@article {pmid40837691,
year = {2025},
author = {Zhai, ZQ and Yang, LK and Zhu, LB and Zhao, FJ and Xie, WY and Wang, P},
title = {Early Life Exposure to Manure-Fertilized Soil Shapes the Gut Antibiotic Resistome.},
journal = {Environment & health (Washington, D.C.)},
volume = {3},
number = {8},
pages = {931-941},
pmid = {40837691},
issn = {2833-8278},
abstract = {The global rise of antimicrobial resistance (AMR) presents a pressing public health challenge with agricultural practices such as the use of manure fertilization, excessive antibiotic use in livestock, and the irrigation of crops with contaminated water contributing to the spread of antibiotic resistance genes (ARGs). Despite growing concerns, the pathways through which ARGs migrate from environmental reservoirs to animal microbiomes are poorly understood. In this study, we raised mice from birth in pig manure-fertilized red (Ultisols) and black (Mollisols) soils or unfertilized controls, sampling their gut microbiomes at 8 weeks, to show that early life exposure to manure-fertilized soil profoundly shapes the gut antibiotic resistome in mice. Application of organic manure significantly enriched tetracycline-resistant ARGs in both red and black soils. Mice living in these environments harbored markedly higher abundances of ARGs, particularly the tet-(Q) gene, compared to those in nonfertilized environments. Notably, Muribaculaceae and Bacteroidaceae were identified as key hosts of tet-(Q), with evidence suggesting a horizontal gene transfer between these families. These findings indicate that manure fertilization not only increases ARG abundance in soils but also facilitates its transfer to animal microbiomes, thereby amplifying the risk of AMR dissemination. This research underscores the importance of improved agricultural management practices to mitigate the environmental transmission of AMR.},
}

@article {pmid40837528,
year = {2025},
author = {Trejo-Meléndez, VJ and Contreras-Garduño, J},
title = {Master of Puppets: How Microbiota Drive the Nematoda Ecology and Evolution?.},
journal = {Ecology and evolution},
volume = {15},
number = {8},
pages = {e71549},
pmid = {40837528},
issn = {2045-7758},
abstract = {In recent decades, the microbiota has emerged as a key driver of biological functions in metazoans, and nematodes are no exception. Advances in genomic technologies have enabled detailed exploration of nematode-microbiota interactions, revealing compelling insights. However, much of our current understanding is derived from studies on the model organism Caenorhabditis elegans, where the microbiota's role in shaping host phenotypes and genotypes has been extensively characterized. These studies have uncovered the selective pressures influencing the function, structure, and assembly of the microbiota, highlighting the dynamic interplay between nematodes and their associated microbial communities. Despite these findings, the ecological and evolutionary implications of the microbiota in nematodes remain underappreciated. Emerging evidence indicates that the microbiota can modulate nematode life-history traits and mediate trade-offs among fitness components. Moreover, mechanisms such as horizontal gene transfer from bacteria have been shown to alter nematode phenotypes and genotypes, facilitating adaptation to novel or challenging environments. In this review, we integrate life-history theory into the nematodes-microbiota interactions, offering a framework to identify the mechanisms driving phenotypic variation in nematodes. Understanding these processes is essential for uncovering the evolutionary and ecological bases of metazoan diversification, with the microbiota acting as a crucial source of phenotypic and genetic variability.},
}

@article {pmid40835192,
year = {2025},
author = {Bui-Nguyen, TA and Huynh, TB and Tran-Van, H},
title = {Molecular Epidemiology of Acute Hepatopancreatic Necrosis Disease: A Review.},
journal = {Developmental and comparative immunology},
volume = {},
number = {},
pages = {105444},
doi = {10.1016/j.dci.2025.105444},
pmid = {40835192},
issn = {1879-0089},
abstract = {Acute hepatopancreatic necrosis disease (AHPND) is one of the major shrimp diseases worldwide which affects global economy up to 44 billion USD from 2010 to 2016. The causative agent of AHPND is the binary toxin PirAB, a toxin that causes sloughing effect on shrimp hepatopancreatic cells. This toxin is encoded by pirAB[vp] gene located within a 5.5-kb composite transposon Tn6264, on a ∼70-kb plasmid pVA carried by Vibrio parahaemolyticus. Up to date, the pathogenesis and epidemiological links between AHPND-causing strains are still unclear. Therefore, this review aims to collect achieved results about the distribution, origin, transmission, and antibiotic resistance status of AHPND-causing strains, the molecular mechanism of PirAB toxin, and the mobile genetic elements that promote the spread of AHPND to provide valuable insights for future studies. Phylogenetic studies on AHPND reveal its evolutionary history, transmission routes, and genetic variations, with findings suggesting diverse origins of AHPND strains across different regions, facilitated by horizontal gene transfer and adaptation mechanisms in V. parahaemolyticus populations. Antimicrobial resistance profiles of AHPND-causing strains are also diverse and prevalent, particularly in Vietnam, South Korea, and Thailand, encompassing antibiotics like ampicillin, amoxicillin, sulfadiazine sodium, streptomycin, colistin, cefalexin, erythromycin, ceftazidime, and neomycin, raising concerns regarding multidrug resistance. PirAB toxin might function through the pore-forming activity of PirB[vp] and the receptor-binding activity of PirA[vp], as predicted by Cry toxin model, while its expression is regulated by the quorum sensing system in V. parahaemolyticus. The pVA plasmid and the composite transposon Tn6264 both facilitates the dissemination of AHPND-causing strains, while the evolutionary mechanisms of these elements have not been widely understood. Transcriptomic and metabolomic studies also identify numerous differentially expressed genes in shrimp infected by AHPND-causing V. parahaemolyticus, and its immunity is also dependent on developmental stage and gut microbiota.},
}

@article {pmid40834228,
year = {2025},
author = {Mariault, L and Puginier, C and Keller, J and El Baidouri, M and Delaux, PM},
title = {Mechanisms, Detection, and Impact of Horizontal Gene Transfer in Plant Functional Evolution.},
journal = {The Plant cell},
volume = {},
number = {},
pages = {},
doi = {10.1093/plcell/koaf195},
pmid = {40834228},
issn = {1532-298X},
abstract = {Horizontal gene transfers (HGT) have been observed across the tree of life. While their adaptive importance in bacteria is conspicuous, the occurrence of HGT and their evolutionary significance in Eukaryotes has only recently started to be considered. In this review, we explore the extent of HGT in the plant kingdom, indicating the widespread occurrence of microbe - plant HGT and Plant - Plant HGT. We propose mechanisms that mediate these transfers, and detail the methods available to identify and test the robustness of putative HGT using both sequence-based and phylogenomic approaches. Exploring recently sequenced plant genomes across the green lineage has revealed hundreds of such HGT. We discuss the impact of these transfers on plant adaptation and functional diversification. In the future, expanding the phylogenomic scrutinization of the plant kingdom should reveal the full extent of HGT. In situ sequencing and combinations of synthetic biology and experimental evolution may allow catching ongoing HGT and testing the functional relevance of such events.},
}

@article {pmid40831643,
year = {2025},
author = {Meza, C and Sepulveda, B and Flores-Castañón, N and Valenzuela, F and Ormeño, C and Castillo, A and Echeverría-Vega, A and Jasem Mohammed Breig, S and Alardhi, SM and Gonzalez, A and Mora-Lagos, B and Banerjee, A},
title = {Genomic basis and functional characterization of the exopolysaccharide production by a thermotolerant Bacillus isolated from Tolhuaca hot spring.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1622325},
pmid = {40831643},
issn = {1664-302X},
abstract = {Bacillus licheniformis Tol1, a thermotolerant bacterial strain isolated from the Tolhuaca hot spring in Chile, was investigated for its genomic features and the functional properties of its exopolysaccharide (EPS). The whole-genome sequencing revealed ∼4.25 Mbp genome with a GC content of 45.9% and a rich repertoire of genes associated with environmental stress adaptation, antibiotic resistance, sporulation, biofilm formation, and EPS biosynthesis, including the presence of epsD and epsC. The strain also harbored intact prophage elements and a Type I-A CRISPR-Cas system, indicating potential horizontal gene transfer and genome plasticity. Confocal microscopy revealed robust biofilm formation at 45-55°C under neutral to slightly alkaline pH, with strong EPS matrix development. EPS production was optimized using OFAT and Response Surface Methodology (RSM), achieving a yield of 2.11 g L[-1] under optimized conditions, which was further validated using an Artificial Neural Network (ANN) model (R [2] = 0.9909). The EPS exhibited promising antioxidant activity and significant emulsification potential across various vegetable oils, which were comparable or superior to commercial bacterial EPS xanthan gum. Notably, the EPS also showed cytotoxic effects against AGS gastric adenocarcinoma cells, reducing viability by 38.38 and 37% at 50-100 μg μL[-1] concentrations, respectively, suggesting potential anticancer activity. Altogether, the study highlights B. licheniformis Tol1 as a multifunctional thermophile with valuable biotechnological potential, particularly for applications in food, pharmaceutical, and biomedical industries.},
}

@article {pmid40831357,
year = {2025},
author = {Cerda-Herrera, JD and Zhang, H and Wafula, EK and Adhikari, S and Park, SY and Carey, SB and Harkess, A and Ralph, PE and Westwood, JH and Axtell, MJ and dePamphilis, CW},
title = {Chromosome level assembly and annotation of Cuscuta campestris Yunck. ("field dodder"), a model parasitic plant.},
journal = {G3 (Bethesda, Md.)},
volume = {},
number = {},
pages = {},
doi = {10.1093/g3journal/jkaf193},
pmid = {40831357},
issn = {2160-1836},
abstract = {We present the first chromosome-level genome assembly and annotation for the genus Cuscuta, a twining and leafless parasitic plant of the morning glory family (Convolvulaceae). C. campestris, the study species, is a widely studied model parasite, due in part to its worldwide occurrence as a weed of agricultural and natural plant communities. The species has served as a model parasite for studies of parasite biology, haustorium development, growth responses to chemical and light stimuli, gene content and expression, horizontal gene transfer, interspecies RNA movement, and has a recently developed transformation system. The 505 Mb (1C) genome is assembled into 31 chromosomes and supports annotation of 47,199 protein-coding genes, 214 small RNA loci (including 146 haustoria-specific miRNAs), and 3,238 interspecies mobile mRNA loci. C. campestris is a recent tetraploid with a high retention of duplicated genes and chromosomes, and less than 8% nucleotide divergence between homoeologous chromosomes. We also show that transformation of C. campestris with the RUBY marker system allows visualization of transformed Cuscuta-derived fluorescent mobile molecules that have entered the host stem. This genome will be of value for scientists performing fundamental research in a wide range of molecular, developmental, population and evolutionary biology, as well as a research tool for studying interspecies mobile molecules, generating genetic markers for species and genotype identification, and for the development of highly specific herbicides.},
}

@article {pmid40830872,
year = {2025},
author = {Saffari Natanzi, A and Poudineh, M and Karimi, E and Khaledi, A and Haddad Kashani, H},
title = {Innovative approaches to combat antibiotic resistance: integrating CRISPR/Cas9 and nanoparticles against biofilm-driven infections.},
journal = {BMC medicine},
volume = {23},
number = {1},
pages = {486},
pmid = {40830872},
issn = {1741-7015},
mesh = {*Biofilms/drug effects ; *CRISPR-Cas Systems ; Humans ; *Nanoparticles ; *Anti-Bacterial Agents/administration & dosage/pharmacology ; Gene Editing/methods ; *Drug Resistance, Bacterial/genetics ; *Bacterial Infections/drug therapy ; Pseudomonas aeruginosa/drug effects ; },
abstract = {The increasing prevalence of antibiotic-resistant bacterial infections is a major global health concern, with biofilms playing a key role in bacterial persistence and resistance. Biofilms provide a protective matrix that limits antibiotic penetration, enhances horizontal gene transfer, and enables bacterial survival in hostile environments. Conventional antimicrobial therapies are often ineffective against biofilm-associated infections, necessitating the development of novel therapeutic strategies. The CRISPR/Cas9 gene-editing system has emerged as a revolutionary tool for precision genome modification, offering targeted disruption of antibiotic resistance genes, quorum sensing pathways, and biofilm-regulating factors. However, the clinical application of CRISPR-based antibacterials faces significant challenges, particularly in efficient delivery and stability within bacterial populations. Nanoparticles (NPs) present an innovative solution, serving as effective carriers for CRISPR/Cas9 components while exhibiting intrinsic antibacterial properties. Nanoparticles can enhance CRISPR delivery by improving cellular uptake, increasing target specificity, and ensuring controlled release within biofilm environments. Recent advances have demonstrated that liposomal CRISPR-Cas9 formulations can reduce Pseudomonas aeruginosa biofilm biomass by over 90% in vitro, while gold nanoparticle carriers enhance editing efficiency up to 3.5-fold compared to non-carrier systems. These hybrid platforms also enable co-delivery with antibiotics, producing synergistic antibacterial effects and superior biofilm disruption. Additionally, they can facilitate co-delivery of antibiotics or antimicrobial peptides, further enhancing therapeutic efficacy. This review explores the synergistic integration of CRISPR/Cas9 and nanoparticles in combating biofilm-associated antibiotic resistance. We discuss the mechanisms of action, recent advancements, and current challenges in translating this approach into clinical practice. While CRISPR-nanoparticle hybrid systems hold immense potential for next-generation precision antimicrobial therapies, further research is required to optimize delivery platforms, minimize off-target effects, and assess long-term safety. Understanding and overcoming these challenges will be critical for developing effective biofilm-targeted antibacterial strategies.},
}

*Biofilms/drug effects
*CRISPR-Cas Systems
Humans
*Nanoparticles
*Anti-Bacterial Agents/administration & dosage/pharmacology
Gene Editing/methods
*Drug Resistance, Bacterial/genetics
*Bacterial Infections/drug therapy
Pseudomonas aeruginosa/drug effects

@article {pmid40829589,
year = {2025},
author = {Sibbald, SJ and Lawton, M and Maclean, C and Roger, AJ and Archibald, JM},
title = {Pangenome biology and evolution in harmful algal-bloom-forming pelagophytes.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2025.07.055},
pmid = {40829589},
issn = {1879-0445},
abstract = {In prokaryotes, lateral gene transfer (LGT) is a key mechanism leading to intraspecies variability in gene content and the phenomenon of pangenomes. In microbial eukaryotes, however, the extent to which LGT-driven pangenomes exist is unclear. Pelagophytes are ecologically important marine algae that include Aureococcus anophagefferens-a species notorious for causing harmful algal blooms. To investigate genome evolution across Pelagophyceae and within Ac. anophagefferens, we used long-read sequencing to produce high-quality genome assemblies for five strains of Ac. anophagefferens (52-54 megabase pairs [Mbp]), a telomere-to-telomere assembly for Pelagomonas calceolata (32 Mbp), and the first reference genome for Aureoumbra lagunensis (41 Mbp). Using comparative genomics and phylogenetics, we show remarkable strain-level genetic variation in Ac. anophagefferens, with a pangenome (23,356 orthogroups) that is 81.1% core and 18.9% accessory. Although gene content variation within Ac. anophagefferens does not appear to be largely driven by recent prokaryotic LGTs (2.6% of accessory orthogroups), 368 orthogroups were acquired from bacteria in a common ancestor of all analyzed strains and are not found in P. calceolata or Au. lagunensis. A total of 1,077 recent LGTs from prokaryotes and viruses were identified within Pelagophyceae overall, constituting 3.5%-4.0% of the orthogroups in each species. This includes genes likely contributing to the ecological success of pelagophytes globally and in long-lasting harmful blooms.},
}

@article {pmid40829401,
year = {2025},
author = {Zhang, J and Chen, J and Wang, C and Wang, P and Feng, B and Gao, H and Chen, D},
title = {Nitrate input enriched the antibiotic resistance genes in lake sediments by shaping co-host community and promoting horizontal gene transfer.},
journal = {Journal of hazardous materials},
volume = {497},
number = {},
pages = {139580},
doi = {10.1016/j.jhazmat.2025.139580},
pmid = {40829401},
issn = {1873-3336},
abstract = {The impact of various non-antibiotic factors on antibiotic resistance has garnered widespread attention. However, there has been little investigation into whether the coexistence of nutrients with antibiotic resistance genes (ARGs) in aquatic ecosystems contributes to the increasing abundance of ARGs. We employed a microcosm experiment and metagenomic analysis to investigate the impact of nitrate on ARG profiles in lake sediments. Our results revealed that increased nitrate input correspondingly elevated the abundance of sediment ARGs, virulence factor genes (VFGs), mobile genetic elements (MGEs), and nitrate reduction genes (NRGs). Among the metagenome-assembled genomes (MAGs) harboring ARGs found by binning analysis, nitrate inputs increased the abundance of 78.4 % ARG-carried MAGs, especially in genera Nitrosomonas and Sulfuriomonas. All MAGs carrying ARGs simultaneously encoded NRGs, suggesting that ARG-NRG co-hosts are important factors for ARG proliferation. Co-localization and Pearson's correlation analyses suggested that nitrate input most likely accelerated the acquisition of ARGs by particular bacterial taxa via horizontal gene transfer (HGT). Genes involved in HGT, including those related to reactive oxygen species production, membrane permeability, ATP synthesis, and pili synthesis, were also upregulated by nitrate input, thus potentially enhancing ARG transfer. Based on the partial least squares path modeling analysis, abundances of genes involved in HGT (r = 0.43) and ARG-NRG co-hosts (r = 0.41) had the highest direct positive impact on the ARG abundance. Our study suggests the increased nitrate levels may drive the dissemination of antibiotic resistance, consequently affecting human health.},
}

@article {pmid40828659,
year = {2025},
author = {Wang, X and Chen, Z and Liu, C and Zhang, Z and Deng, Y and Tao, L and Tiedje, JM and Deng, J},
title = {Type I-F CRISPR-associated transposons contribute to genomic plasticity in Shewanella and mediate efficient programmable DNA integration.},
journal = {Microbial genomics},
volume = {11},
number = {8},
pages = {},
doi = {10.1099/mgen.0.001476},
pmid = {40828659},
issn = {2057-5858},
abstract = {The genome plasticity of species and strains in the genus Shewanella is closely associated with the diverse mobile genetic elements embedded in its genomes. One mobile element with potential for accurate and efficient DNA insertion in Shewanella is the type I-F3 CRISPR-associated transposon (I-F3 CAST). However, relatively little is known about the distribution and ecological significance of I-F3 CASTs and whether they could be suitable as a tool for targeted genetic manipulation in situ. To better understand the distribution of I-F3 CASTs in Shewanella, we analysed 602 Shewanella genomes. We found that I-F3 CASTs were present in 12% of all genomes, although differences in both gene arrangement and integration locus were observed. These Shewanella I-F3 CASTs carried up to 89 cargo genes, which were associated with diverse functions, including defence, resistance and electron transfer, demonstrating an important role in genomic diversification and ecological adaptation. We tested whether the I-F3 CAST present in Shewanella sp. ANA-3 enhanced gene insertion, both in situ and in a heterologous host. We observed I-F3 CAST-mediated crRNA-targeted integration of the supplied genes into the pyrF locus in Shewanella sp. ANA-3. Heterologous gene insertion with high integration efficiency in Escherichia coli was also demonstrated using a simplified version of ANA-3 I-F3 CAST. Altogether, this work highlights the important role of I-F3 CASTs in promoting genomic plasticity of the Shewanella genus and demonstrates the gene-editing capability of ANA-3-CAST both endogenously and heterologously.},
}

@article {pmid40825471,
year = {2025},
author = {Suzuki, H and Moriguchi, K and Shintani, M and Suzuki, M and Nojiri, H},
title = {Insights from public database sequences related to the replication initiation protein TrfA of the IncP-1 plasmid RK2.},
journal = {Plasmid},
volume = {},
number = {},
pages = {102756},
doi = {10.1016/j.plasmid.2025.102756},
pmid = {40825471},
issn = {1095-9890},
abstract = {Replicon typing identifies sequences similar to known DNA replication initiators and is widely used to detect specific plasmid groups (e.g., IncP-1) in genome and metagenome sequencing data. However, the characteristics of these homologous sequences in public databases have not been systematically assessed, making it difficult to determine whether detecting a specific replicon type reliably indicates the presence of a particular plasmid group. Here, we conducted amino acid sequence alignments to identify sequences similar to the replication initiation protein TrfA of the IncP-1 plasmid RK2 in the NCBI non-redundant (nr) database. In the nr nucleotide database, TrfA-matched nucleotide sequences were found across diverse taxonomic groups and replicons, including complete and partial plasmids and chromosomes. In total, 76 protein sequences from the reference plasmid RK2 were screened against the nucleotide sequences of the trfA-harboring plasmids to identify candidate IncP-1 plasmids. TrfA-related proteins, originating from bacterial chromosomes, plasmids, and phages, were selected from the nr amino acid database and used to infer phylogenetic trees. Our phylogenetic analyses reveal that TrfA homologs have diverged through vertical inheritance within IncP-1 and horizontal gene transfer across replicons and taxa. These findings caution against overreliance on single-gene replicon typing to infer plasmid group identity from sequence data.},
}

@article {pmid40823826,
year = {2025},
author = {Sadler, MC and Wietz, M and Mino, S and Morris, RM},
title = {Genomic diversity and adaptation in Arctic marine bacteria.},
journal = {mBio},
volume = {},
number = {},
pages = {e0155525},
doi = {10.1128/mbio.01555-25},
pmid = {40823826},
issn = {2150-7511},
abstract = {Arctic marine bacteria experience seasonal changes in temperature, salinity, light, and sea ice cover. Time-series and metagenomic studies have identified spatiotemporal patterns in Arctic microbial communities, but a lack of complete genomes has limited efforts to identify the extent of genomic diversity in Arctic populations. We cultured and sequenced the complete genomes of 34 Arctic marine bacteria to identify patterns of gene gain, loss, and rearrangement that structure genomes and underlie adaptations to Arctic conditions. We found that the most abundant lineage in the Arctic (SAR11) is comprised of diverse species and subspecies, each encoding 50-150 unique genes. Half of the 16 SAR11 genomes harbor a genomic island with the potential to enhance survival in the Arctic by utilizing the osmoprotectant and potential methyl donor glycine betaine. We also cultured and sequenced four species representing an uncultured family of Pseudomonadales, four subspecies of Pseudothioglobus (SUP05), a genus of high GC Puniceispirillales (SAR116), and a family of low GC SAR116. Time-series 16S rRNA amplicon data indicate that this culture collection represents up to 60% of the marine bacterial community in Arctic waters. Their genomes provide insights into the evolutionary processes that underlie bacterial diversity and adaptation to Arctic waters.IMPORTANCEGenetic diversity has limited efforts to assemble and compare whole genomes from natural populations of marine bacteria. We developed a cultivation-based population genomics approach to culture and sequence the complete genomes of bacteria from the Arctic Ocean. Cultures and closed genomes obtained in this study represent previously uncultured families, genera, and species from the most abundant lineages of bacteria in the Arctic. We report patterns of gene gain, loss, rearrangement, and adaptation in the dominant lineage (SAR11), as well as the size, composition, and structure of genomes from several other groups of marine bacteria. This work demonstrates the potential for cultivation-based high-throughput genomics to enhance understanding of the processes underlying genomic diversity and adaptation.},
}

@article {pmid40822392,
year = {2025},
author = {Teixeira, P and Ramos, M and Rivière, R and Azevedo, M and Ferreira, M and Cano, MM and Vieira, P and Reis, L and Matias, R and Rodrigues, J and Menezes, C and Rosado, T and Sequeira, A and Moreira, O and Ruppitsch, W and Cabal-Rosel, A and Mo, SS and Dias, E and Woegerbauer, M and Caniça, M and Manageiro, V},
title = {Genomic epidemiology and resistome dynamics of Enterobacter species in a Portuguese Open Air Laboratory: the emergence of the FRI-8 carbapenemase.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1593872},
pmid = {40822392},
issn = {1664-302X},
abstract = {Interconnected reservoirs contribute to the global spread of antimicrobial resistance (AMR), including carbapenem- and colistin-resistant Enterobacterales, highlighting the need for a One Health approach. We assessed the genomic epidemiology, diversity and AMR mechanisms of Enterobacter spp. across interconnected human, animal, plant, and environmental reservoirs in a Portuguese Open Air Laboratory. Over a one year monitoring period, samples from 12 different compartments were collected and processed using selective media to isolate Enterobacter spp., which were subjected to antibiotic susceptibility testing, whole-genome sequencing and subsequent analyses to identify AMR determinants, characterize plasmids and phylogenetic relationships. We established a collection of 61 Enterobacter isolates spanning nine species and 32 sequence types, including 16 novel ones, across nine compartments (river water, wastewater, soil, manure, feed, air, farmers, pigs, wild animals), reflecting the diversity and ubiquity of Enterobacter species. Core-genome analysis revealed eight genetic clusters, suggesting clonal transmission across compartments. In total, 29 antibiotic resistance genes were detected across all isolates. Notably, this is the first documentation of bla FRI-harbouring Enterobacterales in European environmental settings and the first to describe bla FRI, bla IMI and mcr-10 genes in Portugal. bla FRI-8 was detected in all E. vonholyi isolates (n = 17), located on four different IncFII(Yp) plasmids, and bla IMI-6 in an E. asburiae isolate, flanked by IS3 family transposases. E. vonholyi and the bla IMI-6-harbouring E. asburiae isolate were resistant to carbapenems. A mcr-10.1 gene was identified in an E. roggenkampii isolate on an IncFII(pECLA) plasmid. These plasmids exhibited high sequence similarity with global counterparts, indicating potential for horizontal gene transfer. Other antimicrobial resistance genes included qnrE1, sul1, and aadA2. Our findings underscore the importance of Enterobacter as vectors for AMR and the critical role of environmental compartments in its dissemination, reinforcing the importance of adopting a One Health approach to fully understand AMR dynamics.},
}

@article {pmid40822141,
year = {2025},
author = {Li, X and Chen, H and Chen, Y and Chen, X and Liu, S and Patil, S and Wen, F},
title = {In-silico Analysis of a Novel MCR-1.1 Variant on an IncX4 Plasmid Attenuating Colistin Resistance in Multidrug-Resistant Escherichia coli ST131.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {4053-4066},
pmid = {40822141},
issn = {1178-6973},
abstract = {INTRODUCTION: The emergence of mcr-1.1-mediated colistin resistance in Escherichia coli poses a significant threat to last-resort antibiotic therapy. This study investigates a novel variant of mcr-1.1 found in a highly virulent E. coli ST131 strain isolated from a pediatric patient with severe aplastic anemia and recurrent infections.

