethoxazole biodegradation and preventing antibiotic resistance genes transfer in halotolerant fungal-bacterial sludge treating saline aquaculture wastewater.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135312},
doi = {10.1016/j.biortech.2026.135312},
pmid = {42402282},
issn = {1873-2976},
abstract = {To address low biological treatment efficiency in saline antibiotic wastewater and antibiotic resistance gene (ARGs) transmission risk, a static magnetic field (SMF) was applied to a salt-tolerant fungal-bacterial consortium to enhance sulfamethoxazole (SMX) biodegradation; additionally, associated ARGs transmission risks were assessed. Results demonstrated that 40 mT was the optimal SMF intensity, under which the SMX degradation efficiency achieved a relative improvement of 62.8% compared to the control. At the mechanistic level, SMF alleviated oxidative stress by stimulating extracellular polymeric substance (EPS) secretion and upregulating antioxidant defenses, thereby reducing intracellular reactive oxygen species (ROS) accumulation. Furthermore, SMF significantly suppressed the absolute abundance of mobile genetic elements (MGEs), effectively restricting the horizontal gene transfer of ARGs. SMF application is an effective strategy for improving SMX removal and reducing ARGs transfer, providing new insights for developing advanced saline aquaculture wastewater biological treatment technologies.},
}

@article {pmid42405344,
year = {2026},
author = {Monte, DFM and Thakur, S},
title = {One Health transmission of plasmid-mediated antimicrobial resistance: genomic insights at the interface of food, animals, humans and the environment.},
journal = {JAC-antimicrobial resistance},
volume = {8},
number = {4},
pages = {dlag130},
pmid = {42405344},
issn = {2632-1823},
abstract = {Antimicrobial resistance (AMR) is increasingly recognized as a complex issue that requires an interdisciplinary One Health approach to find solutions. While early surveillance efforts have emphasized clonal expansion of resistant pathogens, recent genomic studies demonstrate that plasmid-mediated horizontal gene transfer is a dominant force shaping the global AMR landscape. Mobile resistance determinants conferring reduced susceptibility to critically important antimicrobials, including extended-spectrum β-lactams, quinolones, colistin, tigecycline and carbapenems, are now widely detected across food-producing animals, retail foods, environmental waters and human clinical isolates. In this review, we synthesize genomic evidence supporting cross-sector transmission of plasmid-mediated AMR, with a focus on key resistance genes (bla CTX-M, qnr, mcr, tet(X), bla NDM), and their associated plasmid backbones. We discuss why certain plasmids are particularly successful across diverse ecological niches and highlight implications for surveillance and mitigation strategies within a One Health framework. Rather than proposing a new One Health framework, this review synthesizes current genomic evidence highlighting the role of plasmids as major vehicles of AMR dissemination across interconnected reservoirs.},
}

@article {pmid42133993,
year = {2026},
author = {Carvalho, L and Corvalán, L and Dias, R and Braga-Ferreira, R and Targueta, C and Diniz-Filho, J and Telles, M and Nunes, R},
title = {The mitochondrial genome of pequi tree (Caryocar brasiliense Cambess.): genome structure, gene transfers, and evolutionary insights within Malpighiales.},
journal = {Genome},
volume = {69},
number = {},
pages = {1-14},
doi = {10.1139/gen-2025-0097},
pmid = {42133993},
issn = {1480-3321},
mesh = {*Genome, Mitochondrial ; *Evolution, Molecular ; Phylogeny ; *Gene Transfer, Horizontal ; *Magnoliopsida/genetics/classification ; Genome, Plant ; },
abstract = {The complete mitochondrial genome of Caryocar brasiliense (Caryocaraceae), an ecologically and economically important species native to the Brazilian savannas, was assembled and annotated. Using a hybrid assembly approach combining Oxford Nanopore and Illumina sequencing data, we assembled a 533 641 bp bipartite mitogenome organized into two circular chromosomes. A high density of dispersed repeats and simple sequence repeats was detected, along with extensive DNA transfers from the chloroplast and nuclear genomes (MTPTs and NUMTs). The variation of mitogenome size is positively correlated with the number of dispersed repeats (R[2] = 0.88). Genome annotation revealed 74 protein-coding genes, including sequences derived from both mitochondrial and chloroplast origins, as well as 376 predicted RNA editing sites, particularly concentrated in energy metabolism genes such as ccm and nad gene family. Comparative analysis across 10 Malpighiales species identified conserved core mitochondrial genes and revealed topological differences between mitochondrial and plastid phylogenies. These findings offer new insights into the structural and evolutionary dynamics of angiosperm mitochondrial genomes and provide a foundational resource for future genetic, evolutionary, and conservation studies in Caryocar brasiliense and related taxa.},
}

*Genome, Mitochondrial
*Evolution, Molecular
Phylogeny
*Gene Transfer, Horizontal
*Magnoliopsida/genetics/classification
Genome, Plant

@article {pmid42395547,
year = {2026},
author = {Kokroko, N and Jayanti, R and Sapoval, N and Nute, MG and Nakhleh, L and Treangen, TJ},
title = {Kente: A Graph-based Pangenomic Approach for Horizontal Gene Transfer Detection in Microbiomes.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.06.22.733643},
pmid = {42395547},
issn = {2692-8205},
abstract = {MOTIVATION: Horizontal gene transfer (HGT) shapes bacterial evolution and microbial ecosystems, yet detecting HGT within microbiomes remains a challenge due to fragmented metagenomic assemblies, reference bias, reliance on gene boundaries, and limited ability to model structural mosaicism and patterns across genomes.

METHODS: We present Kente, a novel pangenome graph-based framework designed for HGT detection that aligns metagenomic assembly contigs to a curated database of >600 genus-level bacterial pangenome graphs constructed using minigraph. Kente infers local taxonomic composition along contigs using alignment evidence and classifies candidate transfers using structured clade-transition topologies (e.g., A-B-A sandwich, open tips, and mosaic patterns). A complementary intra-genus module detects inter-species transfers within a single genus graph using segment-level clade annotations.

RESULTS: Across simulated intra- and inter-genus transfer scenarios, Kente achieves higher precision and comparable recall relative to existing gene-centric microbiome HGT detection approaches while reducing false positives from fragmented assemblies. Application to real human gut metagenomes (HMP2, n = 26) demonstrates Kente's ability to detect candidate cross-lineage transfer regions in complex microbial communities. Runtime profiling shows near-linear scaling with input size, enabling efficient analysis of large metagenomic assemblies.

https://github.com/treangenlab/Kente.},
}

@article {pmid42391838,
year = {2026},
author = {Yu, YH and Marín Arancibia, M},
title = {Mesorhizobium bavaricum sp. nov. and Mesorhizobium monacense sp. nov., two novel Lotus-associated species harbouring symbiotic plasmids.},
journal = {Systematic and applied microbiology},
volume = {49},
number = {5},
pages = {126739},
doi = {10.1016/j.syapm.2026.126739},
pmid = {42391838},
issn = {1618-0984},
abstract = {Legumes establish a mutualistic interaction with nitrogen-fixing rhizobia. Lotus japonicus is a model for studying this symbiosis; however, only a limited number of rhizobial species nodulating this host have been taxonomically described. Here, we characterise four Mesorhizobium strains (DC-1.1[T], Qj1B1, DC-1.5[T], and Qj2B2) isolated from root nodules of Lotus japonicus and Lotus burttii. Multi-locus phylogeny and phylogenomic analyses resolved these isolates into two well-supported monophyletic clades. Genome-based comparisons supported their classification as distinct taxa, with strains DC-1.1[T] and Qj1B1 showing 95.2% average nucleotide identity (ANI) and 62.9-63.5% digital DNA-DNA hybridisation (dDDH) values relative to Mesorhizobium newzealandense ICMP 19545[T], whereas DC-1.5[T] and Qj2B2 exhibited 92.5-92.8% ANI and 49.9-50.5% dDDH compared with Mesorhizobium waimense ICMP 19557[T]. Together with chemotaxonomic and physiological traits, these data support the proposal of two novel species, Mesorhizobium bavaricum sp. nov. (DC-1.1[T] and Qj1B1) and Mesorhizobium monacense sp. nov. (DC-1.5[T] and Qj2B2). Metagenomic analyses predicted high environmental prevalence for these novel taxa, particularly within soil habitats. Isolates DC-1.1[T], Qj1B1, and DC-1.5[T] effectively nodulated Lotus burttii and significantly promoted plant growth, whereas Qj2B2 neither nodulated nor enhanced growth. Comparative genomic analysis revealed that the nodulating isolates harbour symbiotic genes (nod, fix, and nif) on symbiotic plasmids, a rare feature in Mesorhizobium strains, whereas Qj2B2 lacks essential nod and nif genes. Consistent with these genomic features, symbiotaxonomic analysis assigned the nodulating isolates to symbiovar loti. These results highlight the potential of these isolates as models for comparative analyses of symbiotic plasmid evolution and horizontal gene transfer.},
}