METHODS: Blood samples were collected from a 4-year-old patient, and the E. coli isolate underwent antimicrobial susceptibility testing, multi-locus sequence typing, serotyping, and whole-genome sequencing. In-silico analyses included molecular docking and molecular dynamics simulations to assess the structural and functional impact of the mcr-1.1 variant. Horizontal gene transfer experiments evaluated plasmid mobility.

RESULTS: The E. coli ST131 isolate harboured a mcr-1.1 gene located on a stable IncX4 plasmid and exhibited a multidrug-resistant phenotype. A missense mutation (T797C) led to an F265L substitution in the MCR-1.1 enzyme, reducing its phosphoethanolamine transferase activity. This mutation likely impairs lipid A modification, decreasing colistin resistance. Molecular modeling supported the reduced binding affinity of the mutated MCR-1.1 for lipid A. The plasmid demonstrated a horizontal transfer frequency of 1.3 × 10[-]². Phylogenetic analysis showed close relatedness to global ST131 clones.

CONCLUSION: This novel mcr-1.1 variant potentially restores colistin susceptibility in a globally prevalent E. coli lineage. The findings highlight a unique resistance attenuation mechanism and offer a promising avenue for restoring colistin efficacy. Further in-vivo validation is warranted to explore therapeutic strategies exploiting such mutations.},
}

@article {pmid40821579,
year = {2025},
author = {Gómez-Rubio, E and Arana, L and Vicario-Martín, R and Arbé-Carton, K and Garbisu, C and Martín-Cámara, O and Alkorta, I and Martín-Santamaría, S},
title = {Exploring Inhibition of Bacterial Conjugation Coupling Protein TrwB: Novel Ligands to Fight Antimicrobial Resistance Spread.},
journal = {ACS omega},
volume = {10},
number = {31},
pages = {34645-34658},
pmid = {40821579},
issn = {2470-1343},
abstract = {Bacterial conjugation is the most sophisticated mechanism for horizontal gene transfer. Conjugative plasmids allow the recipient bacterium to acquire new traits from the donor, such as antimicrobial resistance (AMR). Among the proteins involved in the plasmid transfer machinery, the Type IV Coupling Protein (T4CP) links the relaxosome and the Type IV Secretion System (T4SS). However, despite their biological relevance and their potential as a target to control AMR, only a few T4CPs have been exhaustively studied. The archetype of the T4CP family is the coupling protein of the conjugative plasmid R388, TrwB. The inhibition of TrwB ATPase activity or oligomerization with small-molecule modulators is expected to control the transfer of R388, contributing to combat AMR spread. Following a drug repurposing approach, we have combined in silico screening studies, molecular dynamics (MD) simulations, and in vitro bacterial conjugation assays to identify a small collection of compounds that selectively decrease the frequency of conjugation of the plasmid R388 (30-40%). Our results suggest that this inhibition is the result of the specific interaction of these drugs with TrwB. The search for conjugation inhibitors, via the inactivation of proteins such as T4CPs, rises as a strategy to advance in solutions to combat the silent pandemic of AMR.},
}

@article {pmid40816182,
year = {2025},
author = {Li, H and Yan, Y and Shi, Y and Zhang, X and Wang, X and Wang, X and Zhou, L and Zheng, G},
title = {Mechanisms underlying the role of Fe3O4 in enhancing antibiotic degradation and mitigating the spread of antibiotic resistance in aquaculture sediment: Coupling dissimilatory iron reduction with methanogenesis.},
journal = {Journal of hazardous materials},
volume = {496},
number = {},
pages = {139526},
doi = {10.1016/j.jhazmat.2025.139526},
pmid = {40816182},
issn = {1873-3336},
abstract = {Ferric oxides play a critical role in transforming organic contaminants within anaerobic aquaculture sediments; however, their effect on the removal of antibiotics and antibiotic resistance genes (ARGs) remains unexplored. This study revealed that the addition of Fe3O4 significantly promoted microbial Fe(III) reduction, SMX degradation, and methanogenesis by enhancing metabolic activity and facilitating electron transfer. While nutrient supplementation similarly improved SMX removal, it notably increased ARG abundance, unlike Fe3O4, which effectively suppressed ARGs. Although the presence of the electron shuttle AQDS in Fe3O4-amended systems further stimulated dissimilatory iron reduction, no additional benefit to SMX degradation was observed. Inhibition of methanogenesis reduced SMX degradation by 48 %, whereas Fe3O4 supplementation enriched the methane metabolic pathway, suggesting that SMX removal occurred through a conductive network involving Fe3O4 and methanogens. Moreover, Fe3O4 supplementation induced significant shifts in bacterial community composition, enhanced antioxidase activity, and reduced reactive oxygen species levels. These alterations were associated with the repression of genes related to horizontal gene transfer and a decrease in ARG hosts. Overall, these results indicate that Fe3O4 serves as an effective conductor, enhancing antibiotic degradation and limiting ARG propagation in aquaculture sediments.},
}

@article {pmid40815942,
year = {2025},
author = {McDonagh, F and Ryan, K and Kovářová, A and Tumeo, A and Clarke, C and Cormican, M and Miliotis, G},
title = {Identification of blaESBL- and blaCARBA- Positive Multi-Drug Resistant Mixta calida Isolates from Distinct Human Hosts.},
journal = {International journal of medical microbiology : IJMM},
volume = {320},
number = {},
pages = {151669},
doi = {10.1016/j.ijmm.2025.151669},
pmid = {40815942},
issn = {1618-0607},
abstract = {OBJECTIVE: This study aimed to investigate the identification of blaCARBA-positive multidrug-resistant Mixta calida isolates from human hosts and to elucidate their genomic determinants in a species-wide context.

METHODS: Two carbapenemase-producing M. calida isolates were received by the Galway Reference Laboratory Service in Ireland between June and July 2024. One isolate originated from a sputum sample, while the other was recovered from a routine screening rectal swab. Initial identification was performed using MALDI-ToF mass spectrometry, with genomic confirmation via 16S rRNA sequencing, digital DNA-DNA hybridization, and Average Nucleotide Identity analysis. Antimicrobial susceptibility testing was conducted using a MicroScan panel, following EUCAST and CLSI guidelines. Whole-genome sequencing, plasmid replicon typing, and antibiotic-resistance-gene and virulence-factor profiling were employed. Comparative analysis included all additional canonical M. calida genomes from NCBI database.

RESULTS: Both Irish isolates were taxonomically placed as M. calida and exhibited multidrug resistance against penicillins, cephalosporins, monobactams and ertapenem. The acquired genes blaKPC-3, blaOXA-9, and blaTEM-122 were detected on plasmid-borne contigs, indicating horizontal acquisition. Seven plasmid replicon types were shared between the two isolates. Both plasmid replicons and acquired antimicrobial-resistance-genes (ARGs) were seldomly identified across the species. Phylogenetic inference based on core genome analysis identified a monophyletic cluster, suggesting a single introductory event.

CONCLUSION: This study documents a dual occurrence of blaCARBA-positive M. calida in human colonisation and infection. The findings highlight the potential for horizontal-gene-transfer to drive the emergence of multidrug-resistant profiles in the species, underscoring the need for enhanced surveillance, diagnostic precision, and targeted infection control strategies to mitigate public health risks.

IMPACT STATEMENT: This study reports blaESBL and blaCARBA-positive multi-drug resistant Mixta calida isolates from distinct human hosts. Genomic analysis revealed the co-occurrence of plasmid-borne resistance genes blaKPC-3, blaOXA-9, and blaTEM-122. Species-wide phylogenetic analysis grouped the two isolates into a monophyletic cluster, suggesting a single introductory event.},
}

@article {pmid40815008,
year = {2025},
author = {},
title = {Pathway to Independence - an interview with Sonya Widen.},
journal = {Development (Cambridge, England)},
volume = {152},
number = {16},
pages = {},
doi = {10.1242/dev.205117},
pmid = {40815008},
issn = {1477-9129},
abstract = {Sonya Widen is a Postdoctoral Fellow in Alejandro Burga's lab at the Vienna BioCenter, Austria. She is interested in large DNA transposons called Polintons (or Mavericks) that facilitate horizontal gene transfer across nematodes and how they and other transposons with viral-like properties can influence development and evolution. Sonya is part of the 2025 cohort of Development's Pathway to Independence programme, which aims to support postdocs in their transition towards establishing their own labs and securing independent funding. We spoke to Sonya online to learn about her research interests in genome evolution, hopes for the programme and plans for her future lab.},
}

@article {pmid40813371,
year = {2025},
author = {Kiu, R and Darby, EM and Alcon-Giner, C and Acuna-Gonzalez, A and Camargo, A and Lamberte, LE and Phillips, S and Sim, K and Shaw, AG and Clarke, P and van Schaik, W and Kroll, JS and Hall, LJ},
title = {Impact of early life antibiotic and probiotic treatment on gut microbiome and resistome of very-low-birth-weight preterm infants.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {7569},
pmid = {40813371},
issn = {2041-1723},
support = {100974/C/13/Z//Wellcome Trust (Wellcome)/ ; BB/R012490/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; BB/X011054/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; BB/S017941/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; },
abstract = {Preterm infants (<37 weeks' gestation) are commonly given broad-spectrum antibiotics due to their risk of severe conditions like necrotising enterocolitis and sepsis. However, antibiotics can disrupt early-life gut microbiota development, potentially impairing gut immunity and colonisation resistance. Probiotics (e.g., certain Bifidobacterium strains) may help restore a healthy gut microbiota. In this study, we investigated the effects of probiotics and antibiotics on the gut microbiome and resistome in two unique cohorts of 34 very-low-birth-weight, human-milk-fed preterm infants - one of which received probiotics. Within each group, some infants received antibiotics (benzylpenicillin and/or gentamicin), while others did not. Using shotgun metagenomic sequencing on 92 longitudinal faecal samples, we reconstructed >300 metagenome-assembled genomes and obtained ~90 isolate genomes via targeted culturomics, allowing strain-level analysis. We also assessed ex vivo horizontal gene transfer (HGT) capacity of multidrug-resistant (MDR) Enterococcus using neonatal gut models. Here we show that probiotic supplementation significantly reduced antibiotic resistance gene prevalence, MDR pathogen load, and restored typical early-life microbiota profile. However, persistent MDR pathogens like Enterococcus, with high HGT potential, underscore the need for continued surveillance. Our findings underscore the complex interplay between antibiotics, probiotics, and HGT in shaping the neonatal microbiome and support further research into probiotics for antimicrobial stewardship in preterm populations.},
}

@article {pmid40811916,
year = {2025},
author = {Chen, Y and Liu, S and Ouyang, T and Jiang, R and Ma, J and Lu, G and Yuan, S and Yan, Z},
title = {Reshaping the antibiotic resistance genes in plastisphere upon deposition in sediment-water interface: Dynamic evolution and propagation mechanism.},
journal = {Journal of hazardous materials},
volume = {496},
number = {},
pages = {139532},
doi = {10.1016/j.jhazmat.2025.139532},
pmid = {40811916},
issn = {1873-3336},
abstract = {Microplastics (MPs) could provide unique niches for microbiota and aggravate their gravity, leading to vertical travel from waters to sediments. Although the plastisphere functions as hotspots for antibiotic resistance genes (ARGs) enrichment, the dynamic evolution and mechanisms of ARGs remain poorly understood when MPs deposited at sediment-water interface (SWI). Herein, this study investigated the dynamic response and reshaping mechanism of ARGs in plastisphere across SWI. It reveals that in deep waters, the ARGs abundance in biodegradable polylactic acid (PLA) plastisphere was higher than non-biodegradable polyethylene terephthalate (PET). However, when plastisphere deposited at SWI from deep waters, the ARGs abundance in PET plastisphere was increased by 45.71-65.10 %, while that decreased by 52.15-53.25 % in PLA. The plastisphere across SWI possessed higher species richness and diversity, more complex interactions, and more key species regulating ARGs compared to deep waters. During sedimentation, the horizontal gene transfer potential was enhanced in PET plastisphere but inhibited PLA. In addition, the function response related to oxidative stress response, cell membrane permeability, and energy metabolism may be underlying mechanisms in regulating ARGs propagation during the travel of plastisphere across SWI. This study highlights the critical roles of SWI in regulating the ARGs propagation in the traveling plastisphere.},
}

@article {pmid40809044,
year = {2025},
author = {Liu, G and Mao, C and Li, Q and Huo, D and Li, T},
title = {Comparative genomic analysis reveals the adaptive traits of Ralstonia spp. in aquatic environments.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1625651},
pmid = {40809044},
issn = {1664-302X},
abstract = {Ralstonia spp. are highly adaptable bacteria that are widely distributed across diverse environments. Here, we isolated four Ralstonia pickettii (R. pickettii) genomes from cultures of Dolichospermum spp., and using a comparative genomic framework of 228 Ralstonia genomes. We performed phylogenetic analyses that grouped them into water, soil, plant, and human-associated clades based on their predominant isolation habitats. Fluorescence in situ hybridization revealed minimal physical interactions between R. pickettii and cyanobacterial cells, indicating a commensal or independent ecological relationship. Distinct differences in carbohydrate-active enzymes (CAZymes) and secondary metabolite profiles were observed between water and human-associated dominant groups compared to plant-associated dominant groups, highlighting potential niche-specific adaptations. The water-associated dominant groups harbored antibiotic resistance genes, including CeoB and OXA-type β-lactamase genes. These genes are typically linked to human-associated strains, suggesting potential horizontal gene transfer or shared selective pressures, and the gene content of T3SS is reduced. Notably, water-associated dominant groups exhibited a unique pyrimidine degradation pathway, potentially enabling the utilization of exogenous pyrimidines to support survival in nutrient-limited aquatic environments. We propose that the gene content loss of T3SS and the acquisition of specialized metabolic pathways reflect adaptive strategies of Ralstonia spp. for thriving in aquatic free-living niches.},
}

@article {pmid40802789,
year = {2025},
author = {Sadikalay, S and Cavé, L and Ducat, C and Mauriello, G and Berchel, M and Boismoreau, D and Guyomard, S and Nazaret, S and Talarmin, A and Ferdinand, S},
title = {Tracking Enterobacteria, microbiomes, and antibiotic resistance genes from waste to soil with repeated compost applications.},
journal = {PloS one},
volume = {20},
number = {8},
pages = {e0329200},
pmid = {40802789},
issn = {1932-6203},
abstract = {The dissemination of antibiotic resistant bacteria (ARB) and genes is one factor responsible for the increasing antibiotic resistance and the environment plays a role in resistance spread. Animal excreta can contribute to the contamination of the environment with ARBs and antibiotics and in some cases, environmental bacteria under antibiotic pressure may acquire antibiotic resistance genes (ARGs) from ARBs by horizontal gene transfer. In Guadeloupe, a French overseas department, organic amendments derived from human and animal waste are widely used in soil fertilization, but their contribution to antibiotic resistance remains unknown. The objective of this study was to evaluate the impact of composting animal and human raw waste and the repeated application of their derived-composts, on the fate of ARGs and antibiotic resistant Enterobacteria, for the first time, in tropical soils of Guadeloupe used for vegetable production. An unculturable approach was used to characterize the bacterial community composition and ARG content from raw waste to composts. A cultivable approach was used to enumerate Enterobacteria, and resistant isolates were further characterized phenotypically and genotypically. Based on this original approach, we demonstrated that the raw poultry droppings exhibited a depletion of Escherichia and Shigella populations during the composting treatment, which was corroborated by the results on the culturable resistant Enterobacteria. Significant differences in the abundance of ARGs were also observed, with some gene levels increasing or decreasing after composting. In addition, other bacterial genera potentially involved in the spread of antimicrobial resistance were identified. Taken together, these results demonstrate that successive applications of raw waste-derived-composts from green waste, sewage sludge, and poultry droppings reshape the Enterobacterial community and influences the abundance of ARGs, with some gene levels increasing or decreasing, in Guadeloupe's tropical vegetable production soils.},
}

@article {pmid40802478,
year = {2025},
author = {Vesel, N and Stare, E and Štefanič, P and Floccari, VA and Mulec, IM and Dragoš, A},
title = {Naturally competent bacteria and their genetic parasites - A battle for control over horizontal gene transfer?.},
journal = {FEMS microbiology reviews},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsre/fuaf035},
pmid = {40802478},
issn = {1574-6976},
abstract = {Host-mediated natural competence for transformation of DNA and mobile genetic element (MGE)-driven conjugation and transduction are key modes of horizontal gene transfer. While these mechanisms are traditionally believed to shape bacterial evolution by enabling the acquisition of new genetic traits, numerous studies have elucidated an antagonistic relationship between natural transformation and MGEs. A new role of natural transformation as a chromosome curing mechanism has now been proposed. Experimental data, along with mathematical models, suggest that transformation can eliminate deleterious MGEs. Supporting this hypothesis, MGEs have been shown to use various mechanisms to decrease or block transformability, such as disrupting competence genes, regulating the development of competence, hindering DNA uptake machinery, producing DNases that target the exogenous (transforming) DNA, and causing lysis of competent cells. A few examples of synergistic relationships between natural transformation and MGEs have also been reported, with natural transformation facilitating MGE transfer and phages enhancing transformation by supplying extracellular DNA through lysis and promoting competence via kin discrimination. Given the complexity of the relationships between natural transformation and MGEs, the balance between antagonism and synergy likely depends on specific selection pressures in a given context. The evidence collected here indicates a continuous conflict over horizontal gene transfer in bacteria, with semiautonomous MGEs attempting to disrupt host-controlled DNA acquisition, while host competence mechanisms work to resist MGE interference.},
}

@article {pmid40801289,
year = {2025},
author = {Mougin, J and Labreuche, Y and Boulo, V and Goudenège, D and Saad, J and Courtay, G and Le Grand, J and Chevalier, O and Pouzadoux, J and Montagnani, C and Travers, MA and Petton, B and Destoumieux-Garzón, D},
title = {Antibiotic Use in Oyster Hatcheries Promotes Rapid Spread of a Highly Transferable and Modular Resistance Plasmid in Vibrio.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf163},
pmid = {40801289},
issn = {1751-7370},
abstract = {Plasmids play a key role in the horizontal gene transfer of antibiotic resistance genes, particularly in aquaculture where ARG-carrying Vibrio bacteria are frequently detected. Given the expansion of global aquaculture and its reliance on antibiotics, we investigated how these practices influence the emergence, dynamics, and spread of ARGs, focusing on Magallana gigas hatcheries - the world's most widely farmed shellfish. Among the three antibiotics tested, only chloramphenicol led to a pronounced selection and dissemination of chloramphenicol-resistant Vibrio isolates. Resistance was mediated by catA2, located in a highly modular, insertion sequence- and transposase-rich region of a conjugative plasmid, alongside tet(B). This plasmid was closely related to emerging pAQU-type plasmids unreported in Europe. pAQU-MAN, derived from Marine ANtimicrobial resistance, is a low-copy, highly transferable plasmid that rapidly spread throughout the hatchery following CHL treatment. Though naturally found in commensal Vibrio, it exhibited a broad host range, transferring efficiently to both oyster- and human-pathogenic Vibrio strains, as well as to E. coli, with high conjugation rates. Additionally, it remained stable in Vibrio hosts and was transmitted from oyster parents to progenies, even in the absence of antibiotic. It eventually disappeared from the microbial community associated to adults. Our findings highlight that antibiotic use in oyster hatcheries can select for highly modular and transferable multidrug-resistant plasmids, posing a risk of environmental dissemination, although their limited persistence in juvenile oyster reduces the likelihood of transmission to humans. We discuss the human and ecological factor driving pAQU-MAN spread and control in aquaculture settings.},
}

@article {pmid40800031,
year = {2025},
author = {Gichure, J and Hald, T and Buys, E},
title = {Exploring the Genetic Diversity, Virulence and Antimicrobial Resistance of Diarrhoeagenic Escherichia coli From Southern Africa Using Whole-Genome Data.},
journal = {Public health challenges},
volume = {4},
number = {3},
pages = {e70098},
pmid = {40800031},
issn = {2769-2450},
abstract = {Introduction: Previous studies, including our research, provide critical insights on the contamination of food, water and environment in the Southern African Development Community (SADC) with diarrhoeagenic Escherichia coli (DEC). This study used whole-genome sequencing to investigate the genetic diversity, virulence-associated factors and antimicrobial resistance (AMR) patterns of DEC isolated from children under 5 years old and food sources in Maputo and compared these findings with publicly available DEC genome assemblies from the Southern Africa region. Methods: Whole-genome sequence data from 11 DEC isolates from food, children under 5 and water sources in Maputo, Mozambique, were analysed alongside 125 publicly available DEC genomic assemblies from the SADC region. The latter were retrieved from the EnteroBase database (http://enterobase.warwick.ac.uk) and included isolates previously collected from food, animals and environmental sources. Genomic analyses were performed using the online pipelines provided by the Centre for Genomic Epidemiology (CGE), Denmark. Unsupervised hierarchical clustering was applied to visualize patterns in genetic diversity, AMR, virulence-associated genes and plasmid content using the R software. Results: Clustering based on single nucleotide polymorphism (SNP) and core genome multilocus sequence typing (cgMLST) alleles revealed associations based on geographic locations, sample niche, pathovar and O:H antigen, pointing to evolutionary relatedness between the clades with principal coordinate analysis uncovering this accounted for 27.55% of the genetic diversity. Virulence-associated genes encoding for attaching and effacing (eae) (63.97%), heat-labile toxin (LT) (25.00%) and Shiga toxin 1 (Stx1) (15.44%) were most abundant, with an inverse association between genes encoding for the presence of LT and eae. Resistance to folate pathway antagonists (sulfamethoxazole-55.9%), β-lactamases (amoxicillin, ampicillin and piperacillin-all 54.4%) and aminoglycoside (streptomycin-55.1%) was most abundant. Conclusions: The study revealed region-specific lineages, evidence of horizontal gene transfer and the clustering patterns suggest both localized and cross-border transmission. The study provides insightful evidence on DEC transmission patterns associated with antimicrobial and disinfectant resistance and associated virulence factors.},
}

@article {pmid40796304,
year = {2025},
author = {Qing, Y and Liao, Z and An, D and Zeng, Y and Zhu, Q and Zhang, X},
title = {Comparative genomics reveals the genetic diversity and plasticity of Clostridium tertium.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxaf201},
pmid = {40796304},
issn = {1365-2672},
abstract = {AIMS: Clostridium tertium, increasingly recognized as the emerging human pathogen frequently isolated from environmental and clinical specimens, remains genetically underexplored despite its clinical relevance. This study aims to explore the genetic characteristics of C. tertium by genomic analysis.

METHODS AND RESULTS: This study presented a comprehensive genomic investigation of 45 C. tertium strains from the GenBank database. Genome sizes (3.27-4.55 Mbp) and coding gene counts varied markedly across strains. Phylogenetic analyses based on 16S rRNA gene and core genome uncovered distinct intra-species lineages, including evolutionarily divergent clusters likely shaped by niche specialization. Pan-genomic analysis confirmed an open genome, with accessory and strain-specific genes enriched in functions related to environmental adaptation and regulation. Functional annotation further identified diverse virulence factor genes (e.g. clpP, nagK) and antibiotic resistance genes (e.g. vatB, tetA(P)) co-occurring with mobile genetic elements (MGEs), suggesting that horizontal gene transfer (HGT) may be a key driver of genome plasticity in C. tertium. Notably, one-third of the strains carried CRISPR-Cas systems, indicating the defense potential against exogenous genetic elements.

CONCLUSIONS: C. tertium exhibited extensive genetic diversity and genome plasticity, probably driven by MGE-mediated HGT, defense mechanisms of CRISPR-Cas systems, and functional adaptation related to virulence and resistance. These traits may underlie its ability to colonize diverse environments and acquire pathogenicity and resistance.},
}

@article {pmid40794765,
year = {2025},
author = {Mazzamurro, F and Touchon, M and Charpentier, X and Rocha, EPC},
title = {Impact of Natural Transformation on the Acquisition of Novel Genes in Bacteria.},
journal = {Molecular biology and evolution},
volume = {42},
number = {8},
pages = {},
pmid = {40794765},
issn = {1537-1719},
abstract = {Natural transformation is the only process of gene exchange under the exclusive control of the recipient bacteria. It has often been considered as a source of novel genes, but quantitative assessments of this claim are lacking. To investigate the potential role of natural transformation in gene acquisition, we analyzed a large collection of genomes of Acinetobacter baumannii (Ab) and Legionella pneumophila (Lp) for which transformation rates were experimentally determined. Natural transformation rates are weakly correlated with genome size. But they are negatively associated with gene turnover in both species. This might result from a negative balance between the transformation's ability to cure the chromosome from mobile genetic elements (MGEs), resulting in gene loss, and its facilitation of gene acquisition. By comparing gene gains by transformation and MGEs, we found that transformation was associated with the acquisition of small sets of genes per event, which were also spread more evenly in the chromosome. We estimated the contribution of natural transformation to gene gains by comparing recombination-driven gene acquisition rates between transformable and non-transformable strains, finding that it facilitated the acquisition of ca. 6.4% (Ab) and 1.1% (Lp) of the novel genes. This moderate contribution of natural transformation to gene acquisition implies that most novel genes are acquired by other means. Yet, 15% of the recently acquired antibiotic resistance genes in A. baumannii may have been acquired by transformation. Hence, natural transformation may drive the acquisition of relatively few novel genes, but these may have a high fitness impact.},
}

@article {pmid40792260,
year = {2025},
author = {Jiang, Y and Shu, L and Wen, H and Wei, Y and Liu, S and Ye, C and Cheng, L and Zeng, Z and Liu, J},
title = {Enhancement of bla IMP-carrying plasmid transfer in Klebsiella pneumoniae by hospital wastewater: a transcriptomic study.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1626123},
pmid = {40792260},
issn = {1664-302X},
abstract = {INTRODUCTION: Klebsiella pneumoniae is a critical ESKAPE pathogen that presents a significant challenge to public health because of its multidrug-resistant strains. This study investigates the impact and mechanisms of hospital wastewater on the horizontal gene transfer of carbapenem resistance genes, particularly bla IMP, in K. pneumoniae.

METHODS: LB broth was prepared using sterile filtered wastewater as the substrate to investigate the impact of wastewater on the transfer of carbapenem-resistant gene bla IMP in K. pneumoniae. The mechanisms of sewage effects on the horizontal transfer of bla IMP were explored by integrating transcriptome sequencing with the detection of extracellular membrane permeability, intracellular reactive oxygen species (ROS), and other test results.

RESULTS: Hospital wastewater significantly enhances the conjugation frequency of plasmids containing bla IMP, showing a two-fold increase in wastewater-based LB broth compared to regular LB broth. In comparison to regular LB broth culture, the wastewater-based LB broth culture group showed significant alterations in the expression of 1,415 genes, with 907 genes upregulated and 508 genes downregulated. Genes related to conjugation transfer systems and the type IV secretion system were significantly upregulated, indicating a potential role in promoting plasmid transfer. Moreover, the treatment of wastewater resulted in elevated intracellular ROS production and increased permeability of bacterial outer membranes, potentially facilitating the spread of antibiotic resistance genes.

DISCUSSION: This research shows that hospital wastewater facilitates the transfer of drug-resistant plasmids containing bla IMP and elucidates its potential mechanisms. A more detailed investigation into these mechanisms may facilitate the prevention of resistance transmission between healthcare and environmental contexts and inform future strategies for managing carbapenem resistance.},
}

@article {pmid40791418,
year = {2025},
author = {Hamrock, FJ and Guest, T and Daum, MN and Connell, O and Ershova, AS and Hokamp, K and Fleming, AB and Gebhardt, MJ and Westermann, AJ and Kröger, C},
title = {DNA uptake and twitching motility are controlled by the small RNA Arp through repression of pilin translation in Acinetobacter baumannii.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.07.19.665661},
pmid = {40791418},
issn = {2692-8205},
abstract = {UNLABELLED: Acinetobacter baumannii is a major opportunistic pathogen capable of natural transformation, a process driven by type IV pili (T4P) that facilitates horizontal gene transfer and accelerates the spread of antimicrobial resistance. While the transcriptional regulation of T4P is increasingly understood, post-transcriptional mechanisms controlling pilus assembly remain unexplored. Here, we identify and characterise a small RNA, Arp (Acinetobacter repressor of pilin), as a post-transcriptional repressor of T4P-mediated functions in A. baumannii . In a previous Hi-GRIL-seq experiment, we detected specific ligation events between Arp and the ribosome binding site of the pilA mRNA, encoding the major pilin subunit PilA. In-line probing and translational reporter assays revealed that Arp represses pilA translation by sequestering the Shine-Dalgarno sequence and the first 17 codons of the mRNA. Overexpression of Arp significantly impairs DNA uptake and twitching motility, two hallmark T4P-dependent phenotypes. Together, our findings identify a native A. baumannii sRNA that modulates natural competence by targeting pilin synthesis, revealing a new regulatory layer that could be exploited to disrupt horizontal gene transfer in multidrug-resistant strains.

SIGNIFICANCE STATEMENT: Acinetobacter baumannii is a multidrug-resistant WHO #1 priority pathogen that acquires antibiotic resistance genes through natural transformation, a process dependent on type IV pili (T4P). This work reveals Arp, the first native post-transcriptional repressor of natural competence in A. baumannii , uncovering a novel regulatory layer that modulates horizontal gene transfer. The widespread presence of arp in pathogenic Acinetobacter strains suggests that sRNA is an important regulator in those organisms. Furthermore, these findings broaden our understanding of RNA-based regulation in this priority pathogen and open potential avenues for interfering with antibiotic resistance dissemination.},
}

@article {pmid40784676,
year = {2025},
author = {Luo, L and Chen, X and Liu, B and Nie, Y and Wu, XL},
title = {Strengthen or Weaken: Evolutionary Directions of Cross-Feeding After Formation.},
journal = {Environmental microbiology reports},
volume = {17},
number = {4},
pages = {e70175},
pmid = {40784676},
issn = {1758-2229},
support = {32130004//National Natural Science Foundation of China/ ; 32161133023//National Natural Science Foundation of China/ ; 32170113//National Natural Science Foundation of China/ ; 2024YFA0919000//National Key Research and Development Program of China/ ; },
mesh = {*Biological Evolution ; *Microbial Consortia/physiology ; *Bacteria/genetics/metabolism ; *Microbial Interactions ; Symbiosis ; },
abstract = {Interactions between species and the evolution of strains are important biotic factors determining the microbial community dynamics, with these two processes being deeply intertwined. Cross-feeding is a prevailing mutualistic interaction in natural microbial communities in which metabolites secreted by one microbe can be utilised by another. Constructing synthetic microbial consortia based on cross-feeding is a promising strategy for bioremediation and bioproduction. But how to improve the performance and the stability of consortia remains a challenge. This review discusses the features of two opposite evolutionary directions of cross-feeding consortia over time, providing insights into the factors affecting the evolutionary process. While coevolving, cross-feeding may strengthen with stronger metabolic coupling, deeper growth dependence, and/or deeper evolutionary dependence; then the consortia become reinforced. Conversely, unsuitable environmental conditions can lead to the direct collapse of the cross-feeding consortia due to metabolic decoupling, partner extinction, or cheater dominance. The loss of the fitness advantage and the constraints on the evolutionary ability can also lead to the weakening of cross-feeding. Cross-feeding partners can affect the evolution of focal strains from different aspects, such as niche space, selective pressure, horizontal gene transfer, and evolutionary rate. Analysing cross-feeding from an evolutionary perspective will advance our understanding of microbial community dynamics and enable rational designs of efficient and stable synthetic microbial consortia.},
}

*Biological Evolution
*Microbial Consortia/physiology
*Bacteria/genetics/metabolism
*Microbial Interactions
Symbiosis

@article {pmid40780628,
year = {2025},
author = {Feng, X and Li, S and Huang, D and Tan, N and Li, X and Xia, S and Hu, L and Cai, R and Li, Y and Wang, J and Luo, M and Li, H and Ye, X and Lv, Z and Shi, X and Wu, S and Dyer, N and Li, H and Hu, Q and Zhou, Z},
title = {Emergence of carbapenem-resistant XDR Salmonella enterica in pediatric patients in South China: a genomic perspective study.},
journal = {International journal of antimicrobial agents},
volume = {},
number = {},
pages = {107589},
doi = {10.1016/j.ijantimicag.2025.107589},
pmid = {40780628},
issn = {1872-7913},
abstract = {BACKGROUND AND AIM: Carbapenem-resistant Salmonella enterica (CRSE), mostly driven by plasmids, poses a growing public health threat, especially in pediatric populations. This study investigates a cluster of pediatric CRSE infections in pediatric populations, characterizes genomic features of CRSE isolates, assesses global CRSE prevalence, and explores plasmid-mediated horizontal gene transfer.

METHODS: An epidemiological investigation of 18 pediatric CRSE cases was conducted. Genomic analysis included resistome profiling, plasmid typing, and phylogenetic clustering to assess genetic diversity. A global analysis of 530,113 Salmonella genomes identified carbapenemase-carrying isolates. Plasmid transfer experiments between S. enterica and E. coli were performed to evaluate horizontal gene transmission.

RESULTS: Respiratory co-infections (67% of cases, primarily RSV and HPIVs) were associated with severe clinical outcomes. Genomic analysis revealed multiple genetically distinct CRSE clones carrying blaNDM-5, predominantly on IncI-gamma/K1 and IncHI2A plasmids. Plasmid-mediated transfer of carbapenem resistance genes between S. enterica and E. coli was confirmed. Global surveillance identified 228 carbapenemase-positive Salmonella isolates (2000-2023) across 35 genetically diverse populations and 24 countries, demonstrating widespread dissemination.

CONCLUSION: Respiratory co-infections may exacerbate CRSE severity in children, while plasmid circulation drives carbapenem resistance transmission. The high genetic diversity and global distribution of CRSE highlight urgent needs for integrated surveillance, antimicrobial stewardship, and interventions targeting co-infections and environmental reservoirs.},
}

@article {pmid40779699,
year = {2025},
author = {Bao, Y and Ho, YW and Shen, Z and Lam, EY and Fang, JKH and Leung, KMY and Lee, PKH},
title = {Ecological Roles and Shared Microbes Differentiate the Plastisphere from Natural Particle-Associated Microbiomes in Urban Rivers.},
journal = {Environmental science & technology},
volume = {59},
number = {32},
pages = {17298-17309},
doi = {10.1021/acs.est.5c06538},
pmid = {40779699},
issn = {1520-5851},
abstract = {The "plastisphere," comprising microbes associated with microplastics (MPs), may have substantial ecological impacts on riverine ecosystems. However, little is known about how the microbiomes associated with anthropogenic MPs compare with those associated with natural particles (NPs) in urban rivers with varying MP pollution levels. We therefore conducted a comparative analysis of the metagenomes associated with MPs and NPs (100-5000 μm) and river water (RW) across 10 urban river systems. Although we found similarities in taxonomic and functional compositions between the microbiomes associated with MPs and NPs, the plastisphere exhibited distinct associations with specialized taxa and life-history strategies. These unique traits enhanced the potential of the plastisphere for complex carbohydrate and plastic degradation, nitrate and nitric oxide reduction, and antibiotic resistance and virulence compared with the NP or RW microbiomes. Furthermore, MPs supported the sharing of unique microbes with the surrounding RW; these shared microbes possessed enhanced horizontal gene transfer capabilities and potentially could disperse traits of the plastisphere into the broader RW microbiomes. This study highlights the distinct ecological roles and shared microbes of the plastisphere, indicating that MP pollution may substantially and uniquely impact the function and health of riverine ecosystems.},
}

@article {pmid40778777,
year = {2025},
author = {Phimphong, T and Hashimoto, S and Songwattana, P and Wongdee, J and Greetatorn, T and Teamtisong, K and Boonchuen, P and Masuda, S and Shibata, A and Shirasu, K and Sibounnavong, P and Tittabutr, P and Boonkerd, N and Sato, S and Gully, D and Giraud, E and Piromyou, P and Teaumroong, N},
title = {Diversity of bradyrhizobial T3SS systems and their roles in symbiosis with peanut (Arachis hypogaea) and Vigna species (V. radiata and V. mungo).},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0060025},
doi = {10.1128/aem.00600-25},
pmid = {40778777},
issn = {1098-5336},
abstract = {Symbiosis between Bradyrhizobium strains isolated from Lao People's Democratic Republic (Lao PDR) and intercropped legumes (Arachis hypogaea, Vigna radiata, and V. mungo) was regulated by the type III secretion system (T3SS), which delivers effector proteins (T3Es) into host plant cells to modulate nodulation. To explore this mechanism, we sequenced and analyzed seven Bradyrhizobium genomes, identifying putative T3Es across five T3SS groups (G.1-G.5), which were classified based on the sequence of rhcN, a conserved ATPase gene essential for T3SS function. Phylogenetic analysis of rhcN more closely reflected the evolutionary relationships of nodulation genes than those based on 16S rRNA or whole-genome comparisons, underscoring its symbiotic relevance. Functional assays using rhcN mutants revealed group-specific effects on nodulation; G.1 strains showed neutral effects on A. hypogaea, negative effects on V. radiata, and positive effects on V. mungo. G.2 strains consistently promoted nodulation across all hosts and lacked effectors related to SUMO (small ubiquitin-like modifier) pathways, which have been implicated in host defense regulation. G.3 strains reduced nodulation in A. hypogaea but enhanced it in Vigna species. G.4 strains suppressed nodulation in A. hypogaea, and G.5 strains inhibited nodulation across all tested legumes. These findings highlight the diversity in T3SS organization, effector composition, and symbiotic responses among native Bradyrhizobium strains. The identification of known and uncharacterized effectors suggests roles in host compatibility and specificity. These strains, along with their effector profiles, provide a foundation for future functional studies to better understand T3SS-mediated interactions and support the development of targeted inoculants for legume hosts.IMPORTANCEThis study advances our understanding of legume-Bradyrhizobium symbiosis by examining the genetic organization and evolutionary patterns of T3SS genes. Our findings revealed that T3SS gene evolution does not always align with phylogenies based on 16S rRNA or whole-genome sequences, suggesting that horizontal gene transfer and functional adaptation may shape diversification. The observed variation in T3SS architecture and effector profiles among the five distinct Bradyrhizobium groups was correlated with host-specific nodulation outcomes in A. hypogaea, V. radiata, and V. mungo. We also identified novel candidate genes influencing symbiotic signaling and compatibility. These insights into the diversity and function of T3SS components contribute to a broader understanding of host-microbe communication and may support the development of more targeted and efficient rhizobial inoculants for sustainable legume cultivation and improved biological nitrogen fixation.},
}

@article {pmid40763861,
year = {2025},
author = {Singh, R and Lim, CS and Kim, H and Kang, S and Kim, K},
title = {Sustainable material platforms for multi-log removal of antibiotic-resistant bacteria and genes from wastewater: A review.},
journal = {International journal of biological macromolecules},
volume = {321},
number = {Pt 4},
pages = {146561},
doi = {10.1016/j.ijbiomac.2025.146561},
pmid = {40763861},
issn = {1879-0003},
abstract = {Antibiotic-resistant bacteria (ARB) and the associated resistance genes (ARGs) are now recognized as emerging contaminants that can disseminate via wastewater streams, posing significant risks to both human and ecosystem health. Conventional physicochemical treatment approaches (e.g., chlorination, ozonation, advanced oxidation processes) typically suppress these contaminants but may also result in the formation of hazardous by-products. This critical review comprehensibly evaluates bio-based and other sustainable materials designed for the removal of ARB and ARGs from aqueous environments. The materials are systematically categorized into (i) biopolymers and their composites (chitosan, alginate, cellulose), (ii) carbon-rich adsorbents and (photo-)catalysts (biochar, activated carbon, graphene), (iii) metal- and semiconductor-based nanomaterials, and (iv) nature-based treatment solutions (constructed wetlands, soil-aquifer treatment, clay sorbents). Observed log-reduction value range from 2 to 7 for ARB with platforms such as zinc oxide/activated-carbon alginate beads, Fe/N-doped biochars, and graphene-supramolecular-porphyrin hybrids demonstrating high multifunctional efficacy. Mechanistic studies reveal that removal involves synergistic adsorption, photodynamic or Fenton-like oxidation, cell-membrane disruption, and inhibition of horizontal gene transfer. This review emphasizes the advancing potential of sustainable material solutions for mitigating antibiotic resistance and highlights the urgent need to develop scalable, environmentally sustainable treatment methods for protecting water resources and public health.},
}

@article {pmid40743727,
year = {2025},
author = {Vinogradov, E and Zou, L and Stupak, J and Martynova, Y and Arbour, M and St Michael, F and Williams, D and Beaudoin, G and Li, J and Chen, W and Zou, W and Peters, DL},
title = {Capsular Polysaccharide of Acinetobacter baumannii MRSN 31196 (a KL1 Variant Strain) and its Degradation by a Recombinant Depolymerase from Bacteriophage vB_AbaP_B5.},
journal = {Carbohydrate research},
volume = {556},
number = {},
pages = {109621},
doi = {10.1016/j.carres.2025.109621},
pmid = {40743727},
issn = {1873-426X},
abstract = {Acinetobacter baumannii MRSN 31196 was assigned as KL1, but has now been reassigned as KL1-v as new polymerase wzy and acetyl transferase (atr25) genes are discovered outside of its gene locus due to horizontal gene transfer. Its capsular polysaccharide (CPS), namely K1v, was isolated by a standard water-phenol extraction and an aqueous base extraction. K1v is degradable by a recombinant phage depolymerase B5 which is known to hydrolyze A. baumannii K9 CPS. The structure of oligosaccharides obtained were determined by NMR and mass spectroscopic analysis. The results showed that the K1v structure is closely related to K1 CPS, with the same sugar composition and linkages except β-QuiNAcNR-(1-3)-GlcNAc in K1v replaced β-QuiNAcNR-(1-4)-GlcNAc in K1, due to an altered Wzy. However, the atr25 gene is likely silenced, or the transferase activity is inhibited, as K1v is not O-acetylated. We also found that the N-acetyl and N-3-hydroxybutyryl (HBu) substitutions (R) in QuiNAcNR has approximately a 1:1 ratio. The mass spectroscopic analysis provided evidence that structural blocks with consecutive QuiNAcNAc or QuiNAcNHBu are present in the polysaccharide. The K1v CPS structure has the following trisaccharide repeating unit.},
}

@article {pmid40738074,
year = {2025},
author = {Yang, X and Heng, H and Zhang, H and Peng, M and Chan, EW and Shum, HP and Zhang, R and Chen, S},
title = {IncFIBK/FIIK conjugative iuc3-carrying virulence plasmids of clinical hypervirulent Klebsiella pneumoniae are multi-drug resistant.},
journal = {Microbiological research},
volume = {300},
number = {},
pages = {128288},
doi = {10.1016/j.micres.2025.128288},
pmid = {40738074},
issn = {1618-0623},
mesh = {*Klebsiella pneumoniae/genetics/pathogenicity/drug effects/isolation & purification ; *Plasmids/genetics ; *Drug Resistance, Multiple, Bacterial/genetics ; *Klebsiella Infections/microbiology ; Virulence/genetics ; *Virulence Factors/genetics ; Humans ; Anti-Bacterial Agents/pharmacology ; Conjugation, Genetic ; Animals ; Multigene Family ; Hydroxamic Acids/metabolism ; Genetic Variation ; Siderophores/metabolism ; Bacterial Proteins/genetics ; },
abstract = {Aerobactin encoding loci is the key virulence factor in the virulence plasmid of Klebsiella pneumoniae (Kp). The iuc1 and iuc2 loci are most commonly detected and well-studied, while the iuc3 lineage is less understood. The study investigated comprehensively the iuc3-carrying plasmids in Kp strains providing insights into the diversity, transmission potential and contribution to Kp virulence. The iuc3 was encoded on plasmids ranging from 177,328 bp to 249,880 bp, primarily of the IncFIBK/FIIK5 type, often carrying multi-drug resistance (MDR) regions. Conjugation experiments demonstrated the transferability of iuc3-carrying plasmids, conferring additional resistance to recipient strains. Siderophore production assays indicated that the iuc3 gene cluster significantly enhanced iron acquisition in transconjugants. Analysis of 69,969 Kp isolates from the NCBI Pathogen Detection database identified 872 iuc3-carrying strains across 205 STs and 69 KLs, indicating widespread genetic diversity. These strains were increasingly detected in human clinical samples over time, with additional reservoirs in animals, food, and the environment. The findings underscore the public health threat posed by iuc3-carrying Kp strains, emphasizing the need for surveillance and control measures to prevent the spread of MDR-HvKp clones. This study highlights the complex interplay between plasmid-mediated resistance, virulence, and the potential for horizontal gene transfer in Klebsiella spp.},
}

*Klebsiella pneumoniae/genetics/pathogenicity/drug effects/isolation & purification
*Plasmids/genetics
*Drug Resistance, Multiple, Bacterial/genetics
*Klebsiella Infections/microbiology
Virulence/genetics
*Virulence Factors/genetics
Humans
Anti-Bacterial Agents/pharmacology
Conjugation, Genetic
Animals
Multigene Family
Hydroxamic Acids/metabolism
Genetic Variation
Siderophores/metabolism
Bacterial Proteins/genetics