@article {pmid42391956,
year = {2026},
author = {Sun, Y and Wang, XG and Chen, XJ and Zhou, Z and Huang, YJ and Wang, DS and Xi, BD and He, XS},
title = {Leachate treatment reduces but does not eliminate antibiotic resistance gene contamination: Associations between Pseudomonadota and resistome persistence in treated leachate.},
journal = {Journal of hazardous materials},
volume = {514},
number = {},
pages = {142868},
doi = {10.1016/j.jhazmat.2026.142868},
pmid = {42391956},
issn = {1873-3336},
abstract = {Landfill leachate is a hotspot for pharmaceuticals and personal care products (PPCPs) and antibiotic resistance genes (ARGs), but systematic research on their removal and ecological risks remains limited. This study investigated 30 leachate treatment plants using four techniques: biological + advanced oxidation (AOP), membrane bioreactor + nanofiltration/reverse osmosis (MBR+NF/RO), pretreatment + two-stage disc tube reverse osmosis (DTRO), and pretreatment + mechanical vapor recompression (MVR). Overall, 86.67% of target PPCPs achieved 90100% removal, though diethyltoluamide, caffeine, ibuprofen (IP), ofloxacin, and carbamazepine showed inconsistent results. Pretreatment + DTRO exhibited the most stable removal (coefficient of variation 0.013.21%). Despite the limited sample size (n = 2), pretreatment + MVR achieved high PPCP removal efficiencies (95.8100%), except for IP. IP presented high risk in effluents from biological + AOP and MBR + NF/RO. Treatment reduced 252 ARG subtypes and plasmid abundance, but chromosomally encoded multidrug and aminoglycoside resistance genes increased by 24.6100% in effluent, likely driven by selective enrichment of intrinsic resistance in persistent bacterial hosts. Pretreatment + DTRO (n = 6) and MVR (n = 2) showed relatively higher ARGs removal performance than the other techniques. Treatment weakened bacterial-ARGs associations and reduced selection pressures from PPCPs, heavy metals, and nutrients. However, horizontal gene transfer potential remained, associated with residual Pseudomonadota and five mobile genetic elements. Importantly, high-risk Rank I human pathogen-associated genes (bacA, mdtB, ompR, sul1) persisted in effluent. This first systematic study of four full-scale leachate treatment techniques provides a scientific basis for risk management under the One Health framework.},
}

@article {pmid42392292,
year = {2026},
author = {Zhang, Y and Ren, CY and Cao, X and Zhao, HP},
title = {The Role of Intracellular ROS in the Development of Antimicrobial Resistance:A Convergent Mediator Linking Mutations and Horizontal Gene Transfer.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {128683},
doi = {10.1016/j.envpol.2026.128683},
pmid = {42392292},
issn = {1873-6424},
abstract = {The development of antimicrobial resistance (AMR) is a major threat to global public health and environmental security. While antibiotics are known drivers, a wide range of non-antibiotic pollutants also promote antibiotic resistance genes (ARG) dissemination, yet the underlying unifying mechanism remains poorly integrated. This paper systematically analyzes how reactive oxygen species (ROS) act as major convergent mediator that drive the evolution of ARGs by promoting mutation and horizontal gene transfer (HGT) under various environmental stress conditions. The mechanisms of antibiotic-induced ROS generation and the controversial role of ROS in bacterial lethality are first delineated. It is then revealed that numerous non-antibiotic stressors, including disinfectants, heavy metals, nanoparticles, pharmaceuticals, and organic pollutants, convergently promote ARG conjugation, transformation, and transduction. Within these processes, moderate levels of intracellular ROS promote ARG dissemination, whereas excessive oxidative stress inhibits transfer or compromises cell viability. Based on these observations, we propose the concept of an "oxidative window" to describe the bidirectional regulatory effect of ROS on ARG dissemination at different concentrations. Furthermore , strategies to suppress ARG spread by modulating intracellular ROS are discussed, shifting from total elimination to precise regulation within the permissive window. Building upon this mechanistic framework, we further discuss the potential of incorporating ROS-related metrics into machine-learning-assisted risk assessment models and evaluate emerging ROS-regulation strategies for mitigating ARG dissemination. By reframing ROS from a passive byproduct into a measurable and potentially predictive indicator of ARG dissemination risk, this review provides a new conceptual basis for predicting and controlling environmental resistance risks.},
}

@article {pmid42388939,
year = {2026},
author = {Bhati, DG and Patil, HV and Patil, SR},
title = {Clinical Impact of Biofilm-Producing Carbapenem-Resistant Acinetobacter baumannii: Diagnosis and Treatment Challenges.},
journal = {Cureus},
volume = {18},
number = {6},
pages = {e110019},
pmid = {42388939},
issn = {2168-8184},
abstract = {Carbapenem-resistant Acinetobacter baumannii (CRAB) has emerged as a major nosocomial pathogen associated with significant morbidity and mortality, particularly in intensive care unit (ICU) settings. Its remarkable ability to survive in adverse environments, persist on medical devices, and rapidly acquire multidrug resistance has made it a critical global healthcare concern. This review aims to provide a comprehensive overview of the epidemiology, risk factors, antimicrobial resistance mechanisms, and pathogenicity of CRAB, with a special emphasis on the role of biofilm formation. CRAB infections are strongly associated with prolonged hospitalization, mechanical ventilation, previous antibiotic exposure, and invasive procedures. The organism exhibits multiple resistance mechanisms, including carbapenemase production, efflux pumps, porin modifications, and horizontal gene transfer, which significantly limit therapeutic options. A key virulence factor is its capacity to form biofilms on biotic and abiotic surfaces, enhancing bacterial survival, immune evasion, and resistance to antimicrobial agents. Biofilm-associated infections are often chronic, recurrent, and difficult to eradicate, particularly in device-related infections. The interplay between biofilm formation and antimicrobial resistance further complicates treatment outcomes. Current management strategies rely on last-resort antibiotics, combination therapy, antimicrobial stewardship, and strict infection control practices, while emerging therapies targeting biofilms offer promising alternatives. Understanding these complex mechanisms is essential for developing effective therapeutic and preventive strategies against CRAB infections.},
}