@article {pmid40701356,
year = {2025},
author = {Hu, L and Ye, Y and Li, Y and Tan, X and Liu, X and Zhang, T and Wang, J and Du, Z and Ye, M},
title = {Bacteria-algae synergy in carbon sequestration: Molecular mechanisms, ecological dynamics, and biotechnological innovations.},
journal = {Biotechnology advances},
volume = {83},
number = {},
pages = {108655},
doi = {10.1016/j.biotechadv.2025.108655},
pmid = {40701356},
issn = {1873-1899},
mesh = {*Biotechnology/methods ; *Microalgae/metabolism ; *Carbon Sequestration ; *Bacteria/metabolism ; Carbon Dioxide/metabolism ; Photosynthesis ; Carbon/metabolism ; },
abstract = {Rising atmospheric CO2 levels require innovative strategies to increase carbon sequestration. Bacteria-algae interactions, as pivotal yet underexplored drivers of marine and freshwater carbon sinks, involve multiple mechanisms that amplify CO2 fixation and long-term storage. This review systematically describes the synergistic effects of bacteria-algae consortia spanning both microalgae (e.g., Chlorella vulgaris and Phaeodactylum tricornutum) and macroalgae (e.g., Macrocystis and Laminaria) on carbon sequestration. These effects include (1) molecular-level regulation (e.g., signal transduction via N-acyl-homoserine lactones (AHLs), and horizontal gene transfer), (2) ecological facilitation of recalcitrant dissolved organic carbon (RDOC) formation, and (3) biotechnological applications in wastewater treatment and bioenergy production. We highlight that microbial crosstalk increases algal photosynthesis by 20-40 % and contributes to 18.9 % of kelp-derived RDOC storage. Furthermore, engineered systems integrating algal-bacterial symbiosis achieve greater than 80 % nutrient removal and a 22-35 % increase in CO2 fixation efficiency (compared with axenic algal systems), demonstrating their dual role in climate mitigation and a circular economy. This review is the first to integrate molecular mechanisms (e.g., quorum sensing), ecological carbon transformation processes (e.g., the formation of RDOC), and applications in synthetic biology (e.g., CRISPR-engineered consortia) into a unified framework. Moreover, the novel strategy "microbial interaction network optimization" for enhancing carbon sinks is proposed. However, scalability challenges persist, including light limitations in photobioreactors and the ecological risks of synthetic consortia. By bridging microbial ecology with synthetic biology, this work provides a roadmap for harnessing bacteria-algae synergy to achieve carbon neutrality.},
}

*Biotechnology/methods
*Microalgae/metabolism
*Carbon Sequestration
*Bacteria/metabolism
Carbon Dioxide/metabolism
Photosynthesis
Carbon/metabolism

@article {pmid40651546,
year = {2025},
author = {Tang, J and Hu, Z and Zhang, X and Mou, Q and Du, L and Daroch, M},
title = {Evolutionary insights from the pangenome and pigment profiles of Parasynechococcus.},
journal = {Molecular phylogenetics and evolution},
volume = {212},
number = {},
pages = {108408},
doi = {10.1016/j.ympev.2025.108408},
pmid = {40651546},
issn = {1095-9513},
abstract = {Parasynechococcus is one of the two essential alongside Prochlorococcus photosynthetic cyanobacteria that contribute primary productivity in the ocean. Despite its global importance its specie delimitation remains controversial. Herein, a pangenome analysis of 39 high-quality genomes was conducted to delineate Parasynechococcus species. Core-gene phylogram revealed the classification of these genomes into 18 well-defined putative genospecies, which was corroborated by ANI index and GTDB classification. Moreover, numerous interspecies and intraspecies HGT events were detected, some of which may be responsible for the inconsistencies between core-gene and pan-gene phylograms. Besides, the profiling of phycobilisome rod region in Parasynechococcus genomes unraveled intriguing diversity of their genomic organization, pigment type and genomic cluster variants. The diversification process was hypothesized to be mediated by the putative mobile elements located in these regions. Moreover, phylogeny incongruence between the genes within phycobilisome rod region and the core genome indicate distinct evolutionary history, which could be ascribed to lateral gene transfer. Conclusively, the results provide insights into the diversity and evolution of Parasynechococcus from the perspective of pangenome and pigment type, facilitating the evolutionary research and exploration of this important taxon.},
}

@article {pmid40572258,
year = {2025},
author = {Gonzalez Moreno, PJ and Nishiguchi, MK},
title = {The Competitive Edge: T6SS-Mediated Interference Competition by Vibrionaceae Across Marine Ecological Niches.},
journal = {Microorganisms},
volume = {13},
number = {6},
pages = {},
pmid = {40572258},
issn = {2076-2607},
support = {NSF DBI-2214028//U.S. National Science Foundation/ ; EXO 80NSSC18K1053/NASA/NASA/United States ; School of Natural Sciences//University of California, Merced/ ; },
abstract = {Interference competition, wherein bacteria actively antagonize and damage their microbial neighbors, is a key ecological strategy governing microbial community structure and composition. To gain a competitive edge, bacteria can deploy a diverse array of antimicrobial weapons-ranging from diffusible toxins to contact-mediated systems in order to eliminate their bacterial rivals. Among Gram-negative bacteria, the type VI secretion system (T6SS) has emerged as a potent and sophisticated contact-dependent mechanism that enables the delivery of toxic cargo into neighboring cells, thereby promoting the colonization and dominance of a bacterial taxon within an ecological niche. In this review, we examine the ecological significance of T6SS-mediated interference competition by members of the Vibrionaceae family across a range of marine habitats that include free-living microbial communities and host-associated niches such as coral and squid symbioses. Additionally, we explore the ecological impact of T6SS-mediated competition in modulating biofilm community structure and promoting horizontal gene transfer within those complex microbial populations. Together, these insights underscore the ecological versatility of the T6SS and emphasize its role in driving antagonistic bacterial interactions and shaping microbial community dynamics within marine ecosystems.},
}

@article {pmid40572111,
year = {2025},
author = {Lucero, J and Nishiguchi, MK},
title = {Host-Associated Biofilms: Vibrio fischeri and Other Symbiotic Bacteria Within the Vibrionaceae.},
journal = {Microorganisms},
volume = {13},
number = {6},
pages = {},
pmid = {40572111},
issn = {2076-2607},
support = {1T32GM141862-24S3/NH/NIH HHS/United States ; DBI 2214038//National Science Foundation/ ; },
abstract = {Biofilm formation is important for microbial survival, adaptation, and persistence within mutualistic and pathogenic systems in the Vibironaceae. Biofilms offer protection against environmental stressors, immune responses, and antimicrobial treatments by increasing host colonization and resilience. This review examines the mechanisms of biofilm formation in Vibrio species, focusing on quorum sensing, cyclic-di-GMP signaling, and host-specific adaptations that influence biofilm structure and function. We discuss how biofilms differ between mutualistic and pathogenic species based on environmental and host signals. Recent advances in omics technologies such as transcriptomics and metabolomics have enhanced research in biofilm regulation under different conditions. Horizontal gene transfer and phase variation promote the greater fitness of bacterial biofilms due to the diversity of environmental isolates that utilize biofilms to colonize host species. Despite progress, questions remain regarding the long-term effects of biofilm formation and persistence on host physiology and biofilm community dynamics. Research integrating multidisciplinary approaches will help advance our understanding of biofilms and their implications for influencing microbial adaptation, symbiosis, and disease. These findings have applications in biotechnology and medicine, where the genetic manipulation of biofilm regulation can enhance or disrupt microbiome stability and pathogen resistance, eventually leading to targeted therapeutic strategies.},
}

@article {pmid40556036,
year = {2025},
author = {Li, Y and Liu, X and Yang, J and Li, R and Wang, M and Kuang, S},
title = {Characteristics of intracellular/extracellular antibiotic resistance genes and microbial community in sludge compost under sulfadiazine stress.},
journal = {Environmental technology},
volume = {},
number = {},
pages = {1-11},
doi = {10.1080/09593330.2025.2522480},
pmid = {40556036},
issn = {1479-487X},
abstract = {The accumulation of emerging antibiotics in sewage sludge, which serves as a repository for antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs), is raising growing concern. To accurately assess the environmental risks, it is essential to separately investigate intracellular and extracellular ARGs (iARGs and eARGs) due to their distinct roles in resistance persistence and horizontal gene transfer. However, the impact of sulfadiazine (SDZ) on iARGs and eARGs, and the mechanisms involved in the composting process remain under further investigation. In this study, composts with SDZ concentrations of 5 and 50 mg/kg were constructed, and ARGs, microbial community composition and functional pathways were analyzed. The results showed that the abundance of iARGs varied significantly under SDZ selective pressure, while eARGs showed no significant differences. Specifically, i-erm decreased in the 50SDZ group, likely due to competition for ecological niches. The abundance of ermA, ermB and ermF decreased by approximately 97%, 85%, and 84%, respectively. i-sul increased by 127% to 156% in SDZ-added groups but not dose-dependently. Bacillus, Paracoccus, Pseudomonas, and Caproiciproducens were predominant in the SDZ-added groups. The abundance of potential ARG hosts, such as Bacillus and Paracoccus, increased significantly, with Paracoccus showing 2.3-fold and 1.8-fold higher abundance in the 50SDZ and 5SDZ treatments, respectively, compared to the CK. Functional genes related to the ABC-2 type transport system, signal transduction, and genome maintenance decreased with SDZ application. These findings suggested that the dynamics of ARGs should be continuously monitored during sludge composting and land application of compost products to reduce their environmental risks.},
}

@article {pmid40516407,
year = {2025},
author = {Fang, C and Liu, H and Chen, X and Lu, H and Ren, C and Hu, Z and Wang, Y and Zhang, J},
title = {Thioredoxin-mediated sulfur cycling and biogenic sulfur encapsulation synergistically enhance co-removal of nitrogen, sulfamethoxazole, and resistance genes in constructed wetlands.},
journal = {Water research},
volume = {284},
number = {},
pages = {123939},
doi = {10.1016/j.watres.2025.123939},
pmid = {40516407},
issn = {1879-2448},
mesh = {*Sulfamethoxazole/metabolism ; *Wetlands ; *Sulfur/metabolism ; *Thioredoxins/metabolism ; *Nitrogen/metabolism ; Denitrification ; Drug Resistance, Microbial/genetics ; },
abstract = {The interplay between sulfur-driven denitrification and antibiotic resistance genes (ARGs) proliferation remains unresolved in constructed wetlands (CWs), where sulfide accumulation and reactive oxygen species generation paradoxically enhance nitrogen removal while compromising microbial integrity. To resolve this conflict, this study engineered a FeS2@S° composite filler that synergized thioredoxin (Trx)-mediated sulfur cycling and biogenic sulfur (bio-S[0]) encapsulation. Upregulation of trxA/B genes (2.3-fold increase) enabled Trx to convert toxic sulfide into adhesive bio-S[0], exhibiting higher microbial adhesion that shielded functional denitrifiers like Thiomonas (84.03 % viability under SMX stress). Concurrently, sulfur vacancies (SVs) at FeS2 {210}
crystal facets generated hydroxyl radicals (•OH) and singlet oxygen ([1]O2) via vacancy-activated pathways, selectively degrading about 73.00 % of extracellular polymeric substance (EPS)-bound ARGs while suppressing horizontal gene transfer (tolC downregulation). The 6:4 FeS2@S[0] system achieved 68.66 % total nitrogen removal and 50.17 % sulfamethoxazole degradation, outperforming conventional substrates by 28.00-39.00 %, alongside a 61.24-67.31 % reduction in ARG abundance. A self-sustaining sulfur cycle recycled about 89.00 % of sulfides into bio-S[0] or FeS2, minimizing H2S emissions (0.045 mg·m[-2]·h[-1]) and maintaining electron flux. By bridging Trx-driven redox homeostasis and bio-S[0]'s physical protection, this work redefines CWs as robust systems capable of simultaneous nitrogen retention, antibiotic degradation, and ARGs suppression, establishing a transformative paradigm for sustainable wastewater treatment.},
}

*Sulfamethoxazole/metabolism
*Wetlands
*Sulfur/metabolism
*Thioredoxins/metabolism
*Nitrogen/metabolism
Denitrification
Drug Resistance, Microbial/genetics

@article {pmid40319560,
year = {2025},
author = {Gross, N and Brodard, I and Overesch, G and Kittl, S},
title = {Genetic basis of β-lactam resistance in Corynebacterium auriscanis and association with otitis externa in dogs and cats.},
journal = {Veterinary microbiology},
volume = {305},
number = {},
pages = {110526},
doi = {10.1016/j.vetmic.2025.110526},
pmid = {40319560},
issn = {1873-2542},
mesh = {Animals ; Dogs ; *Corynebacterium/genetics/drug effects ; *Dog Diseases/microbiology ; *Corynebacterium Infections/veterinary/microbiology ; *Otitis Externa/veterinary/microbiology ; Cats ; *Cat Diseases/microbiology ; Anti-Bacterial Agents/pharmacology ; *beta-Lactam Resistance/genetics ; Microbial Sensitivity Tests ; Whole Genome Sequencing ; Switzerland/epidemiology ; beta-Lactams/pharmacology ; beta-Lactamases/genetics ; },
abstract = {Corynebacterium (C.) auriscanis is an opportunistic pathogen regularly isolated from canine otitis externa, an important condition often hard to treat. We found a surprisingly high prevalence of β-lactam resistant isolates of C. auriscanis (47 %), even though β-lactams are not routinely used for otitis externa treatment in Switzerland. To determine the genetic base of this phenotype, a selection of isolates of C. auriscanis with high and low minimal inhibitory concentration values were subjected to whole genome sequencing. Comparative analysis revealed a gene cassette containing three genes (hdfR encoding a LysR-family transcriptional regulator, blaB encoding a β-lactamase related protein and pbp2c encoding a D,D-transpeptidase) as the likely resistance-encoding determinant in the isolates from otitis externa. This locus had previously been described in C. jeikeium as well as C. diphtheriae and was associated with mobile genetic elements. In our six C. auriscanis isolates the pbp2c locus was always associated with the same IS3 family transposase, an association also found on C. diphtheriae plasmid CP091096, indicating horizontal gene transfer between species. To elucidate the function of the three genes in the pbp2c locus, we constructed plasmids with different combinations of these genes, transformed β-lactam sensitive isolates with the plasmids and tested resistance in the mutants phenotypically. By doing so we confirmed Pbp2c to be the primary factor conferring β-lactam resistance and HdfR and BlaB being important for expression and regulation. Interestingly, resistance to all β-lactams including carbapenems was constitutive in one C. auriscanis transformant while an induction effect was visible for the other transformed C. auriscanis strain, C. glutamicum and C. rouxii as previously described for C. jeikeium. Therefore, testing of β-lactam resistance should be done in combination including induction in Corynebacterium spp.},
}

Animals
Dogs
*Corynebacterium/genetics/drug effects
*Dog Diseases/microbiology
*Corynebacterium Infections/veterinary/microbiology
*Otitis Externa/veterinary/microbiology
Cats
*Cat Diseases/microbiology
Anti-Bacterial Agents/pharmacology
*beta-Lactam Resistance/genetics
Microbial Sensitivity Tests
Whole Genome Sequencing
Switzerland/epidemiology
beta-Lactams/pharmacology
beta-Lactamases/genetics

@article {pmid40262895,
year = {2025},
author = {Lind, AL and McDonald, NA and Gerrick, ER and Bhatt, AS and Pollard, KS},
title = {Contiguous and complete assemblies of Blastocystis gut microbiome-associated protists reveal evolutionary diversification to host ecology.},
journal = {Genome research},
volume = {35},
number = {6},
pages = {1377-1390},
pmid = {40262895},
issn = {1549-5469},
support = {K22 AI173181/AI/NIAID NIH HHS/United States ; R01 AI143757/AI/NIAID NIH HHS/United States ; R01 AI148623/AI/NIAID NIH HHS/United States ; R01 HL160862/HL/NHLBI NIH HHS/United States ; },
mesh = {*Blastocystis/genetics/classification ; *Gastrointestinal Microbiome/genetics ; Phylogeny ; Animals ; Humans ; *Evolution, Molecular ; Genome, Protozoan ; },
abstract = {Blastocystis, an obligate host-associated protist, is the most common microbial eukaryote in the human gut, and is widely distributed across vertebrate hosts. The evolutionary transition of Blastocystis from its free-living stramenopile ancestors to a radiation of host-associated organisms is poorly understood. To explore this, we cultured and sequenced eight strains representing the significant phylogenetic diversity of the genus using long-read, short-read, and Hi-C DNA sequencing, alongside gene annotation and RNA sequencing. Comparative genomic analyses reveal significant variation in gene content and genome structure across Blastocystis. Notably, three strains from herbivorous tortoises, phylogenetically distant from human subtypes, have markedly larger genomes with longer introns and intergenic regions, and retain canonical stop codons absent in the human-associated strains. Despite these genetic differences, all eight isolates exhibit gene losses linked to the reduced cellular complexity of Blastocystis, including losses of cilia and flagella genes, microtubule motor genes, and signal transduction genes. Isolates from herbivorous tortoises contain higher numbers of plant carbohydrate-metabolizing enzymes, suggesting that, like gut bacteria, these protists ferment plant material in the host gut. We find evidence that some of these carbohydrate-metabolizing enzymes were horizontally acquired from bacteria, indicating that horizontal gene transfer is an ongoing process in Blastocystis that has contributed to host-related adaptation. Together, these results highlight substantial genetic and metabolic diversity within the Blastocystis genus, indicating that different lineages of Blastocystis have varied ecological roles in the host gut.},
}

*Blastocystis/genetics/classification
*Gastrointestinal Microbiome/genetics
Phylogeny
Animals
Humans
*Evolution, Molecular
Genome, Protozoan

@article {pmid39981300,
year = {2025},
author = {Proença, M and Tanoeiro, L and Fox, JG and Vale, FF},
title = {Prophage dynamics in gastric and enterohepatic environments: unraveling ecological barriers and adaptive transitions.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf017},
pmid = {39981300},
issn = {2730-6151},
support = {R01 CA281732/CA/NCI NIH HHS/United States ; },
abstract = {Phage predation plays a critical role in shaping bacterial genetic diversity, with prophages playing a comparable role. However, the prevalence and genetic variability of prophages within the Helicobacter genus remain inadequately studied. Helicobacter species are clinically significant and occupy distinct digestive system regions, with gastric species (e.g. Helicobacter pylori) residing in the gastric mucosa and enterohepatic species colonizing the liver and intestines of various vertebrates. Here, we address this knowledge gap by analyzing prophage presence and diversity across 343 non-pylori Helicobacter genomes, mapping their distribution, comparing genomic features between gastric and enterohepatic prophages, and exploring their evolutionary relationships with hosts. We identified and analyzed a catalog of 119 new complete and 78 incomplete prophages. Our analysis reveals significant differences between gastric and enterohepatic species. Gastric prophages exhibit high synteny, and cluster in a few groups, indicating a more conserved genetic structure. In contrast, enterohepatic prophages show greater diversity in gene order and content, reflecting their adaptation to varied host environments. Helicobacter cinaedi stands out, harboring a large number of prophages among the enterohepatic species, forming a distinct cohesive group. Phylogenetic analyses reveal a co-evolutionary relationship between several prophages and their bacterial hosts-though exceptions, such as the enterohepatic prophages from H. canis, H. equorum, H. jaachi, and the gastric prophage from H. himalayensis-suggesting more complex co-evolutionary dynamics like host jumps, recombination, and horizontal gene transfer. The insights gained from this study enhance our understanding of prophage dynamics in Helicobacter, emphasizing their role in bacterial adaptation, virulence, and host specificity.},
}

@article {pmid39592962,
year = {2024},
author = {Mane, A and Sanderson, H and White, AP and Zaheer, R and Beiko, R and Chauve, C},
title = {Plaseval: a framework for comparing and evaluating plasmid detection tools.},
journal = {BMC bioinformatics},
volume = {25},
number = {1},
pages = {365},
pmid = {39592962},
issn = {1471-2105},
mesh = {*Plasmids/genetics/metabolism ; Software ; Genome, Bacterial ; Sequence Analysis, DNA/methods ; },
abstract = {BACKGROUND: Plasmids play a major role in the transfer of antimicrobial resistance (AMR) genes among bacteria via horizontal gene transfer. The identification of plasmids in short-read assemblies is a challenging problem and a very active research area. Plasmid binning aims at detecting, in a draft genome assembly, groups (bins) of contigs likely to originate from the same plasmid. Several methods for plasmid binning have been developed recently, such as PlasBin-flow, HyAsP, gplas, MOB-suite, and plasmidSPAdes. This motivates the problem of evaluating the performances of plasmid binning methods, either against a given ground truth or between them.

RESULTS: We describe PlasEval, a novel method aimed at comparing the results of plasmid binning tools. PlasEval computes a dissimilarity measure between two sets of plasmid bins, that can originate either from two plasmid binning tools, or from a plasmid binning tool and a ground truth set of plasmid bins. The PlasEval dissimilarity accounts for the contig content of plasmid bins, the length of contigs and is repeat-aware. Moreover, the dissimilarity score computed by PlasEval is broken down into several parts, that allows to understand qualitative differences between the compared sets of plasmid bins. We illustrate the use of PlasEval by benchmarking four recently developed plasmid binning tools-PlasBin-flow, HyAsP, gplas, and MOB-recon-on a data set of 53 E. coli bacterial genomes.

CONCLUSION: Analysis of the results of plasmid binning methods using PlasEval shows that their behaviour varies significantly. PlasEval can be used to decide which specific plasmid binning method should be used for a specific dataset. The disagreement between different methods also suggests that the problem of plasmid binning on short-read contigs requires further research. We believe that PlasEval can prove to be an effective tool in this regard. PlasEval is publicly available at https://github.com/acme92/PlasEval.},
}

*Plasmids/genetics/metabolism
Software
Genome, Bacterial
Sequence Analysis, DNA/methods

@article {pmid39219575,
year = {2024},
author = {He, XY and Chen, JM and Li, ZZ},
title = {Complete organelle genomes of the threatened aquatic species Scheuchzeria palustris (Scheuchzeriaceae): Insights into adaptation and phylogenomic placement.},
journal = {Ecology and evolution},
volume = {14},
number = {9},
pages = {e70248},
pmid = {39219575},
issn = {2045-7758},
abstract = {Scheuchzeria palustris, the only species in the Scheuchzeriaceae family, plays a crucial role in methane production and transportation, influencing the global carbon cycle and maintaining ecosystem stability. However, it is now threatened by human activities and global warming. In this study, we generated new organelle genomes for S. palustris, with the plastome (pt) measuring 158,573 bp and the mitogenome (mt) measuring 420,724 bp. We predicted 296 RNA editing sites in mt protein-coding genes (PCGs) and 142 in pt-PCGs. Notably, abundant RNA editing sites in pt-PCGs likely originated from horizontal gene transfer between the plastome and mitogenome. Additionally, we identified positive selection signals in four mt-PCGs (atp4, ccmB, nad3, and sdh4) and one pt-PCG (rps7), which may contribute to the adaptation of S. palustris to low-temperature and high-altitude environments. Furthermore, we identified 35 mitochondrial plastid DNA (MTPT) segments totaling 58,479 bp, attributed to dispersed repeats near most MTPT. Phylogenetic trees reconstructed from mt- and pt-PCGs showed topologies consistent with the APG IV system. However, the conflicting position of S. palustris can be explained by significant differences in the substitution rates of its mt- and pt-PCGs (p < .001). In conclusion, our study provides vital genomic resources to support future conservation efforts and explores the adaptation mechanisms of S. palustris.},
}

@article {pmid39096995,
year = {2024},
author = {Tian, J and Xu, L and Sun, JQ},
title = {Taxonomic characterization and comparative genomic analysis of a novel Devosia species revealed that phenolic acid-degrading traits are ubiquitous in the Devosia genus.},
journal = {Environmental research},
volume = {261},
number = {},
pages = {119724},
doi = {10.1016/j.envres.2024.119724},
pmid = {39096995},
issn = {1096-0953},
mesh = {*Hydroxybenzoates/metabolism ; Hyphomicrobiaceae/genetics/metabolism ; Soil Microbiology ; Genome, Bacterial ; Genomics ; Phylogeny ; Rhizosphere ; Biodegradation, Environmental ; },
abstract = {Phenolic acids (PAs) are widely distributed allelochemicals in various environments. To better understand the fate of PAs in environments, a halotolerant PAs-degrading bacterium (named strain RR2S18[T]) isolated from rhizosphere soil was identified as a novel species of Devosia, named Devosia rhizosphaerae sp. nov. The strain initially degraded PAs into central ring-fission intermediates (protocatechuic acid) using the CoA-dependent non-β-oxidation pathway. The produced ring-fission intermediates were then consecutively degraded by an ortho-cleavage reaction and the β-ketoadipic acid pathway. A comparative genomics analysis of 62 Devosia strains revealed that PAs-degrading genes were ubiquitous in their genomes, indicating that PAs degradation is universal among members of this genus. The analysis also suggested that the genes involved in CoA-dependent non-β-oxidation are inherent to Devosia strains, while those involved in ring-fission and β-ketoadipic acid pathways were obtained by horizontal gene transfer.},
}

*Hydroxybenzoates/metabolism
Hyphomicrobiaceae/genetics/metabolism
Soil Microbiology
Genome, Bacterial
Genomics
Phylogeny
Rhizosphere
Biodegradation, Environmental