@article {pmid42389247,
year = {2026},
author = {Kaçar, B and Williams, TA and Eme, L and Gogarten, JP and Sanchez-Baracaldo, P and Spang, A and Aylward, FO and Travisano, M and Welander, PV and Huber, JA and Cooper, VS and Turner, PE and Lyons, TW and Ellington, AD and Copley, SD and Koonin, EV and Lynch, M},
title = {The Origin of Life in the Light of Evolution.},
journal = {ArXiv},
volume = {},
number = {},
pages = {},
pmid = {42389247},
issn = {2331-8422},
abstract = {The origin of life is often framed primarily as a chemical problem, yet life's defining feature is evolution. Advances in geochemistry, prebiotic chemistry, and molecular biology have produced diverse scenarios for the emergence of genomes, metabolism, and cellular compartments on the early Earth, but most of these models lack a population-genetics framework. Here, we argue that origin-of-life research must expand from asking simply how life began to exploring how it evolved from pre-biological systems. Synthesizing evidence from comparative genomics, phylogenetics, biochemistry, and geoscience, we emphasize that the last universal common ancestor (LUCA) was already a complex, ecologically adapted population far removed from the starting point of life, implying a deep pre-LUCA evolutionary history. We highlight how population genetics, ecology, and synthetic biology can constrain origin-of-life scenarios by making explicit the roles of selection, drift, mutation, horizontal gene transfer, parasites, and compartmentalization in shaping early communities. Finally, we outline an evolutionary research agenda spanning protometabolic and autocatalytic networks, protocells, the emergence of translation, and the transition to DNA genomes, in which qualitative models can now be buttressed and formalized by evolution-driven hypotheses subject to testing using theory and laboratory experiments, including those with synthetic cells.},
}

@article {pmid42390233,
year = {2026},
author = {Peng, Y and Liu, Q and Lin, X and Xing, F and Li, S and Liu, X and Han, Y and Chen, Y and Dong, X},
title = {Salinity-driven microbial adaptation of hydrocarbon-degrading communities in coastal sediments.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0036926},
doi = {10.1128/msphere.00369-26},
pmid = {42390233},
issn = {2379-5042},
abstract = {Salinity is a major abiotic driver of microbial diversity and metabolic function in coastal ecosystems. While its broad ecological impacts are well established, its role in shaping hydrocarbon-degrading communities and their adaptive mechanisms remains poorly understood. Here, we integrated gene- and genome-resolved metagenomics to investigate how salinity regulates the diversity, ecological interactions, and evolutionary dynamics of aerobic hydrocarbon-degrading microbes in Zhenhai Bay sediments (0.17-28.54 practical salinity units [PSU]). Across the natural salinity gradient, 10 types of hydrocarbon-degrading genes and 30 bacterial genomes spanning four phyla were identified, revealing extensive metabolic potential for the aerobic degradation of both aliphatic and aromatic hydrocarbons. The functional diversity and relative abundance of these genes increased significantly with salinity, accompanied by strong correlations with organic carbon parameters and nitrogen availability. Co-occurrence network analyses showed that hydrocarbon degraders, particularly Gammaproteobacteria, acted as key taxa maintaining community stability under saline conditions. Comparative genomics revealed that these bacteria possess multiple halotolerance strategies, including compatible solute biosynthesis and ion transport, supported by diverse energy-generating pathways. Frequent horizontal gene transfer and duplication of alkane monooxygenases (alkB and cyp153) expanded substrate ranges and enhanced functional diversity in hydrocarbon oxidation, highlighting salinity-driven evolutionary innovation. Together, these findings demonstrate that salinity governs the structure, metabolism, and evolution of hydrocarbon-degrading microbes, promoting microbial adaptation and functional diversification in coastal sediments.IMPORTANCESalinity is a defining feature of coastal ecosystems and a major regulator of microbial processes that support carbon cycling and pollutant degradation. This study highlights that salinity plays a central role in structuring hydrocarbon-degrading microbial communities and shaping their functional capacities and evolutionary trajectories in coastal sediments. By integrating osmoadaptation, metabolic potential, and community organization, our work shows that hydrocarbon degraders function as key links between environmental conditions and ecological processes. Salinity-driven shifts in microbial networks and metabolic strategies illustrate how environmental gradients can foster resilience and stability in highly dynamic coastal systems. Beyond advancing understanding of microbial responses, this study has potential implications for the rational design of bioremediation strategies targeting hydrocarbon pollutants in saline and estuarine environments.},
}

@article {pmid42391309,
year = {2026},
author = {Kim, JI and Zaheer, R and Zovoilis, A and Van Domselaar, G and Zaidi, SE and Haight, T and Beiko, RG and McAllister, TA},
title = {Investigating the mobility and host range of mobile genetic elements harbouring antimicrobial resistance genes in enterococci.},
journal = {Microbiology (Reading, England)},
volume = {172},
number = {7},
pages = {},
doi = {10.1099/mic.0.001720},
pmid = {42391309},
issn = {1465-2080},
mesh = {Conjugation, Genetic ; *Interspersed Repetitive Sequences ; Plasmids/genetics ; Gene Transfer, Horizontal ; DNA Transposable Elements ; Enterococcus faecium/genetics/drug effects ; *Host Specificity ; Bacterial Proteins/genetics ; Enterococcus faecalis/genetics/drug effects ; Anti-Bacterial Agents/pharmacology ; *Enterococcus/genetics/drug effects ; *Drug Resistance, Bacterial/genetics ; Multigene Family ; Humans ; Genes, Bacterial ; },
abstract = {In this study, the abundance and conjugation capacity of mobile genetic elements (MGEs) carrying resistance genes such as vanA, tet(M) and erm(B) were investigated to enhance our understanding of antimicrobial resistance (AMR) dissemination across the One Health continuum in high-priority, highly prevalent enterococcal pathogens. The abundance of MGEs was estimated using replicon typing and both reference-based and reference-free clustering approaches. Conjugation potential was assessed using agar plate mating between Enterococcus faecium donors and E. faecium, Enterococcus faecalis and Enterococcus hirae recipients, with conjugated MGE verified via long-read sequencing. Key findings include the identification of a vanA gene cluster from E. faecium VRE0008 associated with a Tn1546-like transposon embedded in a RepA_N-type putative plasmid (232,902 bp). This plasmid successfully conjugated with E. faecium, E. faecalis and E. hirae recipients from clinical, environmental and agricultural sources. The transfer predominantly involved the modular movement of a 46-kb region surrounding the vanA gene cluster, with E. hirae of agricultural origin (i.e. 0093A) being the exception, as it retained the entire plasmid. The tet(M) gene from E. faecium Ent0189 was located on a putative Rep_Trans-like plasmid, with features of Tn916 integrative conjugative elements. The entire plasmid from Ent0189 was successfully transferred to intra-species recipients from clinical and environmental sources, but transfer to E. faecalis and E. hirae was less common. Attempts to transfer tet(M) associated with Tn916 from bovine E. hirae to any of the E. hirae, E. faecium and E. faecalis isolates were unsuccessful. Additionally, the erm(B) gene from E. faecium NS0794 was carried by an MGE matching the RepA_N-type plasmid, but lacking the vanA gene cluster. Successful conjugative transfer of this plasmid was observed with E. faecium, E. faecalis and E. hirae of various origins, except one clinical E. faecalis isolate. These findings highlight the broad conjugation capabilities and modular mobility of MGEs carrying ARGs in enterococci, enhancing our understanding of dynamic MGE-mediated ARG dissemination and informing strategies to address the spread of AMR between species and habitats.},
}

Conjugation, Genetic
*Interspersed Repetitive Sequences
Plasmids/genetics
Gene Transfer, Horizontal
DNA Transposable Elements
Enterococcus faecium/genetics/drug effects
*Host Specificity
Bacterial Proteins/genetics
Enterococcus faecalis/genetics/drug effects
Anti-Bacterial Agents/pharmacology
*Enterococcus/genetics/drug effects
*Drug Resistance, Bacterial/genetics
Multigene Family
Humans
Genes, Bacterial

@article {pmid42379816,
year = {2026},
author = {Ni, Y and Bi, W and Yu, H and Chen, L and Yu, Y and Han, J and Wang, Y},
title = {Ecological and evolutionary implications of a mobile genetic element-richhaloarchaeon with unique osmotic resilience.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0340325},
doi = {10.1128/spectrum.03403-25},
pmid = {42379816},
issn = {2165-0497},
abstract = {We isolated a novel halophilic archaeon, strain DSL9, representing the proposed new species Haloliberatus hailidukes gen. nov., sp. nov., from Dishui Lake, China. Unlike most obligate halophiles, DSL9 survives in low salinity, even distilled water, without lysis. Genomic analysis revealed dual salinity adaptation strategies: salt-in and compatible solutes, including a complete trehalose biosynthesis pathway. The strain harbors multiple plasmids, notably a 111,311 bp large plasmid (pHdsl9-3) encoding replication (Orc1/Cdc6, SSB), transcription (TFIIB), transmission (T4SS cluster, ArdC-like protein), and recombination (XerA) modules. pHdsl9-3 provides auxiliary functions such as defense, genome diversification, ion detoxification, and suggests active horizontal gene transfer. Similar elements are widespread in Halobacteriales, highlighting their role in haloarchaeal genetic diversity and plasticity. The encoded XerA hinted at a function beyond DNA dimer resolution, suggesting it may have been adapted by other archaeal mobile genetic elements. These findings underscore the need to investigate plasmid-driven evolution and environmental adaptation mechanisms in haloarchaea.IMPORTANCEThis study reports the isolation and characterization of DSL9, a novel halophilic archaeon from a freshwater lake. Remarkably, DSL9 defies the typical obligate halophilic lifestyle by surviving in low-salinity environments, including distilled water, without cell lysis. A key discovery is the identification of a 111,311 bp large plasmid harboring essential modules for replication, transcription, transmission, and integration. Widespread distribution of similar elements across Halobacteriales suggests their crucial role in haloarchaeal genetic diversity and plasticity, warranting further study of plasmid-mediated evolution and adaptation strategies.},
}

@article {pmid42379824,
year = {2026},
author = {Ballén, V and Delgado, K and Pinar-Méndez, A and Vilaró, C and Galofré, B and Martí, S and González-Díaz, A and Alcalde-Rico, M and Soto, SM},
title = {Emergence and persistence of ESBL- and carbapenemase-producing Klebsiella pneumoniae-related species in Barcelona wastewater treatment plants.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0062126},
doi = {10.1128/spectrum.00621-26},
pmid = {42379824},
issn = {2165-0497},
abstract = {The World Health Organization classifies extended-spectrum beta-lactamase (ESBL) and carbapenemase-producing Klebsiella pneumoniae as critical-priority pathogens due to their high incidence, mortality, transmissibility, rapid resistance acquisition, and limited treatment options. Beyond clinical settings, their detection in wastewater treatment plants (WWTPs) provides an opportunity to assess their prevalence, persistence, and circulation within wastewater systems. This study characterized 37 antibiotic-resistant K. pneumoniae-related species strains isolated from two WWTPs in the metropolitan area of Barcelona, analyzing their antimicrobial resistance (AMR) profiles, antimicrobial resistance genes (ARGs), biocide and heavy metal tolerance genes (HMTGs), virulence factor genes (VFGs), biofilm-forming capacity, and conjugation ability. Among them, 70.3% were multidrug-resistant (MDR), and 16.2% were extensively drug-resistant. Whole-genome sequencing revealed diverse ARGs; all strains carried β-lactam resistance genes (14 ESBL and 12 carbapenemase producers), nearly all (96.9%) carried biocide or HMTGs, 64.9% harbored integrases, and all carried VFGs. Core-genome SNP analysis identified closely related strains across sampling periods and treatment stages, suggesting long-term persistence within the wastewater treatment system, despite biological and chemical processes in secondary treatment. Most strains (67.6%) displayed biofilm-forming capacity, and conjugation assays confirmed horizontal gene transfer in five of the seven ESBL-producing strains tested. High-risk clones were predominantly detected in the IFAS secondary treatment stage of the Gavà-Viladecans WWTP. The three strains recovered from the reclaimed water of the Baix Llobregat WWTP were ESBL or carbapenemase producers. Altogether, these results provide genomic and phenotypic evidence of the persistence and circulation of antibiotic-resistant K. pneumoniae-related species within wastewater treatment systems.IMPORTANCEWWTPs are essential for urban sanitation and environmental protection. Understanding how clinically relevant pathogens, such as ESBL and carbapenemase-producing K. pneumoniae-related species strains, behave in these settings may inform public health considerations. Investigating the presence and persistence of high-risk MDR pathogens in WWTPs helps identify circulation of AMR, assess the risk of gene transfer, and evaluate the potential for co-selection with other contaminants. This knowledge supports efforts to improve wastewater treatments, strengthen environmental surveillance, and develop integrated One Health strategies to limit the spread of AMR across human, animal, and environmental sectors.},
}

@article {pmid42380749,
year = {2026},
author = {Kurt, IC and Guner, H and Erdem, ZA and Can, O and Gumustop, I and Sirin, A and Erol, I and Kotil, ES and Ortakci, F},
title = {Genomic evidence of ecological flexibility and cross-niche CRISPR spacerome targeting phage-plasmid hybrids in Latilactobacillus curvatus.},
journal = {BMC genomics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12864-026-13098-8},
pmid = {42380749},
issn = {1471-2164},
support = {MGA-2024-45355//Bilimsel Araştırma Projeleri Birimi, İstanbul Teknik Üniversitesi/ ; },
abstract = {BACKGROUND: Latilactobacillus curvatus is a lactic acid bacterium with a remarkable ability to persist in diverse niches, including fermented foods and gut. Despite its industrial and potential probiotic relevance, the genomic underpinnings of its cross-niche adaptability remain poorly characterized.

METHODS: We conducted a species-contextualized comparative genomic analysis of 53 L. curvatus strains from food and gut isolates. This analysis integrated pangenome structure, metabolic repertoire, CRISPR-Cas immunity profiles, and mobilome analysis. Additionally, binding mode predictions and dynamics simulations were used to evaluate the theoretical binding energies of bacteriocins to the BamA target.

RESULTS: Phylogenomics revealed a polyphyletic population structure, indicating that long-term evolution is not strictly niche-specific. In contrast, genome-wide similarity showed clustering by isolation source, highlighting horizontal gene transfer (HGT) as a plausible contributor to niche adaptation. We identified a highly active mobilome, encompassing diverse plasmids, IS elements, and multiple intact prophages, reflecting high genomic plasticity characteristic of a multihabitat lifestyle. CRISPR-Cas systems were widespread, and analysis of 2,029 spacers revealed a broad immune repertoire targeting mobile genetic elements represented in fermented food, gut, and environmental datasets. We also identified spacer matches to phage-plasmid hybrid-like elements, highlighting the diversity of mobile genetic elements associated with the L. curvatus spacerome.

CONCLUSION: Our study reveals genomic features consistent with ecological flexibility in L. curvatus, including high genomic plasticity and a broad CRISPR spacer repertoire. Rather than demonstrating strict niche-specific evolution or a causal mechanism for cross-niche persistence, these findings support the hypothesis that this species has experienced diverse interactions with mobile genetic elements across multiple ecological contexts.},
}