@article {pmid38983623,
year = {2024},
author = {Chin, HS and Ravi Varadharajulu, N and Lin, ZH and Chen, WY and Zhang, ZH and Arumugam, S and Lai, CY and Yu, SS},
title = {Isolation, molecular identification, and genomic analysis of Mangrovibacter phragmitis strain ASIOC01 from activated sludge harboring the bioremediation prowess of glycerol and organic pollutants in high-salinity.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1415723},
pmid = {38983623},
issn = {1664-302X},
abstract = {The physiological and genotypic characteristics of Mangrovibacter (MGB) remain largely unexplored, including their distribution and abundance within ecosystems. M. phragmitis (MPH) ASIOC01 was successfully isolated from activated sludge (AS), which was pre-enriched by adding 1,3-dichloro-2-propanol and 3-chloro-1,2-propanediol as carbon sources. The new isolate, MPH ASIOC01, exhibited resilience in a medium containing sodium chloride concentration up to 11% (with optimal growth observed at 3%) and effectively utilizing glycerol as their sole carbon source. However, species delimitation of MGBs remains challenging due to high 16S rRNA sequence similarity (greater than 99% ANI) among different MGBs. In contrast, among the housekeeping gene discrepancies, the tryptophan synthase beta chain gene can serve as a robust marker for fast species delimitation among MGBs. Furthermore, the complete genome of MPH ASIOC01 was fully sequenced and circlized as a single contig using the PacBio HiFi sequencing method. Comparative genomics revealed genes potentially associated with various phenotypic features of MGBs, such as nitrogen-fixing, phosphate-solubilizing, cellulose-digesting, Cr-reducing, and salt tolerance. Computational analysis suggested that MPH ASIOC01 may have undergone horizontal gene transfer events, possibly contributing unique traits such as antibiotic resistance. Finally, our findings also disclosed that the introduction of MPH ASIOC01 into AS can assist in the remediation of wastewater chemical oxygen demand, which was evaluated using gas chromatograph-mass spectrometry. To the best of our knowledge, this study offers the most comprehensive understanding of the phenotypic and genotypic features of MGBs to date.},
}

@article {pmid38765968,
year = {2025},
author = {Mancuso, CP and Baker, JS and Qu, E and Tripp, AD and Balogun, IO and Lieberman, TD},
title = {Intraspecies warfare restricts strain coexistence in human skin microbiomes.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {38765968},
issn = {2692-8205},
support = {DP2 GM140922/GM/NIGMS NIH HHS/United States ; },
abstract = {Determining why only a fraction of encountered or applied strains engraft in a given person's microbiome is crucial for understanding and engineering these communities. Previous work has established that metabolic competition can restrict colonization success in vivo, but the relevance of bacterial warfare in preventing commensal engraftment has been less explored. Here, we demonstrate that intraspecies warfare presents a significant barrier to strain coexistence in the human skin microbiome by profiling 14,884 pairwise interactions between Staphylococcus epidermidis isolates cultured from eighteen people from six families. We find that intraspecies antagonisms are abundant, mechanistically diverse, independent of strain relatedness, and consistent with rapid evolution via horizontal gene transfer. Critically, these antagonisms are significantly depleted among strains residing on the same person relative to random assemblages, indicating a significant in vivo role. Together, our results emphasize that accounting for intraspecies warfare may be essential to the design of long-lasting probiotic therapeutics.},
}

@article {pmid38349154,
year = {2024},
author = {Vargas-Gastélum, L and Romer, AS and Ghotbi, M and Dallas, JW and Alexander, NR and Moe, KC and McPhail, KL and Neuhaus, GF and Shadmani, L and Spatafora, JW and Stajich, JE and Tabima, JF and Walker, DM},
title = {Herptile gut microbiomes: a natural system to study multi-kingdom interactions between filamentous fungi and bacteria.},
journal = {mSphere},
volume = {9},
number = {3},
pages = {e0047523},
pmid = {38349154},
issn = {2379-5042},
mesh = {Bacteria/genetics ; Fungi/genetics ; *Gastrointestinal Microbiome ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Animals ; },
abstract = {Reptiles and amphibians (herptiles) are some of the most endangered and threatened species on the planet and numerous conservation strategies are being implemented with the goal of ensuring species recovery. Little is known, however, about the gut microbiome of wild herptiles and how it relates to the health of these populations. Here, we report results from the gut microbiome characterization of both a broad survey of herptiles, and the correlation between the fungus Basidiobolus, and the bacterial community supported by a deeper, more intensive sampling of Plethodon glutinosus, known as slimy salamanders. We demonstrate that bacterial communities sampled from frogs, lizards, and salamanders are structured by the host taxonomy and that Basidiobolus is a common and natural component of these wild gut microbiomes. Intensive sampling of multiple hosts across the ecoregions of Tennessee revealed that geography and host:geography interactions are strong predictors of distinct Basidiobolus operational taxonomic units present within a given host. Co-occurrence analyses of Basidiobolus and bacterial community diversity support a correlation and interaction between Basidiobolus and bacteria, suggesting that Basidiobolus may play a role in structuring the bacterial community. We further the hypothesis that this interaction is advanced by unique specialized metabolism originating from horizontal gene transfer from bacteria to Basidiobolus and demonstrate that Basidiobolus is capable of producing a diversity of specialized metabolites including small cyclic peptides.IMPORTANCEThis work significantly advances our understanding of biodiversity and microbial interactions in herptile microbiomes, the role that fungi play as a structural and functional members of herptile gut microbiomes, and the chemical functions that structure microbiome phenotypes. We also provide an important observational system of how the gut microbiome represents a unique environment that selects for novel metabolic functions through horizontal gene transfer between fungi and bacteria. Such studies are needed to better understand the complexity of gut microbiomes in nature and will inform conservation strategies for threatened species of herpetofauna.},
}

Bacteria/genetics
Fungi/genetics
*Gastrointestinal Microbiome
*Microbiota
RNA, Ribosomal, 16S/genetics
Animals

@article {pmid38163572,
year = {2024},
author = {Gaviria-Cantin, T and Fernández-Coll, L and Vargas, AF and Jiménez, CJ and Madrid, C and Balsalobre, C},
title = {Expression of accessory genes in Salmonella requires the presence of the Gre factors.},
journal = {Genomics},
volume = {116},
number = {1},
pages = {110777},
doi = {10.1016/j.ygeno.2023.110777},
pmid = {38163572},
issn = {1089-8646},
mesh = {*Salmonella typhimurium/genetics/metabolism ; Plasmids ; Virulence/genetics ; *Bacterial Proteins/genetics/metabolism ; },
abstract = {Genomic studies with Salmonella enterica serovar Typhimurium reveal a crucial role of horizontal gene transfer (HGT) in the acquisition of accessory cellular functions involved in host-interaction. Many virulence genes are located in genomic islands, plasmids and prophages. GreA and GreB proteins, Gre factors, interact transiently with the RNA polymerase alleviating backtracked complexes during transcription elongation. The overall effect of Gre factors depletion in Salmonella expression profile was studied. Both proteins are functionally redundant since only when both Gre factors were depleted a major effect in gene expression was detected. Remarkably, the accessory gene pool is particularly sensitive to the lack of Gre factors, with 18.6% of accessory genes stimulated by the Gre factors versus 4.4% of core genome genes. Gre factors involvement is particularly relevant for the expression of genes located in genomic islands. Our data reveal that Gre factors are required for the expression of accessory genes.},
}

*Salmonella typhimurium/genetics/metabolism
Plasmids
Virulence/genetics
*Bacterial Proteins/genetics/metabolism

@article {pmid37632379,
year = {2023},
author = {Sabar, MA and Van Huy, T and Sugie, Y and Wada, H and Zhao, B and Matsuura, N and Ihara, M and Watanabe, T and Tanaka, H and Honda, R},
title = {Antimicrobial resistome and mobilome in the urban river affected by combined sewer overflows and wastewater treatment effluent.},
journal = {Journal of water and health},
volume = {21},
number = {8},
pages = {1032-1050},
doi = {10.2166/wh.2023.073},
pmid = {37632379},
issn = {1477-8920},
mesh = {Rivers ; *Anti-Infective Agents ; Anti-Bacterial Agents/pharmacology ; Macrolides ; *Microbiota ; },
abstract = {The dissemination of antimicrobial resistance in the environment is an emerging global health problem. Wastewater treatment effluent and combined sewer overflows (CSOs) are major sources of antimicrobial resistance in urban rivers. This study aimed to clarify the effect of municipal wastewater treatment effluent and CSO on antimicrobial resistance genes (ARGs), mobile gene elements, and the microbial community in an urban river. The ARG abundance per 16S-based microbial population in the target river was 0.37-0.54 and 0.030-0.097 during the CSO event and dry weather, respectively. During the CSO event, the antimicrobial resistome in the river shifted toward a higher abundance of ARGs to clinically important drug classes, including macrolide, fluoroquinolone, and β-lactam, whereas ARGs to sulfonamide and multidrug by efflux pump were relatively abundant in dry weather. The abundance of intI1 and tnpA genes were highly associated with the total ARG abundance, suggesting their potential application as an indicator for estimating resistome contamination. Increase of prophage during the CSO event suggested that impact of CSO has a greater potential for horizontal gene transfer (HGT) via transduction. Consequently, CSO not only increases the abundance of ARGs to clinically important antimicrobials but also possibly enhances potential of HGT in urban rivers.},
}

Rivers
*Anti-Infective Agents
Anti-Bacterial Agents/pharmacology
Macrolides
*Microbiota

@article {pmid37499413,
year = {2023},
author = {Ma, R and Wang, J and Liu, Y and Wang, G and Yang, Y and Liu, Y and Kong, Y and Lin, J and Li, Q and Li, G and Yuan, J},
title = {Dynamics of antibiotic resistance genes and bacterial community during pig manure, kitchen waste, and sewage sludge composting.},
journal = {Journal of environmental management},
volume = {345},
number = {},
pages = {118651},
doi = {10.1016/j.jenvman.2023.118651},
pmid = {37499413},
issn = {1095-8630},
mesh = {Animals ; Swine ; *Anti-Bacterial Agents/pharmacology ; Sewage ; Tetracycline ; *Composting ; Manure/microbiology ; Genes, Bacterial ; Drug Resistance, Bacterial ; Macrolides ; Bacteria ; Sulfanilamide ; },
abstract = {Organic solid wastes (OSWs) are important reservoirs for antibiotic resistance genes (ARGs). Aerobic composting transforms OSWs into fertilizers. In this study, we investigated ARGs dynamics and their driving mechanisms in three OSW composts: pig manure (PM), kitchen waste (KC), and sewage sludge (SG). The dominant ARGs were different in each OSW, namely tetracycline, aminoglycoside, and macrolide resistance (PM); tetracyclines and aminoglycosides (KC); and sulfonamides (SG). ARGs abundance decreased in PM (71%) but increased in KC (5.9-fold) and SG (1.3-fold). Interestingly, the ARGs abundance was generally similar in all final composts, which was contributed to the similar bacterial community in final composts. In particular, sulfonamide and β-lactam resistant genes removed (100%) in PM, while sulfonamide in KC (38-fold) and tetracycline in SG (5-fold) increased the most. Additionally, ARGs abundance rebounded during the maturation period in all treatments. Firmicutes, Proteobacteria, and Actinobacteria were the main ARGs hosts. Several persistent and high-risk genes included tetW, aadA, aadE, tetX, strB, tetA, mefA, intl1, and intl2. The structural equation models showed ARGs removal was mainly affected by physicochemical parameters and bacterial communities in PM, the ARGs enrichment in KC composting correlated with increased mobile genetic elements (MGEs). In general, thermophilic aerobic composting can inhibit the vertical gene transfer (VGT) of pig manure and horizontal gene transfer (HGT) of sludge, but it increases the HGT of kitchen waste, resulting in a dramatic increase of ARGs in KC compost. More attention should be paid to the ARGs risk of kitchen waste composting.},
}

Animals
Swine
*Anti-Bacterial Agents/pharmacology
Sewage
Tetracycline
*Composting
Manure/microbiology
Genes, Bacterial
Drug Resistance, Bacterial
Macrolides
Bacteria
Sulfanilamide

@article {pmid36893903,
year = {2023},
author = {Khan, AA and Nema, V and Ashraf, MT},
title = {Host-microbiota interactions and oncogenesis: Crosstalk and its implications in etiology.},
journal = {Microbial pathogenesis},
volume = {178},
number = {},
pages = {106063},
doi = {10.1016/j.micpath.2023.106063},
pmid = {36893903},
issn = {1096-1208},
mesh = {Humans ; Carcinogenesis ; *Microbiota/genetics ; *Neoplasms ; Host Microbial Interactions ; },
abstract = {A number of articles have discussed the potential of microbiota in oncogenesis. Several of these have evaluated the modulation of microbiota and its influence on cancer development. Even in recent past, a plethora of studies have gathered in order to understand the difference in microbiota population among different cancer and normal individuals. Although in majority of studies, microbiota mediated oncogenesis has been primarily attributed to the inflammatory mechanisms, there are several other ways through which microbiota can influence oncogenesis. These relatively less discussed aspects including the hormonal modulation through estrobolome and endobolome, production of cyclomodulins, and lateral gene transfer need more attention of scientific community. We prepared this article to discuss the role of microbiota in oncogenesis in order to provide concise information on these relatively less discussed microbiota mediated oncogenesis mechanisms.},
}

Humans
Carcinogenesis
*Microbiota/genetics
*Neoplasms
Host Microbial Interactions

@article {pmid36822312,
year = {2023},
author = {Sun, L and Tang, D and Tai, X and Wang, J and Long, M and Xian, T and Jia, H and Wu, R and Ma, Y and Jiang, Y},
title = {Effect of composted pig manure, biochar, and their combination on antibiotic resistome dissipation in swine wastewater-treated soil.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {323},
number = {},
pages = {121323},
doi = {10.1016/j.envpol.2023.121323},
pmid = {36822312},
issn = {1873-6424},
mesh = {*Composting ; *Manure ; *Drug Resistance, Bacterial ; Brassica/microbiology ; Interspersed Repetitive Sequences ; Soil Microbiology ; *Agriculture/methods ; *Swine ; Animals ; Soil/chemistry ; },
abstract = {The prevalence of antibiotic resistance genes (ARGs), owing to irrigation using untreated swine wastewater, in vegetable-cultivated soils around swine farms poses severe threats to human health. Furthermore, at the field scale, the remediation of such soils is still challenging. Therefore, here, we performed field-scale experiments involving the cultivation of Brassica pekinensis in a swine wastewater-treated soil amended with composted pig manure, biochar, or their combination. Specifically, the ARG and mobile genetic element (MGE) profiles of bulk soil (BS), rhizosphere soil (RS), and root endophyte (RE) samples were examined using high-throughput quantitative polymerase chain reaction. In total, 117 ARGs and 22 MGEs were detected. Moreover, we observed that soil amendment using composted pig manure, biochar, or their combination decreased the absolute abundance of ARGs in BS and RE after 90 days of treatment. However, the decrease in the abundance of ARGs in RS was not significant. We also observed that the manure and biochar co-application showed a minimal synergistic effect. To clarify this observation, we performed network and Spearman correlation analyses and used structure equation models to explore the correlations among ARGs, MGEs, bacterial composition, and soil properties. The results revealed that the soil amendments reduced the abundances of MGEs and potential ARG-carrying bacteria. Additionally, weakened horizontal gene transfer was responsible for the dissipation of ARGs. Thus, our results indicate that composted manure application, with or without biochar, is a useful strategy for soil nutrient supplementation and alleviating farmland ARG pollution, providing a justification for using an alternative to the common agricultural practice of treating the soil using only untreated swine wastewater. Additionally, our results are important in the context of soil health for sustainable agriculture.},
}

*Composting
*Manure
*Drug Resistance, Bacterial
Brassica/microbiology
Interspersed Repetitive Sequences
Soil Microbiology
*Agriculture/methods
*Swine
Animals
Soil/chemistry

@article {pmid35699339,
year = {2022},
author = {Ahator, SD and Sagar, S and Zhu, M and Wang, J and Zhang, LH},
title = {Nutrient Availability and Phage Exposure Alter the Quorum-Sensing and CRISPR-Cas-Controlled Population Dynamics of Pseudomonas aeruginosa.},
journal = {mSystems},
volume = {7},
number = {4},
pages = {e0009222},
pmid = {35699339},
issn = {2379-5077},
mesh = {Quorum Sensing/genetics ; Pseudomonas aeruginosa/genetics ; *Bacteriophages/genetics ; CRISPR-Cas Systems/genetics ; Acyl-Butyrolactones/pharmacology ; *Anti-Infective Agents/pharmacology ; },
abstract = {Quorum sensing (QS) coordinates bacterial communication and cooperation essential for virulence and dominance in polymicrobial settings. QS also regulates the CRISPR-Cas system for targeted defense against parasitic genomes from phages and horizontal gene transfer. Although the QS and CRISPR-Cas systems are vital for bacterial survival, they undergo frequent selection in response to biotic and abiotic factors. Using the opportunistic Pseudomonas aeruginosa with well-established QS and CRISPR-Cas systems, we show how the social interactions between the acyl-homoserine lactone (AHL)-QS signal-blind mutants (ΔlasRrhlR) and the CRISPR-Cas mutants are affected by phage exposure and nutrient availability. We demonstrate that media conditions and phage exposure alter the resistance and relative fitness of ΔlasRrhlR and CRISPR-Cas mutants while tipping the fitness advantage in favor of the QS signal-blind mutants under nutrient-limiting conditions. We also show that the AHL signal-blind mutants are less selected by phages under QS-inducing conditions than the CRISPR-Cas mutants, whereas the mixed population of the CRISPR-Cas and AHL signal-blind mutants reduce phage infectivity, which can improve survival during phage exposure. Our data reveal that phage exposure and nutrient availability reshape the population dynamics between the ΔlasRrhlR QS mutants and CRISPR-Cas mutants, with key indications for cooperation and conflict between the strains. IMPORTANCE The increase in antimicrobial resistance has created the need for alternative interventions such as phage therapy. However, as previously observed with antimicrobial resistance, phage therapy will not be effective if bacteria evolve resistance and persist in the presence of the phages. The QS is commonly known as an arsenal for bacteria communication, virulence, and regulation of the phage defense mechanism, the CRISPR-Cas system. The QS and CRISPR-Cas systems are widespread in bacteria. However, they are known to evolve rapidly under the influence of biotic and abiotic factors in the bacterial environment, resulting in alteration in bacterial genotypes, which enhance phage resistance and fitness. We believe that adequate knowledge of the influence of environmental factors on the bacterial community lifestyle and phage defense mechanisms driven by the QS and CRISPR-Cas system is necessary for developing effective phage therapy.},
}

Quorum Sensing/genetics
Pseudomonas aeruginosa/genetics
*Bacteriophages/genetics
CRISPR-Cas Systems/genetics
Acyl-Butyrolactones/pharmacology
*Anti-Infective Agents/pharmacology

@article {pmid34576815,
year = {2021},
author = {Poyntner, C and Kutzner, A and Margesin, R},
title = {Biodegradation Potential and Putative Catabolic Genes of Culturable Bacteria from an Alpine Deciduous Forest Site.},
journal = {Microorganisms},
volume = {9},
number = {9},
pages = {},
pmid = {34576815},
issn = {2076-2607},
abstract = {Microbiota from Alpine forest soils are key players in carbon cycling, which can be greatly affected by climate change. The aim of this study was to evaluate the degradation potential of culturable bacterial strains isolated from an alpine deciduous forest site. Fifty-five strains were studied with regard to their phylogenetic position, growth temperature range and degradation potential for organic compounds (microtiter scale screening for lignin sulfonic acid, catechol, phenol, bisphenol A) at low (5 °C) and moderate (20 °C) temperature. Additionally, the presence of putative catabolic genes (catechol-1,2-dioxygenase, multicomponent phenol hydroxylase, protocatechuate-3,4-dioxygenase) involved in the degradation of these organic compounds was determined through PCR. The results show the importance of the Proteobacteria phylum as its representatives did show good capabilities for biodegradation and good growth at -5 °C. Overall, 82% of strains were able to use at least one of the tested organic compounds as their sole carbon source. The presence of putative catabolic genes could be shown over a broad range of strains and in relation to their degradation abilities. Subsequently performed gene sequencing indicated horizontal gene transfer for catechol-1,2-dioxygenase and protocatechuate-3,4-dioxygenase. The results show the great benefit of combining molecular and culture-based techniques.},
}

@article {pmid34126763,
year = {2021},
author = {Hahn, J and DeSantis, M and Dubnau, D},
title = {Mechanisms of Transforming DNA Uptake to the Periplasm of Bacillus subtilis.},
journal = {mBio},
volume = {12},
number = {3},
pages = {e0106121},
pmid = {34126763},
issn = {2150-7511},
support = {R01 GM057720/GM/NIGMS NIH HHS/United States ; },
mesh = {Bacillus subtilis/*genetics/*metabolism ; Biological Transport ; Cell Membrane/metabolism ; DNA, Bacterial/genetics/*metabolism ; Membrane Proteins/metabolism ; Periplasm/*metabolism ; *Transformation, Bacterial ; },
abstract = {We demonstrate here that the acquisition of DNase resistance by transforming DNA, often assumed to indicate transport to the cytoplasm, reflects uptake to the periplasm, requiring a reevaluation of conclusions about the roles of several proteins in transformation. The new evidence suggests that the transformation pilus is needed for DNA binding to the cell surface near the cell poles and for the initiation of uptake. The cellular distribution of the membrane-anchored ComEA of Bacillus subtilis does not dramatically change during DNA uptake as does the unanchored ComEA of Vibrio and Neisseria. Instead, our evidence suggests that ComEA stabilizes the attachment of transforming DNA at localized regions in the periplasm and then mediates uptake, probably by a Brownian ratchet mechanism. Following that, the DNA is transferred to periplasmic portions of the channel protein ComEC, which plays a previously unsuspected role in uptake to the periplasm. We show that the transformation endonuclease NucA also facilitates uptake to the periplasm and that the previously demonstrated role of ComFA in the acquisition of DNase resistance derives from the instability of ComGA when ComFA is deleted. These results prompt a new understanding of the early stages of DNA uptake for transformation. IMPORTANCE Transformation is a widely distributed mechanism of bacterial horizontal gene transfer that plays a role in the spread of antibiotic resistance and virulence genes and more generally in evolution. Although transformation was discovered nearly a century ago and most, if not all the proteins required have been identified in several bacterial species, much remains poorly understood about the molecular mechanism of DNA uptake. This study uses epifluorescence microscopy to investigate the passage of labeled DNA into the compartment between the cell wall and the cell membrane of Bacillus subtilis, a necessary early step in transformation. The roles of individual proteins in this process are identified, and their modes of action are clarified.},
}

Bacillus subtilis/*genetics/*metabolism
Biological Transport
Cell Membrane/metabolism
DNA, Bacterial/genetics/*metabolism
Membrane Proteins/metabolism
Periplasm/*metabolism
*Transformation, Bacterial

@article {pmid33563283,
year = {2021},
author = {Sela, I and Wolf, YI and Koonin, EV},
title = {Assessment of assumptions underlying models of prokaryotic pangenome evolution.},
journal = {BMC biology},
volume = {19},
number = {1},
pages = {27},
pmid = {33563283},
issn = {1741-7007},
mesh = {Archaea/*genetics ; Bacteria/*genetics ; *Evolution, Molecular ; *Metagenome ; Models, Genetic ; },
abstract = {BACKGROUND: The genomes of bacteria and archaea evolve by extensive loss and gain of genes which, for any group of related prokaryotic genomes, result in the formation of a pangenome with the universal, asymmetrical U-shaped distribution of gene commonality. However, the evolutionary factors that define the specific shape of this distribution are not thoroughly understood.

RESULTS: We investigate the fit of simple models of genome evolution to the empirically observed gene commonality distributions and genome intersections for 33 groups of closely related bacterial genomes. A model with an infinite external gene pool available for gene acquisition and constant genome size (IGP-CGS model), and two gene turnover rates, one for slow- and the other one for fast-evolving genes, allows two approaches to estimate the parameters for gene content dynamics. One is by fitting the model prediction to the distribution of the number of genes shared by precisely k genomes (gene commonality distribution) and another by analyzing the distribution of the number of genes common for k genome sets (k-cores). Both approaches produce a comparable overall quality of fit, although the former significantly overestimates the number of the universally conserved genes, while the latter overestimates the number of singletons. We further explore the effect of dropping each of the assumptions of the IGP-CGS model on the fit to the gene commonality distributions and show that models with either a finite gene pool or unequal rates of gene loss and gain (greater gene loss rate) eliminate the overestimate of the number of singletons or the core genome size.

CONCLUSIONS: We examine the assumptions that are usually adopted for modeling the evolution of the U-shaped gene commonality distributions in prokaryote genomes, namely, those of infinitely many genes and constant genome size. The combined analysis of genome intersections and gene commonality suggests that at least one of these assumptions is invalid. The violation of both these assumptions reflects the limited ability of prokaryotes to gain new genes. This limitation seems to stem, at least partly, from the horizontal gene transfer barrier, i.e., the cost of accommodation of foreign genes by prokaryotes. Further development of models taking into account the complexity of microbial evolution is necessary for an improved understanding of the evolution of prokaryotes.},
}

Archaea/*genetics
Bacteria/*genetics
*Evolution, Molecular
*Metagenome
Models, Genetic

@article {pmid33245329,
year = {2020},
author = {Hammond, JA and Gordon, EA and Socarras, KM and Chang Mell, J and Ehrlich, GD},
title = {Beyond the pan-genome: current perspectives on the functional and practical outcomes of the distributed genome hypothesis.},
journal = {Biochemical Society transactions},
volume = {48},
number = {6},
pages = {2437-2455},
pmid = {33245329},
issn = {1470-8752},
support = {P41 RR006009/RR/NCRR NIH HHS/United States ; R01 AI080935/AI/NIAID NIH HHS/United States ; R01 DC002148/DC/NIDCD NIH HHS/United States ; U01 DK082316/DK/NIDDK NIH HHS/United States ; },
mesh = {Algorithms ; Animals ; Bacterial Infections/microbiology ; Bacterial Physiological Phenomena ; Biodiversity ; Ecology ; Evolution, Molecular ; *Genes, Bacterial ; Genetic Variation ; *Genome, Bacterial ; Genome-Wide Association Study ; Genomics ; Genotype ; Humans ; Mice ; Molecular Biology ; Multigene Family ; Phenotype ; Phylogeny ; Symbiosis ; Whole Genome Sequencing ; },
abstract = {The principle of monoclonality with regard to bacterial infections was considered immutable prior to 30 years ago. This view, espoused by Koch for acute infections, has proven inadequate regarding chronic infections as persistence requires multiple forms of heterogeneity among the bacterial population. This understanding of bacterial plurality emerged from a synthesis of what-were-then novel technologies in molecular biology and imaging science. These technologies demonstrated that bacteria have complex life cycles, polymicrobial ecologies, and evolve in situ via the horizontal exchange of genic characters. Thus, there is an ongoing generation of diversity during infection that results in far more highly complex microbial communities than previously envisioned. This perspective is based on the fundamental tenet that the bacteria within an infecting population display genotypic diversity, including gene possession differences, which result from horizontal gene transfer mechanisms including transformation, conjugation, and transduction. This understanding is embodied in the concepts of the supragenome/pan-genome and the distributed genome hypothesis (DGH). These paradigms have fostered multiple researches in diverse areas of bacterial ecology including host-bacterial interactions covering the gamut of symbiotic relationships including mutualism, commensalism, and parasitism. With regard to the human host, within each of these symbiotic relationships all bacterial species possess attributes that contribute to colonization and persistence; those species/strains that are pathogenic also encode traits for invasion and metastases. Herein we provide an update on our understanding of bacterial plurality and discuss potential applications in diagnostics, therapeutics, and vaccinology based on perspectives provided by the DGH with regard to the evolution of pathogenicity.},
}

Algorithms
Animals
Bacterial Infections/microbiology
Bacterial Physiological Phenomena
Biodiversity
Ecology
Evolution, Molecular
*Genes, Bacterial
Genetic Variation
*Genome, Bacterial
Genome-Wide Association Study
Genomics
Genotype
Humans
Mice
Molecular Biology
Multigene Family
Phenotype
Phylogeny
Symbiosis
Whole Genome Sequencing

@article {pmid30867937,
year = {2019},
author = {Kindle, P and Zurfluh, K and Nüesch-Inderbinen, M and von Ah, S and Sidler, X and Stephan, R and Kümmerlen, D},
title = {Phenotypic and genotypic characteristics of Escherichia coli with non-susceptibility to quinolones isolated from environmental samples on pig farms.},
journal = {Porcine health management},
volume = {5},
number = {},
pages = {9},
pmid = {30867937},
issn = {2055-5660},
abstract = {BACKGROUND: In the last decade, the growth of the pig-farming industry has led to an increase in antibiotic use, including several used in human medicine, e.g. (fluoro)quinolones. Data from several studies suggest that there is a link between the agricultural use of antibiotics and the prevalence of antibiotic-resistant bacteria in the pig farm environment, including (fluoro)quinolone resistance. This poses a threat to human and animal health. Our goal was to phenotypically and genotypically characterize 174 E. coli showing non-susceptibility to quinolones isolated from environmental samples from pig farms. Antimicrobial susceptibility testing (AST) was performed using the disk diffusion method. PCR and sequence analysis were performed to identify chromosomal mutations in the quinolone resistance-determining regions (QRDR) of gyrA and the isolates were screened for the presence of the plasmid-mediated quinolone resistance (PMQR) genes aac-(6')-Ib-cr, qepA, qnrA, qnrB, qnrC, qnrD and qnrS.Strain relatedness was assessed by phylogenetic classification and multilocus sequence typing (MLST).

RESULTS: Of 174 isolates, 81% (n = 141) were resistant to nalidixic acid, and 19% (n = 33) were intermediately resistant. Overall, 68.4% (n = 119) were multidrug resistant. This study revealed a prevalence of 79.9% (n = 139) for gyrA QRDR mutations, and detected 21.8% (n = 38) isolates with at least one PMQR gene. The two most frequently detected PMQR genes were qnrB and qnrS (13.8% (n = 24) and 9.8% (n = 17, respectively). E. coli belonging to phylogenetic group A (48.3%/n = 84) and group B1 (33.3% /n = 58) were the most frequent. E. coli ST10 (n = 20) and ST297 (n = 20) were the most common STs.

CONCLUSIONS: E. coli with non-susceptibility to quinolones are widespread among the environment of Swiss pig farms and are often associated with an MDR phenotype. In several cases these isolates possess at least one PMQR gene, which could spread by horizontal gene transfer. E. coli from pig farms have diverse STs, some of which are associated with human and animal disease.},
}

@article {pmid30034183,
year = {2018},
author = {Lalruatdiki, A and Dutta, TK and Roychoudhury, P and Subudhi, PK},
title = {Extended-spectrum β-lactamases producing multidrug resistance Escherichia coli, Salmonella and Klebsiella pneumoniae in pig population of Assam and Meghalaya, India.},
journal = {Veterinary world},
volume = {11},
number = {6},
pages = {868-873},
pmid = {30034183},
issn = {0972-8988},
abstract = {AIM: The present study was conducted to record the prevalence of extended spectrum β-lactamases (ESBLs) producing Escherichia coli, Salmonella spp., and Klebsiella pneumoniae from pig population of Assam and Meghalaya and to record the ability of the resistant bacteria to transfer the resistance genes horizontally.

MATERIALS AND METHODS: Fecal samples (n=228), collected from pigs of Assam (n=99) and Meghalaya (n=129), were processed for isolation and identification of E. coli and Salmonella spp. All the isolates were tested for ESBLs production by double disc synergy test (DDST) followed by screening for ESBLs producing genes (blaTEM, blaSHV, blaCTX-M, and blaCMY) by polymerase chain reaction (PCR). Possible transfer of resistance encoding genes between enteric bacterial species was carried out by in vitro and in vivo horizontal gene transfer (HGT) method.

RESULTS: A total of 897 enteric bacteria (867 E. coli and 30 Salmonella) were isolated and identified. Altogether 25.41% isolates were confirmed as ESBL producers by DDST method. Majority of the isolates were E. coli followed by Salmonella. By PCR, 9.03% isolates were found positive for at least one of the target resistance genes. blaSHV was absent in all the isolates. blaCMY was the most prevalent gene. All the E. coli isolates from Assam were negative for blaTEM. A total of 2.76% isolates were positive for blaTEM + blaCMY. On the other hand, 0.67% isolates were positive for blaCTX-M + blaCMY genes. Only 0.33% isolates carried all the three genes. Altogether, 4.68% bacteria carried the resistance encoding genes in their plasmids. blaTEM gene could be successfully transferred from Salmonella (donor) to E. coli (recipient) by in vitro (5.5-5.7×10[-5]) and in vivo (6.5×10[-5] to 8.8×10[-4]) methods. In vivo method was more effective than in vitro in the transfer of resistance genes.

CONCLUSION: The pig population of Assam and Meghalaya are carrying multidrug resistance and ESBLs producing E. coli and Salmonella. The isolates are also capable to transfer their resistance trait to other bacterial species by HGT. The present finding could be considered as a serious public health concern as similar trait can also be transmitted to the human commensal bacteria as well as pathogens.},
}

@article {pmid29940436,
year = {2018},
author = {Díaz-Quiroz, CA and Francisco Hernández-Chávez, J and Ulloa-Mercado, G and Gortáres-Moroyoqui, P and Martínez-Macías, R and Meza-Escalante, E and Serrano-Palacios, D},
title = {Simultaneous quantification of antibiotics in wastewater from pig farms by capillary electrophoresis.},
journal = {Journal of chromatography. B, Analytical technologies in the biomedical and life sciences},
volume = {1092},
number = {},
pages = {386-393},
doi = {10.1016/j.jchromb.2018.06.017},
pmid = {29940436},
issn = {1873-376X},
mesh = {Animals ; Anti-Bacterial Agents/*analysis ; Electrophoresis, Capillary/*methods ; *Farms ; Limit of Detection ; Linear Models ; Reproducibility of Results ; Swine ; Wastewater/*chemistry ; Water Pollutants, Chemical/*analysis ; },
abstract = {Pig farming is an important activity in the economic development of Mexico with millions of tons of meat produced annually. Antibiotics are used in therapeutic dose to prevent diseases, and sometimes as growth promoters. These compounds are not completely metabolized; they are carried into the environment in its active form at concentrations that could induce antibiotic resistance in bacteria, which could be transferred to human pathogens by horizontal gene transfer. The objective of this work was to develop methods of analysis for simultaneous quantification of the antibiotics Oxytetracycline (OXT), Chlortetracycline (CLT), Enrofloxacin (ENRO) and Ciprofloxacin (CIPRO) by field-amplified sampling injection in capillary zone electrophoresis (FASI-CZE). The method was validated by parameters of (1) linearity, obtaining a lineal range of 0.05 at 1 μg mL[-1] for ENRO and CIPRO, and from 0.1 to 1 μg mL[-1] for OXT and CLT; (2) precision, obtaining values <5% of standard deviation for CIPRO and ENRO and <10% of standard deviation for OXT and CLT; (3) accuracy, with recovery values from 93 to 115%; (4) selectivity, with values of resolution >2 for the all antibiotics tested. To prove the method, a sample of wastewater from a local pig farm was analyzed, detecting a concentration of 0.140 ± 0.009 for OXT. This concentration was higher than the minimal selective concentration, indicating the point in which resistance to a determined antibiotic could develop. The methods were validated with precision and sensitivity comparable to chromatographic methods, which can be used to analyze wastewater from pig farms directly.},
}

Animals
Anti-Bacterial Agents/*analysis
Electrophoresis, Capillary/*methods
*Farms
Limit of Detection
Linear Models
Reproducibility of Results
Swine
Wastewater/*chemistry
Water Pollutants, Chemical/*analysis

@article {pmid29745854,
year = {2018},
author = {Nute, M and Chou, J and Molloy, EK and Warnow, T},
title = {The performance of coalescent-based species tree estimation methods under models of missing data.},
journal = {BMC genomics},
volume = {19},
number = {Suppl 5},
pages = {286},
pmid = {29745854},
issn = {1471-2164},
mesh = {Algorithms ; Classification/*methods ; Computer Simulation ; Genes ; *Genetic Speciation ; Genomics ; *Models, Genetic ; *Phylogeny ; Species Specificity ; },
abstract = {BACKGROUND: Estimation of species trees from multiple genes is complicated by processes such as incomplete lineage sorting, gene duplication and loss, and horizontal gene transfer, that result in gene trees that differ from each other and from the species phylogeny. Methods to estimate species trees in the presence of gene tree discord due to incomplete lineage sorting have been developed and proved to be statistically consistent when gene tree discord is due only to incomplete lineage sorting and every gene tree includes the full set of species.

RESULTS: We establish statistical consistency of certain coalescent-based species tree estimation methods under some models of taxon deletion from genes. We also evaluate the impact of missing data on four species tree estimation methods (ASTRAL-II, ASTRID, MP-EST, and SVDquartets) using simulated datasets with varying levels of incomplete lineage sorting, gene tree estimation error, and degrees/patterns of missing data.

CONCLUSIONS: All the species tree estimation methods improved in accuracy as the number of genes increased and often produced highly accurate species trees even when the amount of missing data was large. These results together indicate that accurate species tree estimation is possible under a variety of conditions, even when there are substantial amounts of missing data.},
}

Algorithms
Classification/*methods
Computer Simulation
Genes
*Genetic Speciation
Genomics
*Models, Genetic
*Phylogeny
Species Specificity

@article {pmid29047329,
year = {2017},
author = {Guo, X and Li, S and Zhang, J and Wu, F and Li, X and Wu, D and Zhang, M and Ou, Z and Jie, Z and Yan, Q and Li, P and Yi, J and Peng, Y},
title = {Genome sequencing of 39 Akkermansia muciniphila isolates reveals its population structure, genomic and functional diverisity, and global distribution in mammalian gut microbiotas.},
journal = {BMC genomics},
volume = {18},
number = {1},
pages = {800},
pmid = {29047329},
issn = {1471-2164},
mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Evolution, Molecular ; Gastrointestinal Microbiome/*genetics ; Humans ; Mammals/*microbiology ; Mice ; Molecular Sequence Annotation ; Verrucomicrobia/drug effects/*genetics/*physiology ; *Whole Genome Sequencing ; },
abstract = {BACKGROUND: Akkermansia muciniphila is one of the most dominant bacteria that resides on the mucus layer of intestinal tract and plays key role in human health, however, little is known about its genomic content.

RESULTS: Herein, we for the first time characterized the genomic architecture of A. muciniphila based on whole-genome sequencing, assembling, and annotating of 39 isolates derived from human and mouse feces. We revealed a flexible open pangenome of A. muciniphila currently consisting of 5644 unique proteins. Phylogenetic analysis identified three species-level A. muciniphila phylogroups exhibiting distinct metabolic and functional features. Based on the comprehensive genome catalogue, we reconstructed 106 newly A. muciniphila metagenome assembled genomes (MAGs) from available metagenomic datasets of human, mouse and pig gut microbiomes, revealing a transcontinental distribution of A. muciniphila phylogroups across mammalian gut microbiotas. Accurate quantitative analysis of A. muciniphila phylogroups in human subjects further demonstrated its strong correlation with body mass index and anti-diabetic drug usage. Furthermore, we found that, during their mammalian gut evolution history, A. muciniphila acquired extra genes, especially antibiotic resistance genes, from symbiotic microbes via recent lateral gene transfer.

CONCLUSIONS: The genome repertoire of A. muciniphila provided insights into population structure, evolutionary and functional specificity of this significant bacterium.},
}

Animals
Anti-Bacterial Agents/pharmacology
Drug Resistance, Bacterial/genetics
Evolution, Molecular
Gastrointestinal Microbiome/*genetics
Humans
Mammals/*microbiology
Mice
Molecular Sequence Annotation
Verrucomicrobia/drug effects/*genetics/*physiology
*Whole Genome Sequencing

@article {pmid26912404,
year = {2016},
author = {Earl, JP and de Vries, SP and Ahmed, A and Powell, E and Schultz, MP and Hermans, PW and Hill, DJ and Zhou, Z and Constantinidou, CI and Hu, FZ and Bootsma, HJ and Ehrlich, GD},
title = {Comparative Genomic Analyses of the Moraxella catarrhalis Serosensitive and Seroresistant Lineages Demonstrate Their Independent Evolution.},
journal = {Genome biology and evolution},
volume = {8},
number = {4},
pages = {955-974},
pmid = {26912404},
issn = {1759-6653},
support = {AI080935/AI/NIAID NIH HHS/United States ; R01 DC002148/DC/NIDCD NIH HHS/United States ; R01 DC005659/DC/NIDCD NIH HHS/United States ; DC02148/DC/NIDCD NIH HHS/United States ; DC05659/DC/NIDCD NIH HHS/United States ; R01 AI080935/AI/NIAID NIH HHS/United States ; },
mesh = {Cell Line ; Evolution, Molecular ; *Genome, Bacterial ; Genomics ; Humans ; Moraxella catarrhalis/*genetics/growth & development ; Moraxellaceae Infections/microbiology ; Multigene Family ; Phylogeny ; Virulence Factors/genetics ; },
abstract = {The bacterial speciesMoraxella catarrhalishas been hypothesized as being composed of two distinct lineages (referred to as the seroresistant [SR] and serosensitive [SS]) with separate evolutionary histories based on several molecular typing methods, whereas 16S ribotyping has suggested an additional split within the SS lineage. Previously, we characterized whole-genome sequences of 12 SR-lineage isolates, which revealed a relatively small supragenome when compared with other opportunistic nasopharyngeal pathogens, suggestive of a relatively short evolutionary history. Here, we performed whole-genome sequencing on 18 strains from both ribotypes of the SS lineage, an additional SR strain, as well as four previously identified highly divergent strains based on multilocus sequence typing analyses. All 35 strains were subjected to a battery of comparative genomic analyses which clearly show that there are three lineages-the SR, SS, and the divergent. The SR and SS lineages are closely related, but distinct from each other based on three different methods of comparison: Allelic differences observed among core genes; possession of lineage-specific sets of core and distributed genes; and by an alignment of concatenated core sequences irrespective of gene annotation. All these methods show that the SS lineage has much longer interstrain branches than the SR lineage indicating that this lineage has likely been evolving either longer or faster than the SR lineage. There is evidence of extensive horizontal gene transfer (HGT) within both of these lineages, and to a lesser degree between them. In particular, we identified very high rates of HGT between these two lineages for ß-lactamase genes. The four divergent strains aresui generis, being much more distantly related to both the SR and SS groups than these other two groups are to each other. Based on average nucleotide identities, gene content, GC content, and genome size, this group could be considered as a separate taxonomic group. The SR and SS lineages, although distinct, clearly form a single species based on multiple criteria including a large common core genome, average nucleotide identity values, GC content, and genome size. Although neither of these lineages arose from within the other based on phylogenetic analyses, the question of how and when these lineages split and then subsequently reunited in the human nasopharynx is explored.},
}

Cell Line
Evolution, Molecular
*Genome, Bacterial
Genomics
Humans
Moraxella catarrhalis/*genetics/growth & development
Moraxellaceae Infections/microbiology
Multigene Family
Phylogeny
Virulence Factors/genetics

@article {pmid24892910,
year = {2014},
author = {Maguire, F and Richards, TA},
title = {Organelle evolution: a mosaic of 'mitochondrial' functions.},
journal = {Current biology : CB},
volume = {24},
number = {11},
pages = {R518-20},
doi = {10.1016/j.cub.2014.03.075},
pmid = {24892910},
issn = {1879-0445},
mesh = {Eukaryota/*genetics/*metabolism ; Organelles/*metabolism ; *Proteome ; Sulfur/*metabolism ; },
abstract = {An ancient endosymbiosis of an α-proteobacterium produced a diverse range of organelles including mitochondria. Reconstruction of the Pygsuia biforma proteome adds to the mosaic of functional systems present in mitochondrial-related organelles and demonstrates the role of horizontal gene transfer.},
}

Eukaryota/*genetics/*metabolism
Organelles/*metabolism
*Proteome
Sulfur/*metabolism

@article {pmid23204388,
year = {2013},
author = {Roelofs, D and Timmermans, MJ and Hensbergen, P and van Leeuwen, H and Koopman, J and Faddeeva, A and Suring, W and de Boer, TE and Mariën, J and Boer, R and Bovenberg, R and van Straalen, NM},
title = {A functional isopenicillin N synthase in an animal genome.},
journal = {Molecular biology and evolution},
volume = {30},
number = {3},
pages = {541-548},
doi = {10.1093/molbev/mss269},
pmid = {23204388},
issn = {1537-1719},
mesh = {Amino Acid Sequence ; Animals ; Catalytic Domain ; Genome, Insect ; Insect Proteins/chemistry/*genetics ; Insecta/*enzymology/genetics ; Models, Molecular ; Molecular Sequence Data ; Oligopeptides/chemistry ; Oxidoreductases/chemistry/*genetics ; Penicillins/biosynthesis ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Horizontal transfer of genes is widespread among prokaryotes, but is less common between microorganisms and animals. Here, we present evidence for the presence of a gene encoding functional isopenicillin N synthase, an enzyme in the β-lactam antibiotics biosynthesis pathway, in the genome of the soil-living collembolan species, Folsomia candida (FcIPNS). At present, this gene is only known from bacteria and fungi, as is the capacity to produce β-lactam antibiotics. The FcIPNS gene was located on two genomic contigs, was physically linked to a predicted insect ATP-binding cassette transporter gene, and contained three introns each flanked by eukaryotic splicing recognition sites (GT/AG). Homology searches revealed no similarity between these introns and the FcIPNS regions of bacteria or fungi. All amino acids conserved across bacteria and fungi were also conserved in F. candida. Recombinant FcIPNS was able to convert its substrate amino δ-(l-α-aminoadipyl)-l-cysteinyl-d-valine into isopenicillin N, providing strong evidence that FcIPNS is functional. Phylogenetic analysis clustered FcIPNS outside the bacterial IPNS clade, and also outside the fungal IPNS clade, suggesting an ancient gene transfer followed by divergence in the F. candida genome. In conclusion, the data suggest that the soil-living collembolan F. candida has assimilated the capacity for antibacterial activity by horizontal gene transfer, which may be an important adaptive trait in the microbe-dominated soil ecosystem.},
}

Amino Acid Sequence
Animals
Catalytic Domain
Genome, Insect
Insect Proteins/chemistry/*genetics
Insecta/*enzymology/genetics
Models, Molecular
Molecular Sequence Data
Oligopeptides/chemistry
Oxidoreductases/chemistry/*genetics
Penicillins/biosynthesis
Phylogeny
Sequence Analysis, DNA

@article {pmid21159175,
year = {2010},
author = {Kato, O and Youn, JW and Stansen, KC and Matsui, D and Oikawa, T and Wendisch, VF},
title = {Quinone-dependent D-lactate dehydrogenase Dld (Cg1027) is essential for growth of Corynebacterium glutamicum on D-lactate.},
journal = {BMC microbiology},
volume = {10},
number = {},
pages = {321},
pmid = {21159175},
issn = {1471-2180},
mesh = {Bacterial Proteins/genetics/*metabolism ; Benzoquinones/*metabolism ; Corynebacterium glutamicum/*enzymology/genetics/*growth & development/metabolism ; Gene Expression Regulation, Bacterial ; Lactate Dehydrogenases/genetics/*metabolism ; Lactic Acid/*metabolism ; },
abstract = {BACKGROUND: Corynebacterium glutamicum is able to grow with lactate as sole or combined carbon and energy source. Quinone-dependent L-lactate dehydrogenase LldD is known to be essential for utilization of L-lactate by C. glutamicum. D-lactate also serves as sole carbon source for C. glutamicum ATCC 13032.

RESULTS: Here, the gene cg1027 was shown to encode the quinone-dependent D-lactate dehydrogenase (Dld) by enzymatic analysis of the protein purified from recombinant E. coli. The absorption spectrum of purified Dld indicated the presence of FAD as bound cofactor. Inactivation of dld resulted in the loss of the ability to grow with D-lactate, which could be restored by plasmid-borne expression of dld. Heterologous expression of dld from C. glutamicum ATCC 13032 in C. efficiens enabled this species to grow with D-lactate as sole carbon source. Homologs of dld of C. glutamicum ATCC 13032 are not encoded in the sequenced genomes of other corynebacteria and mycobacteria. However, the dld locus of C. glutamicum ATCC 13032 shares 2367 bp of 2372 bp identical nucleotides with the dld locus of Propionibacterium freudenreichii subsp. shermanii, a bacterium used in Swiss-type cheese making. Both loci are flanked by insertion sequences of the same family suggesting a possible event of horizontal gene transfer.