@article {pmid42381546,
year = {2026},
author = {Bruce, J and Barona-Gómez, F and Hoskisson, PA},
title = {Considering internal conflict in the face of natural product biosynthesis and biosynthetic gene cluster evolution.},
journal = {Essays in biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1042/EBC20250017},
pmid = {42381546},
issn = {1744-1358},
support = {BB/T001038/1//UKRI | Biotechnology and Biological Sciences Research Council (AFRC)/ ; NPRONET POC045//UKRI | Biotechnology and Biological Sciences Research Council (AFRC)/ ; RPG-2022-316//Leverhulme Trust (The Leverhulme Trust)/ ; RCSRF2021\11\15//Royal Academy of Engineering (RAENG)/ ; },
abstract = {The present essay attempts to stimulate interest and provide insight into the dynamics of internal conflicts, kin selection, and ecological interactions in multicellular, metabolically gifted microorganisms and how these processes may affect biosynthetic gene cluster (BGC) diversity. The multicellular antibiotic-producing soil bacterium Streptomyces provides a useful model for exploring how internal conflicts emerge and are resolved in biology. These organisms must balance two resource-intensive processes that can create internal conflicts-natural product biosynthesis and sporulation. In Streptomyces, there is potential to mitigate these internal conflicts through division of labour, phenotypic specialisation, and extensive gene duplication and diversification, enabling colonies to optimise both natural product production and reproductive success. Horizontal gene transfer further expands gene families and BGCs, introducing new metabolic capabilities while generating opportunities for functional divergence to reduce internal conflict and potentially promote kin selection. Natural product BGCs also possess features that could identify them as 'greenbeards' (kin selection by trait), promoting cooperation among producers and harming non-producers. The coexistence of multiple natural product BGCs and resistance mechanisms in Streptomyces is discussed in the context of the diverse eco-evolutionary processes occurring in structured natural environments, competition among close relatives, recurrent BGC acquisition, and regulatory compatibility encountered by Streptomyces.},
}

@article {pmid42382359,
year = {2026},
author = {Mannion, A and Hooks, D and Comendul, A and Spirgel, R},
title = {Large-scale comparative genomics and structure-function analysis enables characterization of known and novel genetic determinants of antimicrobial resistance in bacterial pathogens.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1842956},
pmid = {42382359},
issn = {1664-302X},
abstract = {INTRODUCTION: Antibiotics are crucial for preventing infection-induced complications, but their widespread overuse has spurred the evolution of antimicrobial resistance (AMR) mechanisms in pathogens. Data-driven biosurveillance approaches utilizing whole genome sequencing data and computational approaches have the potential to improve the detection and characterization of known and emerging AMR profiles, especially in high-priority ESKAPE, enteric, and sexually-transmitted pathogens.

METHODS: In this study, a large-scale analysis of over 70,000 genomes representing 39 pathogen-antibiotic combinations was performed to identify resistance determinants statistically enriched in antibiotic resistant strains.

RESULTS: Using a kmer-based GWAS approach, over 7,000 unique sequences were identified among all resistant genomes. Of these, 1,925 sequences were homologous to known AMR genes, while over 5,000 sequences lacked homology, suggesting novel AMR-associated genes. In addition to identifying the predominant AMR genes for specific pathogen-antibiotic combinations, the findings for this study suggest that horizontal gene transfer mechanisms may influence AMR gene profiles between phylogenetically similar pathogens and antibiotic classes. Likewise, significant associations in co-harbored, multi-drug resistance mechanisms were identified in select pathogens. Protein domains analysis frequently detected efflux/membrane structure and antibiotic-associated metabolism domains in novel AMR-associated proteins, suggesting additional mechanisms potentiate resistance phenotypes. Furthermore, a Random Forest classifier using protein structure, molecular features, and binding affinity profiles to predict protein-antibiotic interactions was developed, identifying several novel proteins that may interact with antibiotics.

DISCUSSION: This study demonstrates the potential of large-scale comparative genomics coupled with AI/ML-based modeling to advance the understanding of AMR threats, thereby enhancing biosurveillance efforts and promoting new strategies to counteract emerging pathogens.},
}

@article {pmid42384800,
year = {2026},
author = {Ardalani, O and Phaneuf, PV and Krishnan, KJ and Pride, D and Nielsen, LK and Palsson, BO},
title = {Annotating the pangenome reveals the diversity in the genetic basis for metabolic enzymes.},
journal = {Science advances},
volume = {12},
number = {27},
pages = {eaeb3363},
pmid = {42384800},
issn = {2375-2548},
mesh = {*Escherichia coli/genetics/metabolism/enzymology ; *Genome, Bacterial ; *Genetic Variation ; *Metabolic Networks and Pathways/genetics ; *Molecular Sequence Annotation ; Gene Transfer, Horizontal ; Evolution, Molecular ; *Enzymes/genetics/metabolism ; },
abstract = {Affordable sequencing has flooded public databases with bacterial genomes; yet, species-scale maps that connect gene content variation to metabolic functions essential to biotechnology/system biology remain scarce. We address this gap by building a pangenome-wide gene-protein-reaction association and applying it to 2377 Escherichia coli genomes to reconstruct a pangenome-scale metabolic model (panGEM). We validate panGEM against Biolog carbon source utilization assays, achieving ≈0.99 precision in growth/no-growth predictions. Using panGEM, we identify >11,000 rare metabolic genes, yet only 35 metabolic reactions are rare. To explain the mismatch, we examined rare genes and found that most are pseudogenes or diverged orthologs acquired by horizontal gene transfer (HGT). Results indicate a recurrent loss-reacquisition cycle in which a core allele is lost/pseudogenized and its function is restored by HGT, preserving function without expanding the reactome, generating genetic heterogeneity in a small subset (~3.6%) of reactions, marking selection pressure hotspots of metabolism. Thus, pangenome annotation reveals the evolutionary dynamics that shape the genetic basis of metabolism.},
}

*Escherichia coli/genetics/metabolism/enzymology
*Genome, Bacterial
*Genetic Variation
*Metabolic Networks and Pathways/genetics
*Molecular Sequence Annotation
Gene Transfer, Horizontal
Evolution, Molecular
*Enzymes/genetics/metabolism

@article {pmid42387401,
year = {2026},
author = {Kang, SW and Shin, H and Kim, SJ and Lee, J and Cheon, KS},
title = {The first complete assembly and analysis of mitochondrial genome of Pinus thunbergii in Pinaceae.},
journal = {BMC plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12870-026-09408-7},
pmid = {42387401},
issn = {1471-2229},
support = {FG0400-2022-01-2026//National Institute of Forest Science/ ; },
abstract = {BACKGROUNDS: The Korean black pine (Pinus thunbergii) is a coastal conifer native to East Asia, including Korea, China, and Japan. Mitochondria and chloroplast in plants are semi-autonomous organelle that encode a small set of proteins and modulate nuclear genome expressions with retrograde signaling to coordinate stress responses and photosynthesis. Although the chloroplast genome of P. thunbergii has been previously characterized, a complete mitochondrial genome has not yet been reported, limiting genomic insights into the evolutionary dynamics of the genus Pinus.

RESULTS: We assembled the mitogenome using a hybrid sequencing approach that integrates Nanopore long reads with Illumina short reads. The mitogenome comprises two distinct chromosomes-a circular chromosome (~ 2.24 Mb) and a linear chromosome (~ 0.31 Mb)-with a total length of 2,553,981 bp (46.86% of GC), which is two times larger than mitogenome of P. taeda (1.2 Mb). These genomes encode 41 protein-coding genes (PCGs), 17 tRNA genes, and three rRNA genes. Based on these PCGs, we predicted 861 potential C-to-U RNA editing sites. Relative synonymous codon usage (RSCU) analysis identified that 30 codon values exceed 1; among these, 86.6% of codons ended with A/T bases, except UUG (Leu), UCC (Ser), ACC (Thr), and UAG (Ter). Only atp1 is exposed to purifying selection (Ka/Ks < 1). Comparative genomics revealed that 15 fragments were transferred to chromosome 1 and two fragments were transferred to chromosome 2 from the chloroplast of P. thunbergii (Accession number MW599991.31). Moreover, collinearity analysis showed that 217 fragments were similar to the mitogenome of P. taeda, which accounts for 23.92% of the P. thunbergii mitogenome. Phylogenetic analysis with 15 PCGs confirmed the taxonomic position within the family Pinaceae. Notably, rps3 showed a similar distribution to the phylogenetic tree of 30 PCGs.