CONCLUSIONS: Cg1067 encodes quinone-dependent D-lactate dehydrogenase Dld of Corynebacterium glutamicum. Dld is essential for growth with D-lactate as sole carbon source. The genomic region of dld likely has been acquired by horizontal gene transfer.},
}

Bacterial Proteins/genetics/*metabolism
Benzoquinones/*metabolism
Corynebacterium glutamicum/*enzymology/genetics/*growth & development/metabolism
Gene Expression Regulation, Bacterial
Lactate Dehydrogenases/genetics/*metabolism
Lactic Acid/*metabolism

@article {pmid16030235,
year = {2005},
author = {Baldo, L and Lo, N and Werren, JH},
title = {Mosaic nature of the wolbachia surface protein.},
journal = {Journal of bacteriology},
volume = {187},
number = {15},
pages = {5406-5418},
pmid = {16030235},
issn = {0021-9193},
mesh = {Amino Acid Sequence ; Bacterial Outer Membrane Proteins/*genetics ; Molecular Sequence Data ; Phylogeny ; *Recombination, Genetic ; Sequence Alignment ; Wolbachia/*genetics ; },
abstract = {Lateral gene transfer and recombination play important roles in the evolution of many parasitic bacteria. Here we investigate intragenic recombination in Wolbachia bacteria, considered among the most abundant intracellular bacteria on earth. We conduct a detailed analysis of the patterns of variation and recombination within the Wolbachia surface protein, utilizing an extensive set of published and new sequences from five main supergroups of Wolbachia. Analysis of nucleotide and amino acid sequence variations confirms four hypervariable regions (HVRs), separated by regions under strong conservation. Comparison of shared polymorphisms reveals a complex mosaic structure of the gene, characterized by a clear intragenic recombining of segments among several distinct strains, whose major recombination effect is shuffling of a relatively conserved set of amino acid motifs within each of the four HVRs. Exchanges occurred both within and between the arthropod supergroups. Analyses based on phylogenetic methods and a specific recombination detection program (MAXCHI) significantly support this complex partitioning of the gene, indicating a chimeric origin of wsp. Although wsp has been widely used to define macro- and microtaxonomy among Wolbachia strains, these results clearly show that it is not suitable for this purpose. The role of wsp in bacterium-host interactions is currently unknown, but results presented here indicate that exchanges of HVR motifs are favored by natural selection. Identifying host proteins that interact with wsp variants should help reveal how these widespread bacterial parasites affect and evolve in response to the cellular environments of their invertebrate hosts.},
}

Amino Acid Sequence
Bacterial Outer Membrane Proteins/*genetics
Molecular Sequence Data
Phylogeny
*Recombination, Genetic
Sequence Alignment
Wolbachia/*genetics

@article {pmid12834405,
year = {2003},
author = {Kleine, T and Lockhart, P and Batschauer, A},
title = {An Arabidopsis protein closely related to Synechocystis cryptochrome is targeted to organelles.},
journal = {The Plant journal : for cell and molecular biology},
volume = {35},
number = {1},
pages = {93-103},
doi = {10.1046/j.1365-313x.2003.01787.x},
pmid = {12834405},
issn = {0960-7412},
mesh = {Amino Acid Sequence ; Arabidopsis/cytology/genetics/*metabolism ; Arabidopsis Proteins/*chemistry/*metabolism ; Chloroplasts/*metabolism ; Cryptochromes ; Cyanobacteria/*chemistry ; DNA/metabolism ; DNA-Binding Proteins/chemistry/metabolism ; Deoxyribodipyrimidine Photo-Lyase/*chemistry/*metabolism ; *Drosophila Proteins ; *Eye Proteins ; Flavin-Adenine Dinucleotide/metabolism ; Flavoproteins/*chemistry/metabolism ; Mitochondria/*metabolism ; Molecular Sequence Data ; *Photoreceptor Cells, Invertebrate ; Phylogeny ; Protein Transport ; Receptors, G-Protein-Coupled ; Sequence Alignment ; Sequence Homology, Amino Acid ; },
abstract = {Cryptochromes (CRYs) are blue/UV-A photoreceptors related to the DNA repair enzyme DNA photolyase. They have been found in plants, animals and most recently in the cyanobacterium Synechocystis. Closely related to the Synechocystis cryptochrome is the Arabidopsis gene At5g24850. Here, we show that the encoded protein of At5g24850 binds flavin adenine dinucleotide (FAD). It has no photolyase activity, and is likely to function as a photoreceptor. We have named it At-cry3 to distinguish it from the other Arbabidopsis cryptochrome homologues At-cry1 and At-cry2. At-cry3 carries an N-terminal sequence, which mediates import into chloroplasts and mitochondria. Furthermore, we show that At-cry3 binds DNA. DNA binding was also demonstrated for the Synechocystis cryptochrome, indicating that both photoreceptors could have similar modes of action. Based on the finding of a new cryptochrome class in bacteria and plants, it has been suggested that cryptochromes evolved before the divergence of eukaryotes and prokaryotes. However, our phylogenetic analyses are also consistent with an alternative explanation that the presence of cryptochromes in the plant nuclear genome is the result of dual horizontal gene transfer. That is, CRY1 and CRY2 genes may originate from an endosymbiotic ancestor of modern-day alpha-proteobacteria, while the CRY3 gene may originate from an endosymbiotic ancestor of modern-day cyanobacteria.},
}

Amino Acid Sequence
Arabidopsis/cytology/genetics/*metabolism
Arabidopsis Proteins/*chemistry/*metabolism
Chloroplasts/*metabolism
Cryptochromes
Cyanobacteria/*chemistry
DNA/metabolism
DNA-Binding Proteins/chemistry/metabolism
Deoxyribodipyrimidine Photo-Lyase/*chemistry/*metabolism
*Drosophila Proteins
*Eye Proteins
Flavin-Adenine Dinucleotide/metabolism
Flavoproteins/*chemistry/metabolism
Mitochondria/*metabolism
Molecular Sequence Data
*Photoreceptor Cells, Invertebrate
Phylogeny
Protein Transport
Receptors, G-Protein-Coupled
Sequence Alignment
Sequence Homology, Amino Acid

@article {pmid10531001,
year = {1999},
author = {Logsdon, JM and Faguy, DM},
title = {Thermotoga heats up lateral gene transfer.},
journal = {Current biology : CB},
volume = {9},
number = {19},
pages = {R747-51},
doi = {10.1016/s0960-9822(99)80474-6},
pmid = {10531001},
issn = {0960-9822},
mesh = {Databases, Factual ; *Evolution, Molecular ; *Genome, Bacterial ; Phylogeny ; Thermotoga maritima/*genetics ; },
abstract = {The complete sequence of the bacterium Thermotoga maritima genome has revealed a large fraction of genes most closely related to those of archaeal species. This adds to the accumulating evidence that lateral gene transfer is a potent evolutionary force in prokaryotes, though questions of its magnitude remain.},
}

Databases, Factual
*Evolution, Molecular
*Genome, Bacterial
Phylogeny
Thermotoga maritima/*genetics

@article {pmid9515912,
year = {1998},
author = {Bäumler, AJ and Norris, TL and Lasco, T and Voight, W and Reissbrodt, R and Rabsch, W and Heffron, F},
title = {IroN, a novel outer membrane siderophore receptor characteristic of Salmonella enterica.},
journal = {Journal of bacteriology},
volume = {180},
number = {6},
pages = {1446-1453},
pmid = {9515912},
issn = {0021-9193},
support = {R29 AI040124/AI/NIAID NIH HHS/United States ; R01 AI040124/AI/NIAID NIH HHS/United States ; R01 AI022933/AI/NIAID NIH HHS/United States ; AI40124/AI/NIAID NIH HHS/United States ; AI 22933/AI/NIAID NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; *Bacterial Outer Membrane Proteins ; Cloning, Molecular ; Cosmids ; DNA, Bacterial/analysis/genetics ; Escherichia coli/genetics/metabolism ; Gene Expression ; Genes, Bacterial ; Molecular Sequence Data ; Mutagenesis, Insertional ; Operon ; Phylogeny ; Receptors, Cell Surface/*genetics/*metabolism ; Recombination, Genetic ; Restriction Mapping ; Salmonella/genetics/metabolism ; Salmonella enterica/*genetics/metabolism ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Siderophores/metabolism ; Species Specificity ; },
abstract = {Speciation in enterobacteria involved horizontal gene transfer. Therefore, analysis of genes acquired by horizontal transfer that are present in one species but not its close relatives is expected to give insights into how new bacterial species were formed. In this study we characterize iroN, a gene located downstream of the iroBC operon in the iroA locus of Salmonella enterica serotype Typhi. Like iroBC, the iroN gene is present in all phylogenetic lineages of S. enterica but is absent from closely related species such as Salmonella bongori or Escherichia coli. Comparison of the deduced amino acid sequence of iroN with other proteins suggested that this gene encodes an outer membrane siderophore receptor protein. Mutational analysis in S. enterica and expression in E. coli identified a 78-kDa outer membrane protein as the iroN gene product. When introduced into an E. coli fepA cir fiu aroB mutant on a cosmid, iroN mediated utilization of structurally related catecholate siderophores, including N-(2,3-dihydroxybenzoyl)-L-serine, myxochelin A, benzaldehyde-2,3-dihydroxybenzhydrazone, 2-N,6-N-bis(2,3-dihydroxybenzoyl)-L-lysine, 2-N,6-N-bis(2,3-dihydroxybenzoyl)-L-lysine amide, and enterochelin. These results suggest that the iroA locus functions in iron acquisition in S. enterica.},
}

Amino Acid Sequence
*Bacterial Outer Membrane Proteins
Cloning, Molecular
Cosmids
DNA, Bacterial/analysis/genetics
Escherichia coli/genetics/metabolism
Gene Expression
Genes, Bacterial
Molecular Sequence Data
Mutagenesis, Insertional
Operon
Phylogeny
Receptors, Cell Surface/*genetics/*metabolism
Recombination, Genetic
Restriction Mapping
Salmonella/genetics/metabolism
Salmonella enterica/*genetics/metabolism
Sequence Alignment
Sequence Analysis, DNA
Sequence Homology, Amino Acid
Siderophores/metabolism
Species Specificity

@article {pmid9214746,
year = {1997},
author = {Cunningham, CW},
title = {Can three incongruence tests predict when data should be combined?.},
journal = {Molecular biology and evolution},
volume = {14},
number = {7},
pages = {733-740},
doi = {10.1093/oxfordjournals.molbev.a025813},
pmid = {9214746},
issn = {0737-4038},
mesh = {Animals ; Codon ; DNA, Mitochondrial/*genetics ; Genes ; Humans ; *Phylogeny ; Rodentia ; Sequence Analysis/*methods ; Statistics as Topic ; },
abstract = {Advocates of conditional combination have argued that testing for incongruence between data partitions is an important step in data exploration. Unless the partitions have had distinct histories, as in horizontal gene transfer, incongruence means that one or more data support the wrong phylogeny. This study examines the relationship between incongruence and phylogenetic accuracy using three tests of incongruence. These tests were applied to pairs of mitochondrial DNA data partitions from two well-corroborated vertebrate phylogenies. Of the three tests, the most useful was the incongruence length difference test (ILD, also called the partition homogeneity test). This test distinguished between cases in which combining the data generally improved phylogenetic accuracy (P > 0.01) and cases in which accuracy of the combined data suffered relative to the individual partitions (P < 0.001). In contrast, in several cases, the Templeton and Rodrigo tests detected highly significant incongruence (P < 0.001) even though combining the incongruent partitions actually increased phylogenetic accuracy. All three tests identified cases in which improving the reconstruction model would improve the phylogenetic accuracy of the individual partitions.},
}

Animals
Codon
DNA, Mitochondrial/*genetics
Genes
Humans
*Phylogeny
Rodentia
Sequence Analysis/*methods
Statistics as Topic

@article {pmid9055816,
year = {1997},
author = {Achenbach, LA and Yang, W},
title = {The fur gene from Klebsiella pneumoniae: characterization, genomic organization and phylogenetic analysis.},
journal = {Gene},
volume = {185},
number = {2},
pages = {201-207},
doi = {10.1016/s0378-1119(96)00642-7},
pmid = {9055816},
issn = {0378-1119},
mesh = {Bacterial Proteins/biosynthesis/*genetics ; Cloning, Molecular ; Gene Expression Regulation, Bacterial ; Klebsiella pneumoniae/*genetics ; Molecular Sequence Data ; *Phylogeny ; Recombinant Proteins/biosynthesis/genetics ; Repressor Proteins/biosynthesis/*genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Transcription, Genetic ; },
abstract = {The Fur (ferric uptake regulator) protein controls the expression of a number of bacterial virulence determinants including those involved in iron uptake. The fur gene was cloned and characterized from Klebsiella pneumoniae. The gene is preceded by a single autoregulated promoter whose -10 region overlaps the putative Fur binding site. The autoregulated nature of the K. pneumoniae fur gene and functionality of the encoded Fur repressor were tested in Fur titration and complementation assays. A partial open reading frame upstream from the fur gene was identified as a flavodoxin (fldA) gene. An open reading frame located 50 bases downstream from the fur stop codon appears to be a truncated citA gene that, if functional, would encode only the carboxy terminus of a citrate utilization protein. The fldA-fur arrangement is also present in Escherichia coli. However, the fur-citA arrangement found in K. pneumoniae is novel. It appears that the chromosomal region downstream from the fur gene is unstable and, thus, variable even in closely related bacterial lineages. To assess of the ability of the Fur protein sequence to reflect organismal phylogeny, the Fur protein tree was compared to the tree of 16S rRNA (ribosomal RNA). The Fur dataset comprises almost an order of magnitude fewer characters than the 16S rRNA but is nonetheless able to track the phylogenetic signal reasonably well, suggesting that the fur gene, like the 16S rDNA, may not be subject to horizontal gene transfer in these bacteria.},
}

Bacterial Proteins/biosynthesis/*genetics
Cloning, Molecular
Gene Expression Regulation, Bacterial
Klebsiella pneumoniae/*genetics
Molecular Sequence Data
*Phylogeny
Recombinant Proteins/biosynthesis/genetics
Repressor Proteins/biosynthesis/*genetics
Sequence Alignment
Sequence Analysis, DNA
Sequence Homology, Amino Acid
Transcription, Genetic

@article {pmid40815474,
year = {2025},
author = {Gios, E and Mosley, OE and Takeuchi, N and Handley, KM},
title = {Genetic exchange shapes ultra-small Patescibacteria metabolic capacities in the terrestrial subsurface.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0004625},
doi = {10.1128/msystems.00046-25},
pmid = {40815474},
issn = {2379-5077},
abstract = {UNLABELLED: Bacterial genomes are highly dynamic entities, mostly due to horizontal gene transfer (HGT). HGT is thought to be the main driver of genetic variation and adaptation to the local environment in bacteria. However, little is known about the modalities of HGT within natural microbial communities, especially the implications of genetic exchange for streamlined microorganisms such as Patescibacteria (Candidate Phyla Radiation). We searched for evidence of genetic exchange in 125 Patescibacteria genomes recovered from aquifer environments and detected the presence of hundreds of genomic islands, individually transferred genes, and prophages combined, with up to 13% of genome length attributed to HGT. Results show that most individual gene transfer events occurred between Patescibacteria, although putative donors included phylogenetically diverse groundwater microorganisms. For example, results indicate exchange of a lysR transcriptional regulator gene between Omnitrophota and Patescibacteria taxa with highly similar relative abundance patterns across 16 groundwater samples. Overall, results indicate a wide variety of metabolic functions were introduced into Patescibacteria genomes by HGT, including transcription, translation, and DNA replication, recombination and repair. This study illustrates the evolutionarily dynamic nature of Patescibacteria genomes despite the constraints of streamlining and that HGT in these organisms is also mediated via viral infection.

IMPORTANCE: Genomic fluidity and diversity in bacteria are mainly governed by horizontal gene transfer (HGT), leading to a variety of genome structures and physiological diversity. The predominantly uncultivated Patescibacteria comprise highly diverse bacteria that consistently exhibit small cell and genome sizes. Despite strong pressures to reduce genetic content, we predict that these ultra-small bacteria use HGT to the same extent as other bacteria and that HGT may help facilitate recovery and maintenance of critical metabolic functions, niche exploitation, and putative symbiont-host interactions. Here, we determine the contribution of gene exchange to the evolution and diversification of Patescibacteria, despite the constraints of streamlining. We provide evidence of gene gains in Patescibacteria genomes recovered from aquifer environments and describe the large extent to which ultra-small bacterial genomes are subjected to HGT. Results suggest distinct metabolic functions acquired by Patescibacteria compared to general groundwater communities, suggesting specific evolutionary pressures on gene transfer dynamics occurring in ultra-small prokaryotes.},
}

@article {pmid40811910,
year = {2025},
author = {Zhang, D and Sun, J and Peng, S and Wang, Y and Lin, X and Wang, S},
title = {Biodegradable microplastics exacerbate the risk of antibiotic resistance genes pollution in agricultural soils.},
journal = {Journal of hazardous materials},
volume = {496},
number = {},
pages = {139490},
doi = {10.1016/j.jhazmat.2025.139490},
pmid = {40811910},
issn = {1873-3336},
abstract = {The widespread emergence of antibiotic resistance genes (ARGs) poses a severe global health threat, exacerbated by agricultural practices such as fertilization and plastic mulch use. While biodegradable plastics are promoted as environmentally friendly alternatives to conventional plastics, their ecological impact on soil ARGs remains poorly understood. This study conducted incubation experiments using soils with distinct long-term fertilization histories (no fertilization CK, chemical fertilizer CF, and pig manure PM) collected from 14-year field experiment sites at Changshu National Agro-Ecosystem Observation and Research Station. The soils were exposed to four types of microplastics (conventional: polyethylene [PE] and polyvinyl chloride [PVC]; biodegradable: polylactic acid [PLA] and polybutylene adipate terephthalate [PBAT]), and the ARGs and mobile genetic elements (MGEs) were quantified using high-throughput quantitative PCR, targeting 329 ARG subtypes and 34 MGEs. Results revealed that PM soil exhibited the highest ARGs abundance, and exposure to biodegradable microplastics (PLA and PBAT) further enriched ARGs by 21.5 % and 47.9 %, respectively. Microplastic exposure enhanced horizontal gene transfer potential by strengthening ARG-MGE co-occurrence, and altered bacterial communities by promoting the proliferation of generalist taxa (e.g., Proteobacteria) identified as key hosts of risk ARGs. These findings challenge the assumption of biodegradable plastics as environmentally friendly, demonstrating their potential to exacerbate ARGs pollution in agricultural soils. This study provides critical insights into the interactive effects of fertilization and microplastic exposure on the soil resistome, with implications for plastic management and ARGs risk control in agroecosystems.},
}

@article {pmid40810119,
year = {2025},
author = {Kumavath, R and Gupta, P and Tatta, ER and Mohan, MS and Salim, SA and Busi, S},
title = {Unraveling the role of mobile genetic elements in antibiotic resistance transmission and defense strategies in bacteria.},
journal = {Frontiers in systems biology},
volume = {5},
number = {},
pages = {1557413},
pmid = {40810119},
issn = {2674-0702},
abstract = {Irrational antibiotic use contributes to the development of antibiotic resistance in bacteria, which is a major cause of healthcare-associated infections globally. Molecular research has shown that multiple resistance frequently develops from the uptake of pre-existing resistance genes, which are subsequently intensified under selective pressures. Resistant genes spread and are acquired through mobile genetic elements which are essential for facilitating horizontal gene transfer. MGEs have been identified as carriers of genetic material and are a significant player in evolutionary processes. These include insertion sequences, transposons, integrative and conjugative elements, plasmids, and genomic islands, all of which can transfer between and within DNA molecules. With an emphasis on pathogenic bacteria, this review highlights the salient features of the MGEs that contribute to the development and spread of antibiotic resistance. MGEs carry non-essential genes, including AMR and virulence genes, which can enhance the adaptability and fitness of their bacterial hosts. These elements employ evolutionary strategies to facilitate their replication and dissemination, thus enabling survival without positive selection for the harboring of beneficial genes.},
}

@article {pmid40800620,
year = {2025},
author = {Partanen, V and Dekić Rozman, S and Karkman, A and Muurinen, J and Hiltunen, T and Virta, M},
title = {Use of sequence barcodes for tracking horizontal gene transfer of antimicrobial resistance genes in a microbial community.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf113},
pmid = {40800620},
issn = {2730-6151},
abstract = {One of the most important knowledge gaps in the antimicrobial resistance crisis is the lack of understanding regarding how genes spread from their environmental origins to bacteria pathogenic to humans. In this study our aim was to create a system that allows the conduction of experiments in laboratory settings that mimic the complexity of natural communities with multiple resistance genes and mobile genetic elements circulating at the same time. Here we report a new sequence-based barcode system that allows simultaneous tracking of the spread of antimicrobial resistance genes from multiple genetic origins. We tested this concept with an experiment in which we added an antimicrobial resistance gene to different genetic environments in alive and dead donors and let the gene spread naturally in an artificial microbial community under different environmental conditions to provide examples of factors that can be investigated. We used emulsion, paired-isolation, and concatenation polymerase chain reaction to detect the new gene carriers and metagenomic analysis to see changes in the genetic environment. We observed the genes moving and were able to recognise the barcode from the gene sequences, thus validating the idea of barcode use. We also saw that temperature and gene origin had effects on the number of new host species. Our results confirmed that our system worked and can be further developed for more complicated experiments.},
}

@article {pmid40796329,
year = {2025},
author = {Weng, YM and Martinez, JI and Markee, A and Plotkin, D and Sondhi, Y and Mongue, AJ and Frandsen, PB and Kawahara, AY},
title = {Gene family evolution suggests correlated dietary adaptations in butterflies and moths.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evaf156},
pmid = {40796329},
issn = {1759-6653},
abstract = {Butterflies and moths (Lepidoptera) are a megadiverse lineage of more than 160,000 described species. Their evolutionary success is thought to be tightly correlated with the radiation of flowering plants, but mechanisms on how these insects evolved to feed on so many different plant hosts remain largely unknown. Previous studies found emergent gene families of odorant receptors and peptidases in the ancestor of Lepidoptera, suggesting these genetic innovations may be linked to lepidopteran diversification. Here, we examined 62 genomes and identify lineage-specific gene families within the Lepidoptera and its three major clades. We found 54, 88, 77 and four functionally annotated gene families specific to Lepidoptera, Glossata, Ditrysia, and Apoditrysia, respectively. These families are involved in chemosensation, digestion, detoxification, immunity and other diverse functions. Notably, there is a marked increase in gene families presumably associated with chemosensation and immunity in Glossata and Ditrysia which encompass more than 98% of Lepidoptera diversity. We also identified horizontal gene transfer (HGT) events of two putative digestion gene families (Catalytic LigB subunit of aromatic ring-opening dioxygenase and Glycosyl hydrolases family 32) and a detoxification gene family (Cysteine synthase-like) to the common ancestors of Lepidoptera and Ditrysia, respectively. These HGT events likely played a crucial role in facilitating dietary transitions from algae, diatoms, and aquatic plant debris to fungi and primitive terrestrial plants in early Lepidoptera, ultimately enabling their adaptation to feed on and diversify with angiosperms since the emergence of Ditrysia.},
}