CONCLUSIONS: In this study, we present the first complete mitogenome of P. thunbergii, analyze mitochondrial genomic characters, confirm horizontal gene transfer from the chloroplast genome, and reveal similarity and close phylogenetic affinity with P. taeda. This study expands the current organellar genomic resources and provides a foundation for evolutionary research in the genus Pinus. Moreover, the discovery of a multi-chromosomal architecture opens new avenues for investigating genome rearrangement and complex evolutionary dynamics across gymnosperm lineages.},
}

@article {pmid42388304,
year = {2026},
author = {Joest, M and Mollat, CL and Mutschler, L and Rodriguez-Franco, M and Sivabalasarma, S and Drepper, F and Huesgen, PF and Ott, T and Albers, SV},
title = {A multilayered cell envelope of a member of the Chloroflexota offers an anchoring platform for the archaellum.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1850455},
pmid = {42388304},
issn = {1664-302X},
abstract = {In a previous study, we discovered that Litorilinea aerophila, a member of the bacterial phylum Chloroflexota, had acquired a bona fide archaellum gene cluster through horizontal gene transfer from Archaea, a surprising finding given that the archaellum had long been considered an archaeal-specific motility machinery. Here, we hypothesize that the distinctive multilayered cell envelope of L. aerophila provides the structural context that enables the integration and function of the archaellum motility machinery. Using fluorescence microscopy, thin-section electron microscopy, and cryo-electron tomography, we revealed the organisation of the L. aerophila envelope and propose a mechanism for how the archaellum can traverse the peptidoglycan of L. aerophila by using the Type IV pilus alignment complex proteins PilO and PilN. In addition, we identified two other cell surface appendages: (i) pilus-like structures consistent with Tad pili, and (ii) grappling hook-like structures. Structural analysis of the grappling hook by CryoEM revealed an architecture that possibly plays a role in cell-cell interactions. Together, these findings imply that the evolution of a complex, multilayered cell envelope in Chloroflexota has facilitated the functional adaptation of archaeal surface machineries, allowing these bacteria to exploit the archaellum as a simpler, more energy-efficient motility system than the bacterial flagellum.},
}

@article {pmid42388456,
year = {2026},
author = {Kim, H and Kim, DH and Baek, JS and Won, D},
title = {Comprehensive safety evaluation of DW2009, a complex of Lactiplantibacillus C29 and fermented soybean powder.},
journal = {Toxicology reports},
volume = {17},
number = {},
pages = {102299},
pmid = {42388456},
issn = {2214-7500},
abstract = {Probiotics with potential health benefits are increasingly incorporated into a wide range of functional foods. However, the safety profiles of probiotics can vary depending on the strain, necessitating a comprehensive safety assessment prior to human use. In this study, the safety profile of a complex of Lactiplantibacillus plantarum C29 and fermented soybean powder (DW2009) was evaluated through a battery of in vitro and in vivo toxicological assessments. L. plantarum C29 demonstrated susceptibility to all tested antibiotics, thereby minimizing the risk of horizontal gene transfer. Safety tests confirmed the absence of hemolytic activity, virulence factors, toxin production, biogenic amine production, and mucin degradation. The results of a 90-day oral toxicity study with repeated doses established no observable adverse effect for DW2009 at 3000 mg/kg body weight/day. Additionally, all genotoxicity assays yielded negative results, indicating no mutagenic potential. Taken together, these findings support a favorable safety profile of DW2009 for application in functional foods.},
}

@article {pmid42167296,
year = {2026},
author = {Rasmussen, A and Porsbo, LJ and Roer, L and Sydenham, TV and Hallstrøm, S and Schønning, K and Holzknecht, BJ and Søes, LM and Nielsen, MTK and Østergaard, C and Wang, M and Søndergaard, TS and Fulgsang-Damgaard, D and Engsbro, AL and Menichincheri, G and Steinke, K and Agergaard, CN and Kristensen, B and Kjerulf, A and Justesen, US and Hammerum, AM and Hasman, H},
title = {Gene transfer from NDM-5-producing and OXA-48-producing Enterobacter hormaechei ST79 on contaminated dicloxacillin capsules to other Enterobacterales in Europe, 2020-23: a retrospective, observational, molecular epidemiological study.},
journal = {The Lancet. Microbe},
volume = {7},
number = {7},
pages = {101354},
doi = {10.1016/j.lanmic.2026.101354},
pmid = {42167296},
issn = {2666-5247},
mesh = {Humans ; Retrospective Studies ; *beta-Lactamases/genetics/metabolism ; *Enterobacter/genetics/drug effects/enzymology/isolation & purification ; Plasmids/genetics ; *Enterobacteriaceae Infections/epidemiology/microbiology ; Disease Outbreaks ; Denmark/epidemiology ; Anti-Bacterial Agents/pharmacology ; *Bacterial Proteins/genetics/metabolism ; Molecular Epidemiology ; *Gene Transfer, Horizontal ; Drug Contamination ; Capsules ; Europe/epidemiology ; },
abstract = {BACKGROUND: In February, 2023, an outbreak of Enterobacter hormaechei ST79 carrying blaNDM-5 and blaOXA-48 was linked to contaminated dicloxacillin capsules administered to approximately 79 000 individuals in Denmark. Initial clonal outbreak investigations identified 11 patients with the E hormaechei ST79 outbreak strain, which carried blaNDM-5 on a distinct IncX3 plasmid, and in nine cases, blaOXA-48 was on a distinct IncL plasmid. Interspecies plasmid transfer was observed in one patient, suggesting a potential plasmid-mediated outbreak involving other Enterobacterales. However, no studies have characterised the progression of a clonal outbreak originating from a contaminated medicine into plasmid-mediated dissemination of carbapenemase genes. Hence, we aimed to characterise the clonal and plasmid-mediated spread of carbapenemase genes in this outbreak.

METHODS: We conducted a retrospective genomic and epidemiological investigation using existing short-read whole-genome sequencing data from all carbapenemase-producing Enterobacterales (CPE) from the Danish national surveillance, collected between Jan 1, 2014, and Oct 1, 2023. All confirmed CPE isolates were eligible for inclusion. Using in-silico screening for unique fragments of the two outbreak plasmids, we selected 160 isolates for long-read sequencing to obtain complete plasmid sequences for outbreak investigation. Analyses were descriptive and included comparison of sequence identity and coverage to define outbreak-associated plasmids and summary statistics of patient characteristics.

FINDINGS: Data from 1829 isolates were obtained. We detected 16 of 53 isolates involved in the outbreak using conventional outbreak detection methods. The remaining 37 isolates were detected using plasmid-specific screening and long-read sequencing. 15 patients carried the outbreak E hormaechei strain, including the 11 patients previously reported. Three of the 15 patients presented with at least one additional bacterial species carrying one or both outbreak plasmids (pDcap_OXA-48 and pDcap_NDM-5). A further 24 patients, sampled between July 1, 2020, and Oct 1, 2023, presented with other Enterobacterales carrying one or both outbreak-associated plasmids but not the original E hormaechei ST79 strain. In four cases, outbreak-associated plasmids differed structurally from the original outbreak plasmid.

INTERPRETATION: This study describes how a clonal CPE outbreak caused by a contaminated medicine evolved into a complex plasmid-mediated outbreak involving multiple Enterobacterales species. Most patients related to the outbreak did not present with the original E hormaechei ST79 outbreak strain and were therefore not identified using standard outbreak detection methods. These findings highlight the importance of using plasmid-focused approaches in outbreak investigations.

FUNDING: The Danish Ministry of Health, SSI-Seq (cofunded by EU4Health).},
}

Humans
Retrospective Studies
*beta-Lactamases/genetics/metabolism
*Enterobacter/genetics/drug effects/enzymology/isolation & purification
Plasmids/genetics
*Enterobacteriaceae Infections/epidemiology/microbiology
Disease Outbreaks
Denmark/epidemiology
Anti-Bacterial Agents/pharmacology
*Bacterial Proteins/genetics/metabolism
Molecular Epidemiology
*Gene Transfer, Horizontal
Drug Contamination
Capsules
Europe/epidemiology

@article {pmid42378117,
year = {2026},
author = {Ono, E and Shimizu, K and Murata, J and Segawa, T and Shiraishi, A and Yokoyama, R and Toyonaga, H and Takagawa, M and Horikawa, M and Hoshino, A and Aoki, K},
title = {Transposon-colonized intron gain follows parasitism-mediated horizontal transfer of a cytochrome P450 gene.},
journal = {Plant physiology},
volume = {201},
number = {2},
pages = {},
doi = {10.1093/plphys/kiag335},
pmid = {42378117},
issn = {1532-2548},
support = {18H03950//Grants-in-Aid for Scientific Research/ ; 19H00944//Grants-in-Aid for Scientific Research/ ; //JSPS/ ; 25A305//Grant-in-Aid for Transformative Research Areas/ ; //Ohsumi Frontier Science Foundation/ ; 19J14848//Grant-in-Aid for JSPS Fellows/ ; },
mesh = {*Gene Transfer, Horizontal ; *Introns/genetics ; *Cytochrome P-450 Enzyme System/genetics/metabolism ; Phylogeny ; *DNA Transposable Elements/genetics ; *Cuscuta/genetics/enzymology ; Plant Proteins/genetics/metabolism ; Lignans/metabolism ; Sesamum/genetics ; Amino Acid Sequence ; },
abstract = {Specialized metabolites are often distributed sporadically across distantly related plant lineages, a pattern commonly attributed to convergent evolution, although the genomic processes enabling such innovation remain poorly understood. Here, we demonstrate that parasitic dodders (Cuscuta spp.) accumulate the lignan sesamin, a compound previously considered characteristic of sesame (Sesamum indicum) and related Lamiales species. We identified Cuscuta homologs of S. indicum CYP81Q1, which encodes piperitol/sesamin synthase (PSS), and demonstrated that these proteins retain catalytic PSS activity in vitro. Phylogenetic analyses indicate that CYP81Q was horizontally transferred from a Lamiales host to an ancestral Cuscuta lineage. Parasitism by C. campestris induces host CYP81Q expression and enhances interspecific transfer of genetic material across the haustorial interface, providing a mechanistic basis for horizontal gene transfer (HGT). Notably, comparative genomic analyses reveal that following horizontal acquisition, the transferred gene underwent extensive structural remodeling, characterized by sequential intron gains, while its enzymatic function was preserved. Many of the newly acquired introns exhibit hallmarks of insertion and excision of transposable elements, suggesting that mobile genetic elements contributed to post-transfer gene restructuring. The intron-rich architecture of Cuscuta CYP81Q was stably maintained throughout species diversification. Together, these findings suggest that parasitism-mediated HGT can be followed by intronization and transposon colonization, resulting in the generation of structurally complex yet functional genes. This process represents an underappreciated mechanism through which parasitic plants remodel horizontally acquired genes to facilitate metabolic innovation.},
}

*Gene Transfer, Horizontal
*Introns/genetics
*Cytochrome P-450 Enzyme System/genetics/metabolism
Phylogeny
*DNA Transposable Elements/genetics
*Cuscuta/genetics/enzymology
Plant Proteins/genetics/metabolism
Lignans/metabolism
Sesamum/genetics
Amino Acid Sequence

@article {pmid42378417,
year = {2026},
author = {Du, M and Yan, Y and Kang, X and Zhang, Y},
title = {Detection and removal methods of antibiotic-resistance genes in drinking water sources: a review.},
journal = {Journal of water and health},
volume = {24},
number = {6},
pages = {800-829},
pmid = {42378417},
issn = {1477-8920},
mesh = {*Drinking Water/microbiology ; *Water Purification/methods ; *Anti-Bacterial Agents/pharmacology ; *Genes, Bacterial ; *Drug Resistance, Bacterial/genetics ; *Drug Resistance, Microbial/genetics ; *Bacteria/genetics/drug effects ; Water Microbiology ; },
abstract = {The natural evolutionary process of bacterial resistance has been catastrophically amplified into a planetary health crisis through anthropogenic antibiotic pollution. Antibiotic accumulation in the environment has become a key driver of antimicrobial resistance (AMR) proliferation. This is particularly critical in wastewater and drinking water systems (DWSs). The presence of antibiotics selects for resistant strains and facilitates horizontal gene transfer of antibiotic resistance genes (ARGs). This phenomenon arises from excessive antibiotic usage coupled with inefficient removal through conventional water treatments, which fail to eliminate residual antibiotics or impede ARG dissemination. This review systematically summarizes current knowledge on bacterial resistance mechanisms in DWSs and recent advancements in detection methodologies of ARGs. Furthermore, we discussed the efficiency of conventional water treatment processes against antimicrobial containment and the emerging solutions to help curb the menace of AMR effectively. Overall, this study aims to establish a theoretical foundation for accurately assessing health risks posed by ARGs in DWSs and implementing effective prevention and control measures. This review can serve as a foundational resource for guiding policy recommendations to protect drinking water sources and public health.},
}

*Drinking Water/microbiology
*Water Purification/methods
*Anti-Bacterial Agents/pharmacology
*Genes, Bacterial
*Drug Resistance, Bacterial/genetics
*Drug Resistance, Microbial/genetics
*Bacteria/genetics/drug effects
Water Microbiology

@article {pmid42378761,
year = {2026},
author = {Shoaib, M and Tang, M and Munir, A and Shafiq, M and Mohsin, M and Zhang, X and Wu, Z and He, Z and Hao, B and Wang, S and Li, R and Pu, W},
title = {Dairy farm waste as a source of novel and globally disseminated multidrug-resistant Escherichia coli clones: A genomic and phylogeographic study.},
journal = {Journal of hazardous materials},
volume = {514},
number = {},
pages = {142819},
doi = {10.1016/j.jhazmat.2026.142819},
pmid = {42378761},
issn = {1873-3336},
abstract = {Dairy farm waste may serve as a reservoir for multidrug-resistant (MDR) Escherichia coli clones, but the genomic characteristics and dissemination potential of such clones remain incompletely understood. Here, we performed whole-genome sequencing and comprehensive genomic analysis of 64 MDR E. coli strains isolated from feces and sewage samples collected from two large dairy farms in Gansu Province, China. Genomic analysis revealed that strains carried 16-32 antibiotic resistance genes (ARGs), 1-6 plasmid replicon types, and 26-96 virulence genes (VGs), with numerically higher (though not statistically significant) counts in feces compared to sewage isolates. Multi-locus sequence typing (MLST) identified globally disseminated clones (ST10, ST38, ST58, ST155) and, for the first time in China, documented the presence of ST1508 (the predominant clone, 42% of isolates), as well as ST2520, ST7207, and ST7588 from dairy farm waste. Network analysis showed co-occurrence of these clones with transferable IncF plasmids harboring broad-spectrum resistance genes (e.g., rmtB, blaCTX-M-55) and multidrug efflux systems (e.g., acrAB-tolC). Contig-level analysis suggested that tet(A) and aph(3')-IIa were located on IncX1 plasmids, blaTEM-1B on IncFIC(FII), and blaCTX-M-55 on IncI1 plasmids, indicating potential for horizontal gene transfer. These findings identify dairy farm waste as a potential environmental reservoir of MDR E. coli clones with genomic features associated with resistance and virulence. While functional validation of transferability and environmental persistence is needed, the presence of these clones - particularly the emerging ST1508 lineage in untreated farm waste suggests that improved waste management, enhanced surveillance, and integrated One Health strategies may help mitigate dissemination risks. Further studies incorporating environmental sampling, persistence assays, and conjugation experiments are required to establish the actual hazard status.},
}

@article {pmid42379595,
year = {2026},
author = {Fullmer, MS and van Dijk, B and Takeuchi, N},
title = {Interaction range of common goods shapes Black Queen dynamics beyond the cheater-cooperator narrative.},
journal = {Proceedings. Biological sciences},
volume = {293},
number = {2074},
pages = {},
doi = {10.1098/rspb.2026.0911},
pmid = {42379595},
issn = {1471-2954},
support = {//Royal Society of New Zealand | Marsden Fund (Royal Society of New Zealand Marsden Fund)/ ; },
mesh = {*Biological Evolution ; Models, Biological ; Ecosystem ; *Symbiosis ; Ecotype ; *Microbial Interactions ; },
abstract = {Dependencies among microorganisms often appear mutualistic, as microbes grow faster together than alone. However, the Black Queen hypothesis (BQH) posits that these dependencies are underpinned by benefits from 'cheating' when others supply necessary common goods (CGs). The BQH often describes the evolution of a pair of ecotypes, a cooperator producing a CG and a cheater free-riding upon it. With multiple goods, their production can be centralized, with one ecotype producing everything and others cheating. We previously proposed an alternative BQH endpoint describing a community of 'mutual cheating', with production distributed over multiple interdependent ecotypes. Here, we present an individual-based eco-evolutionary model that predicts BQH dynamics resulting in various endpoints, including both distributed and centralizedproduction, and novel intermediate ecosystems involving apparent functional redundancy. These endpoints critically depend on the interaction range, the number of beneficiaries a producer can locally support. The intermediate ecosystems involve stable coexistence among ecotypes partially distributing production, with this coexistence punctuated by rare evolutionary transitions resulting in further distribution. These punctuated dynamics arise from cheaters stalling the division of labour by occupying the limited space within the producers' interaction ranges. Overall, our findings unveil complex evolutionary dynamics beyond the simple cheater-cooperator narrative, broadening the predictions of BQH.},
}

*Biological Evolution
Models, Biological
Ecosystem
*Symbiosis
Ecotype
*Microbial Interactions

@article {pmid42366735,
year = {2026},
author = {Guo, X and Lai, CY and Zhao, HP},
title = {Targeted Acclimation Unlocks Adaptive Evolution of a Methanotrophic Consortium Enabling 3A5MI Elimination and Enhanced Sulfamethoxazole Biodegradation.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.6c02194},
pmid = {42366735},
issn = {1520-5851},
abstract = {Targeted pollutant exposure is widely used to acclimate microbial communities for enhanced biodegradation of recalcitrant contaminants, yet the evolutionary mechanisms underlying functional reinforcement remain poorly understood. Here, we acclimated a methanotrophic consortium achieving efficient removal of 3-amino-5-methyl-isoxazole (3A5MI) (>90%, >5 mg/L/d) and elucidated the adaptive evolutionary processes behind it. Analyses of mobile genetic elements (MGEs) and horizontal gene transfer (HGT) revealed that dominant Methylococcaceae members served as genetic exchange hubs in the acclimation bioreactor. Integrated metagenomic and metatranscriptomic analyses showed that prolonged 3A5MI exposure activated their MGEs and promoted extensive HGT of genes related to energy generation, oxidative stress defense, and biosynthesis. This adaptive evolution enabled community-level metabolic rewiring, including optimized carbon metabolism to relieve energy limitation, niche differentiation, and specialized transcription of C-N bond catalytic functions. Furthermore, batch experiments and transformation product analyses confirmed that 3A5MI-induced functional traits (e.g., heterocycle hydroxylation and C-N bond catalysis) facilitated complete sulfamethoxazole (SMX) biodegradation. Overall, this study demonstrates the evolutionary plasticity of methanotrophic consortia under targeted acclimation and highlights MGE-driven genetic exchange and metabolic adaptation as key mechanisms that both underpin functional enhancement and support the development of methanotroph-based strategies for the biodegradation of recalcitrant isoxazole-based pollutants.},
}

@article {pmid42367189,
year = {2026},
author = {Erdem, ED and Li, B and Berendonk, TU and Klümper, U},
title = {Selective shifts in mobile antibiotic resistance genes under carbamazepine exposure in wastewater microbiomes.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag140},
pmid = {42367189},
issn = {2730-6151},
abstract = {Carbamazepine (CBZ) is a widely used nonantibiotic pharmaceutical that frequently persists through wastewater treatment and enters aquatic environments. CBZ has been, in simplified experimental systems, reported to stimulate horizontal gene transfer (HGT), a major process of antimicrobial resistance gene (ARG) dissemination in microbial communities. Moreover, it may facilitate selection for ARGs, directly or via co-selection. However, whether CBZ significantly modulates these processes in complex microbiomes remains insufficiently characterized. To address this gap, we exposed wastewater microbial communities to a gradient of CBZ concentrations for 3 days to evaluate early responses in community composition, ARG, and mobile genetic element (MGE) dynamics. Community structure remained largely unchanged across environmentally relevant CBZ concentrations. Most ARGs showed no consistent concentration-dependent response. However, a subset of clinically relevant ARGs increased in relative abundance in a dose-dependent manner. For the beta-lactam ARGs (bla CMY, bla OXA-48, bla CTX-M), and the trimethoprim ARG dfrA1, this increase was significantly correlated with IncP and IncW plasmid markers and the transposable element IS26, consistent with enhanced HGT-mediated dissemination. By contrast, the macrolide resistance gene ermF increased independently of the tested MGE markers, suggesting direct or host-specific selection or association with a nontested MGE. The strongest shifts occurred at sub-inhibitory CBZ concentrations within the upper range of concentrations reported in wastewater-impacted environments. These findings show that CBZ exposure can indeed influence the dissemination of selected ARGs in complex microbial communities without major effects on overall community composition, highlighting the potential for nonantibiotic pharmaceuticals to shape early resistome responses to pollutants in the environment.},
}

@article {pmid42368316,
year = {2026},
author = {Zheng, H and Zhuang, J and Lin, Q and Wang, T and Guo, G and Huang, L and Lin, W},
title = {Study on the role and clinical relevance of gut microbiota in diabetic foot ulcers.},
journal = {3 Biotech},
volume = {16},
number = {7},
pages = {287},
pmid = {42368316},
issn = {2190-572X},
abstract = {UNLABELLED: Diabetic foot ulcers (DFU) are severe and costly complications of diabetes, predisposing to infection, amputation, and mortality, highlighting the urgent need to clarify their mechanisms for optimized clinical management. This study integrated clinical biochemistry data and multi-omics analyses (including metagenomic sequencing) from 11 patients to reveal the critical role of gut microbiota in the pathogenesis of DFU. Results showed significant host metabolic disorders in DFU patients, characterized by hypoalbuminemia (mean ± SD:32.35 ± 6.02 g/L), persistent hyperglycemia (mean ± SD:8.25 ± 3.21 mmol/L), and imbalances in trace elements such as magnesium (mean ± SD:0.84 ± 0.08 mmol/L). Concurrently, the gut microbiota composition was markedly altered, with enrichment of the phylum Bacillota_A (formerly Firmicutes; 48.7% in patients vs. 32.1% in controls) and elevated genetic potential of virulence genes (e.g., type VI secretion systems, capsular polysaccharide gene cps4J/L). Metagenomic tracing revealed that antibiotic resistance genes (ARGs) such as tet(A) and blaOXA-1 were co-localized with mobile genetic elements (MGEs) including IncF plasmids and tnpA transposases. 99.2% of key ARGs shared sequence homology with gut-derived metagenome-assembled genomes (MAGs) and co-localized with MGEs, indicating potential cross-niche transfer capacity. Furthermore, renal (mean ± SD:11.81 ± 5.75 mmol/L) and hepatic (ALT: 35.67 ± 18.22 U/L) dysfunction correlated with aggravated gut dysbiosis and ARG enrichment. In conclusion, this study confirms that host metabolic deficiencies contribute to DFU refractoriness by altering gut microbiota ecology and enhancing horizontal gene transfer of virulence and resistance determinants, providing a novel framework for precision therapies targeting the host-microbe metabolic interface.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-026-04745-8.},
}