@article {pmid40794833,
year = {2025},
author = {Frail, S and Steele-Ogus, M and Doenier, J and Moulin, SLY and Braukmann, T and Xu, S and Yeh, E},
title = {Genomes of nitrogen-fixing eukaryotes reveal an alternate path for organellogenesis.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {33},
pages = {e2507237122},
doi = {10.1073/pnas.2507237122},
pmid = {40794833},
issn = {1091-6490},
support = {T32GM007276//HHS | NIH (NIH)/ ; 5T32AI007328-32//HHS | NIH (NIH)/ ; NA//Burroughs Wellcome Fund (BWF)/ ; NA//Chan Zuckerberg Initiative (CZI)/ ; },
mesh = {*Nitrogen Fixation/genetics ; Symbiosis/genetics ; *Diatoms/genetics ; Phylogeny ; *Genome ; Gene Transfer, Horizontal ; Cyanobacteria/genetics ; Evolution, Molecular ; },
abstract = {Endosymbiotic gene transfer (EGT) and import of host-encoded proteins have been considered hallmarks of organelles necessary for stable integration of two cells. However, newer endosymbiotic models have challenged the origin and timing of such genetic integration during organellogenesis. Epithemia diatoms contain diazoplasts, obligate endosymbionts derived from cyanobacteria that are closely phylogenetically related to UCYN-A, a recently described nitrogen-fixing organelle. Diazoplasts function as permanent membrane compartments in Epithemia hosts, but it is unknown if genetic integration has occurred. We report genomic analyses of two Epithemia diatom species, freshwater Epithemia clementina and marine E. pelagica, which are highly divergent but share a common ancestor at the origin of the endosymbiosis <35Mya. We find minimal evidence for genetic integration. Segments of fragmented and rearranged DNA from the diazoplast were detected integrated into the E. clementina nuclear genome, but the transfers that have occurred so far are nonfunctional. No DNA or gene transfers were detected in E. pelagica. In E. clementina, 6 host-encoded proteins of unknown function were identified in the diazoplast proteome, far fewer than detected in recently acquired endosymbiotic organelles. Overall, Epithemia diazoplasts are a valuable counterpoint to existing organelle models, demonstrating that endosymbionts can function as integral compartments-maintained over millions of years of host speciation-absent significant genetic integration. The minimal genetic integration makes diazoplasts valuable blueprints for bioengineering endosymbiotic compartments de novo.},
}

*Nitrogen Fixation/genetics
Symbiosis/genetics
*Diatoms/genetics
Phylogeny
*Genome
Gene Transfer, Horizontal
Cyanobacteria/genetics
Evolution, Molecular

@article {pmid40794100,
year = {2025},
author = {Gewurz, D and Kim, S and Bartu, L and Sharma, A and Harrison, JC and Lee, I and Rondeau, NC and Miranda, JL and Mailloux, BJ and Hamilton, KA and Lopatkin, AJ},
title = {Plasmid prevalence is independent of antibiotic resistance in environmental Enterobacteriaceae.},
journal = {Microbial genomics},
volume = {11},
number = {8},
pages = {},
doi = {10.1099/mgen.0.001453},
pmid = {40794100},
issn = {2057-5858},
mesh = {*Plasmids/genetics ; *Enterobacteriaceae/genetics/drug effects/isolation & purification ; Anti-Bacterial Agents/pharmacology ; Whole Genome Sequencing ; Microbial Sensitivity Tests ; *Drug Resistance, Bacterial/genetics ; Conjugation, Genetic ; },
abstract = {The rapid rise of antibiotic-resistant pathogens poses a critical threat to the treatment of infectious diseases. While the spread of antibiotic resistance genes (ARGs) via plasmid conjugation has been extensively studied both in the lab and the clinic, the prevalence and diversity of plasmids in drug-susceptible isolates (e.g. isolates that do not contain ARGs) remain poorly understood. Yet, plasmids in susceptible isolates play a pivotal role as reservoirs, potentially capturing and disseminating ARGs in situ. To better understand the potential impact of these strains, we investigated the prevalence and characteristics of plasmids in >200 Enterobacteriaceae, including those that are primarily drug susceptible, isolated from diverse environmental sources. Using whole-genome sequencing and a novel bioinformatic pipeline, we quantified the number of large plasmids per isolate and examined the relationship between plasmid abundance and host antibiotic susceptibility profiles. Strikingly, we found a high abundance of plasmids in susceptible strains, with no correlation between plasmid number and susceptibility level to a variety of clinically relevant antibiotics. Moreover, plasmid abundance did not influence a strain's ability to accept additional plasmids via conjugation. These findings reveal that plasmids are widespread in susceptible strains regardless of ARG content and underscore their potential to act as conduits for future resistance dissemination.},
}

*Plasmids/genetics
*Enterobacteriaceae/genetics/drug effects/isolation & purification
Anti-Bacterial Agents/pharmacology
Whole Genome Sequencing
Microbial Sensitivity Tests
*Drug Resistance, Bacterial/genetics
Conjugation, Genetic

@article {pmid40790092,
year = {2025},
author = {Andrade-Oliveira, AL and Prodocimi, F and Silva, R and Rossi, CC and Giambiagi-deMarval, M},
title = {Optimized Plasmid Extraction Uncovers Novel and Mobilizable Plasmids in Staphylococcus nepalensis Sharing Antimicrobial Resistance Across Different Bacterial Genera.},
journal = {Current microbiology},
volume = {82},
number = {10},
pages = {446},
pmid = {40790092},
issn = {1432-0991},
support = {E-26/010.000172/2016; 010.00128/2016; E-26.210.875/2016//Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro/ ; 101056/2018; 001463/2019; 211.554/2019; 201.071/2020//Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro/ ; 200.895/2021//Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro/ ; E-26/204.925/2022//Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro/ ; APQ-01339-25//Fundação de Amparo à Pesquisa do Estado de Minas Gerais/ ; APQ-03498-22//Fundação de Amparo à Pesquisa do Estado de Minas Gerais/ ; 408564/2023-7//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 304839/2022-1//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 23038.002486/2018-26//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; },
mesh = {*Plasmids/genetics/isolation & purification ; *Staphylococcus/genetics/drug effects/isolation & purification/classification ; *Anti-Bacterial Agents/pharmacology ; Phylogeny ; *Drug Resistance, Bacterial/genetics ; Animals ; Gene Transfer, Horizontal ; Whole Genome Sequencing ; Microbial Sensitivity Tests ; Brazil ; },
abstract = {Plasmids are key vectors in the dissemination of antimicrobial resistance (AMR), often transcending species and genus boundaries through horizontal gene transfer. Staphylococcus nepalensis, typically regarded as a commensal species, has emerged as a potential reservoir of resistance genes. In this study, we optimized plasmid extraction protocols to enhance the recovery of low-copy plasmids and applied whole-genome sequencing to characterize plasmids from a S. nepalensis strain isolated from the oral microbiota of a healthy cat in Brazil. Plasmid-enriched extraction using the Qiagen miniprep kit, with an additional enzymatic lysis step, significantly improved assembly outcomes, enabling the recovery of four complete plasmids. Three of them carried mobilizable antimicrobial resistance genes (aadK, cat, and tetK), conferring resistance to streptomycin, chloramphenicol, and tetracycline, respectively. Comparative and phylogenetic analyses revealed a high sequence similarity between these plasmids and mobile elements found in diverse pathogenic and environmental bacteria, including Staphylococcus aureus, S. epidermidis, Enterococcus sp., and Pseudomonas aeruginosa, indicating plasmid circulation across bacterial genera. Additionally, one novel plasmid was identified, displaying limited similarity to any known sequence and suggesting the existence of uncharacterized plasmid lineages in commensal staphylococci. These findings highlight the underestimated role of S. nepalensis as a hidden reservoir of mobilizable resistance genes and reinforce the need to surveil non-pathogenic bacteria in AMR monitoring frameworks.},
}

*Plasmids/genetics/isolation & purification
*Staphylococcus/genetics/drug effects/isolation & purification/classification
*Anti-Bacterial Agents/pharmacology
Phylogeny
*Drug Resistance, Bacterial/genetics
Animals
Gene Transfer, Horizontal
Whole Genome Sequencing
Microbial Sensitivity Tests
Brazil

@article {pmid40788082,
year = {2025},
author = {Kumari, S and Narendrakumar, L and Chawla, M and Das, S and Koley, H and Das, B},
title = {Investigating the molecular transmission dynamics of blaNDM in antibiotic-selective environments.},
journal = {Journal of bacteriology},
volume = {},
number = {},
pages = {e0013325},
doi = {10.1128/jb.00133-25},
pmid = {40788082},
issn = {1098-5530},
abstract = {Carbapenem resistance mediated by blaNDM-encoded metallo-beta-lactamases is often linked to ISAba125, an insertion sequence from the IS30 family, which is widely distributed among critical and high-priority bacterial pathogens. The rapid dissemination of ISAba125-linked blaNDM in both nosocomial and community-acquired infections presents a serious challenge to healthcare systems and pharmaceutical industries. Despite the urgency of this issue, the factors driving blaNDM spread and the molecular mechanisms governing ISAba125 mobility remain poorly understood. In this study, we engineered the genomes of Vibrio cholerae and Escherichia coli to investigate the mobility of blaNDM under controlled conditions both with and without the genetically linked ISAba125. We also examined the transmission efficiency and the stability of blaNDM in environments with and without sublethal antibiotic concentrations. Our in vitro findings were validated in a rabbit ileal loop model. The results revealed that antibiotic pressure significantly influences the mobility of blaNDM, shedding light on the molecular dynamics of its transmission. These insights are crucial for developing strategies to curb the spread of blaNDM and mitigate the growing threat of carbapenem resistance in bacterial pathogens.IMPORTANCEInsertion sequences are the simplest form of mobile genetic elements that play a critical role in the adaptation of bacteria, allowing them to rapidly acquire new traits like resistance genes that enhance their survival. ISAba125 is one such insertion sequence that facilitates the spread of blaNDM, contributing to the global challenge of carbapenem resistance. In this study, we developed reporter strains that could be used as a valuable tool for investigating the dynamics of ISAba125-linked blaNDMsh-ble and evaluated the transposition frequency of ISAba125-linked blaNDMsh-ble in the presence and absence of sublethal concentration of antibiotics. Our results demonstrated that ISAba125 enhances the spread of blaNDMsh-ble under sublethal concentration of antibiotics that induces SOS response.},
}

@article {pmid40773239,
year = {2025},
author = {Gifford, RJ},
title = {Pervasive horizontal transfer of adeno-associated virus capsid genes.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {32},
pages = {e2505928122},
doi = {10.1073/pnas.2505928122},
pmid = {40773239},
issn = {1091-6490},
support = {MC_UU_12014/12//UKRI | Medical Research Council (MRC)/ ; },
mesh = {*Dependovirus/genetics ; *Gene Transfer, Horizontal ; Animals ; *Capsid Proteins/genetics ; Humans ; *Capsid ; Genetic Vectors/genetics ; Recombination, Genetic ; Phylogeny ; Evolution, Molecular ; Cattle ; Genetic Therapy ; },
abstract = {Adeno-associated viruses (AAVs) are nonpathogenic DNA viruses with potent gene delivery capabilities, making them essential tools in gene therapy and biomedical research. Despite their therapeutic importance, key aspects of AAV natural biology remain obscure, complicating efforts to explain rare AAV-associated diseases and optimize gene therapy vectors. By analyzing sequence data from virus isolates and endogenous viral elements (EVEs), I reveal a striking evolutionary pattern: While AAV sublineages, defined by the replication-associated (rep) gene, have broadly codiverged with host groups over millions of years, capsid (cap) diversity has been shaped by extensive recombination. In particular, one capsid lineage, Mammalian-wide (M-wide), has spread horizontally across diverse rep lineages and host taxa through multiple recombination events. Furthermore, several AAVs with M-wide capsids-including AAV-4, AAV-12, and bovine AAV (BAAV)-originate from historical adenovirus (Ad) stocks, raising the possibility that laboratory conditions contributed to capsid transfer. Distinguishing natural from laboratory-driven recombination is essential for understanding AAV ecology and its implications for gene therapy. A systematic sequencing effort in human and primate populations is needed to assess the extent of recombinant capsid acquisition, determine the impact of laboratory-driven recombination on circulating AAV diversity, and track ongoing recombination events that could affect vector safety and efficacy.},
}

*Dependovirus/genetics
*Gene Transfer, Horizontal
Animals
*Capsid Proteins/genetics
Humans
*Capsid
Genetic Vectors/genetics
Recombination, Genetic
Phylogeny
Evolution, Molecular
Cattle
Genetic Therapy

@article {pmid40771950,
year = {2025},
author = {Qi, Y and Lu, Z and Meng, Z and Wang, X and Chen, H and Li, M and Qu, C and Zhang, P and Liu, Y and Liu, J},
title = {Diversity and antibiotic resistance of cultivable bacteria in bulk tank milk from dairy farms in Shandong Province, China.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1649876},
pmid = {40771950},
issn = {2297-1769},
abstract = {INTRODUCTION: This study systematically analyzed bacterial diversity and antimicrobial resistance (AMR) profiles in bulk tank milk from five dairy farms (n = 30) in Shandong Province, China, to assess public health risks associated with microbial contamination and provide critical data for regional quality control and AMR risk assessment in dairy production systems.

METHODS: Total bacterial counts were quantified, revealing significant inter-farm variation (P < 0.05) with a range of 3.94-6.68 log CFU/mL. Among 129 bacterial isolates, genus-level dominance and species prevalence were identified. Antimicrobial susceptibility testing (AST) against 10 agents was performed using integrated resistance criteria combining Clinical and Laboratory Standards Institute (CLSI) standards and epidemiological cutoff values (ECOFFs). Nine resistance genes targeting seven antibiotic classes were detected via PCR.

RESULTS: The highest resistance rate was observed for sulfadiazine (53.2%) and the lowest for levofloxacin (6.0%). Multidrug resistance was detected in 23% (20/87) of isolates, with 14 strains meeting ECOFFs-based resistance criteria. PCR analysis showed sul1 (70.5%) and ant(4')-Ia (54.3%) as the most prevalent resistance genes, while mcr-1, lnu (B), and bla NDM-1 were absent in all isolates. Regional resistance variations correlated significantly with farm management practices.

DISCUSSION: These findings underscore the impact of historical antibiotic use on AMR dissemination. Enhanced AMR surveillance in raw milk, improved antibiotic stewardship, and targeted interventions are crucial to mitigate public health risks from microbial contamination and horizontal gene transfer of resistance determinants.},
}

@article {pmid40770992,
year = {2025},
author = {Moody, ERR and Williams, TA and Álvarez-Carretero, S and Szöllősi, GJ and Pisani, D and Lenton, TM and Donoghue, PCJ},
title = {The emergence of metabolisms through Earth history and implications for biospheric evolution.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {380},
number = {1931},
pages = {20240097},
pmid = {40770992},
issn = {1471-2970},
support = {//John Templeton Foundation/ ; //Leverhulme Trust/ ; /BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {*Archaea/metabolism/genetics ; *Biological Evolution ; *Bacteria/metabolism/genetics ; Earth, Planet ; Phylogeny ; *Metabolic Networks and Pathways/genetics ; Gene Transfer, Horizontal ; },
abstract = {We investigate the evolution of microbial metabolisms from the last universal common ancestor to the extant biota through comparative phylogenomics, reconciling the evolution of the genes that underpin metabolic pathways with a time-calibrated tree of life. We find that the majority of metabolic pathways were established within the first 2 billion years of Earth history, with pathways accreting at different rates. Methanogenesis and acetogenesis are recovered to be among the earliest energy metabolisms, whereas photosynthetic pathways achieved completeness by 2 Ga, much later than most previous studies have envisaged. Horizontal exchange of metabolic genes is widespread, but it has occurred largely among closely related lineages and for some pathways there is a strong signal of vertical inheritance. We also find that the rate of horizontal gene transfer has been higher in Bacteria than in Archaea through evolutionary history. Finally, we evaluate how our reconstructed history of metabolism can help to constrain hypotheses of biospheric evolution, considering the entropic and Darwinized Gaia hypotheses as well as a simple neutral model for the assembly of biogeochemical cycles.This article is part of the discussion meeting issue 'Chance and purpose in the evolution of biospheres'.},
}

*Archaea/metabolism/genetics
*Biological Evolution
*Bacteria/metabolism/genetics
Earth, Planet
Phylogeny
*Metabolic Networks and Pathways/genetics
Gene Transfer, Horizontal

@article {pmid40770987,
year = {2025},
author = {Padalko, A and Karavaeva, V and Zamarreno Beas, J and Neukirchen, S and Sousa, FL},
title = {Bioenergetics evolution: the link between Earth's and Life's history.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {380},
number = {1931},
pages = {20240102},
pmid = {40770987},
issn = {1471-2970},
support = {//H2020 European Research Council/ ; //Vienna Science and Technology Fund/ ; },
mesh = {*Energy Metabolism ; *Biological Evolution ; Earth, Planet ; *Bacteria/metabolism/genetics ; Phylogeny ; Archaea/genetics/metabolism ; *Bacterial Physiological Phenomena ; },
abstract = {The history of life intrigues both researchers and society, as it is human nature to question our origins. Our understanding of microbial evolution comes mainly from genomic data and geological evidence. Recent advances in sequencing technologies are revealing vast insights into microbial diversity, especially among uncultured lineages. While metagenomics indicates the existence of novel lineages, their ecological functions remain unknown. To unlock these mysteries, we need to shift focus from genomics to understanding their physiology. A barrier to understanding environmental microbes lies in our limited knowledge of their energy-harnessing and conservation strategies. Phylogenetic trees built from universal genes can group thousands of lineages but fail to capture the entire genome or reflect key physiological traits, especially with lateral gene transfer complicating evolutionary patterns. To deepen our knowledge of microbial evolution, a promising strategy combines large-scale comparative phylogenetic analyses of genes related to physiology with experimental data. Geochemical records of ancient energy sources can act as evolutionary constraints. This top-down approach would help rule out traits that could not be ancient, narrowing the physiological possibilities of early microbial life. Focusing on how microbes harnessed energy during evolution could bridge the gap between geochemistry and microbiology, providing testable predictions about bioenergetic transitions.This article is part of the discussion meeting issue 'Chance and purpose in the evolution of biospheres'.},
}

*Energy Metabolism
*Biological Evolution
Earth, Planet
*Bacteria/metabolism/genetics
Phylogeny
Archaea/genetics/metabolism
*Bacterial Physiological Phenomena

@article {pmid40770776,
year = {2025},
author = {Kauer, L and Sapountzis, P and Imholt, C and Berens, C and Kuehn, R},
title = {Microbial exchange at the wildlife-livestock interface: insights into microbial composition, antimicrobial resistance and virulence factor gene dynamics in grassland ecosystems.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {84},
pmid = {40770776},
issn = {2524-4671},
abstract = {The transmission of antimicrobial resistance genes (ARGs) and virulence factors (VFs) between wildlife and livestock is an emerging concern for animal and human health, especially in shared ecosystems. ARGs enhance bacterial survival against antibiotics, while VFs contribute to infection processes, and the microbiome composition influences host health. Understanding microbial exchange at the wildlife-livestock interface is essential for assessing risks to both animal and human health. This study addresses the gap in knowledge by investigating the microbial composition, ARGs, and VFs in fecal matter from livestock (Bos taurus, Ovis aries) and wildlife (Microtus arvalis) cohabiting grassland pastures. Sampling was conducted within the DFG Biodiversity Exploratories, which provides valuable and extensive long-term ecological datasets and enables the study of diverse environmental parameters. Using metagenomic sequencing and 16 S rRNA amplicon analysis, we compared bacterial diversity, antimicrobial resistance profiles, and virulence gene presence across the three host species. Metagenomic analysis revealed host-specific differences in bacterial community composition. Livestock samples exhibited higher microbial diversity than those from M. arvalis, likely due to greater environmental exposure and management practices. The most common VFs in livestock were associated with immune modulation, whereas motility-related VFs were prevalent in M. arvalis. ARG profiles differed among hosts, suggesting rare events rather due to environmental acquisition than direct transmission between the hosts. The limited numbers of ARGs and VFs shared between the species indicate that horizontal gene transfer events between wildlife and livestock are infrequent. Notably, M. arvalis harbored diverse ARGs, including resistance to tetracycline and vancomycin, which were likely acquired from the environment rather than from direct livestock contact. These findings highlight the significant role of environmental reservoirs in shaping microbial communities and the spread of resistance. This research underscores the need for enhanced surveillance and ecosystem management strategies to mitigate the risk associated with antimicrobial resistance and the potential impacts on both animal and human health.},
}

@article {pmid40770694,
year = {2025},
author = {Ha, YH and Cho, A and Kim, TH and Gil, HY},
title = {De Novo assembly and characterization of Aria alnifolia Chloroplast and mitochondrial genomes reveal homologous conformational changes mediated by repeat regions and gene transfer.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {730},
pmid = {40770694},
issn = {1471-2164},
support = {KNA 1-1-13, 14-1//Korea National Arboretum/ ; KNA 1-1-13, 14-1//Korea National Arboretum/ ; KNA 1-1-13, 14-1//Korea National Arboretum/ ; KNA 1-1-13, 14-1//Korea National Arboretum/ ; },
mesh = {Phylogeny ; *Genome, Chloroplast ; *Genome, Mitochondrial ; *Repetitive Sequences, Nucleic Acid ; Gene Transfer, Horizontal ; Evolution, Molecular ; *Rosaceae/genetics/classification ; Base Composition ; Chloroplasts/genetics ; },
abstract = {BACKGROUND: Aria alnifolia is an ornamental landscape species widely distributed in East Asia. However, its mitochondrial genome remains largely unexplored. We used PacBio long reads and Illumina short reads to sequence and assemble the organelle genomes, aiming to understand the evolutionary relationship between the plastids and mitochondria of A. alnifolia. This study focused on the homologous conformational changes mediated by repeat regions and gene transfer between organelle genomes. We also conducted comparative genomic and phylogenetic analyses with other Rosaceae species to clarify the evolutionary placement of A. alnifolia within the family.

RESULTS: The mitochondrial genome is 455,361 bp long with a GC content of 45.2%, while the chloroplast genome is 160,303 bp long with a GC content of 36.5%. The mitochondrial genome contains 59 genes, including 35 protein-coding genes, 4 rRNA genes, and 20 tRNA genes. The chloroplast genome comprises 128 genes, with 84 protein-coding genes, 8 rRNA genes, and 37 tRNA genes. The subcircular structure of the mitochondrial genome was inferred from two double-branch structures (DBSs) among 12 identified DBSs in A. alnifolia using a combination of long and short reads. In the mitochondrial genome, 128 simple sequence repeats were identified, compared to 69 in the chloroplast genome. Additionally, both organelles contained 239 dispersed repeats of at least 30 bp. We also confirmed gene transfer between the chloroplasts and mitochondria through shared repeats. Furthermore, we observed a region in the mitochondrial genome with high similarity to the chloroplast-encoded psaA gene, suggesting a possible inter-organellar gene transfer event. Phylogenetic analysis of the mitochondrial genomes revealed that A. alnifolia is closely related to Pyrus communis, albeit with low resolution.

CONCLUSION: This study provides one of the first comprehensive analyses of the organelle genomes (chloroplast and mitochondria) in the genus Aria. These results serve as a valuable reference for future taxonomic and molecular evolutionary studies of the Rosaceae family.},
}

Phylogeny
*Genome, Chloroplast
*Genome, Mitochondrial
*Repetitive Sequences, Nucleic Acid
Gene Transfer, Horizontal
Evolution, Molecular
*Rosaceae/genetics/classification
Base Composition
Chloroplasts/genetics

@article {pmid40768349,
year = {2025},
author = {Zbinden, M and Huisman, JS and Blitvic, N and Stocker, R and Słomka, J},
title = {Fluid flow generates bacterial conjugation hot spots by increasing the rate of shear-driven cell-cell encounters.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {32},
pages = {e2505446122},
doi = {10.1073/pnas.2505446122},
pmid = {40768349},
issn = {1091-6490},
support = {Pivot Fellowship//Simons Foundation (SF)/ ; Pivot Fellowship//Simons Foundation (SF)/ ; 542395FY22//Simons Foundation (SF)/ ; GBMF9197//Gordon and Betty Moore Foundation (GBMF)/ ; LT0045/2023-L//Human Frontier Science Program (HFSP)/ ; 51NF40_180575//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (SNF)/ ; 51NF40_225148//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (SNF)/ ; PZ00P2_202188//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (SNF)/ ; CRSII5-186422//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (SNF)/ ; 205321_207488//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (SNF)/ ; PHY-2309135//National Science Foundation (NSF)/ ; PHY-2309135//National Science Foundation (NSF)/ ; PHY-2309135//National Science Foundation (NSF)/ ; },
mesh = {*Escherichia coli/genetics/physiology ; *Conjugation, Genetic ; Plasmids/genetics ; },
abstract = {Conjugation accelerates bacterial evolution by enabling bacteria to acquire genes horizontally from their neighbors. Plasmid donors must physically encounter and connect with recipients to allow plasmid transfer, and different environments are characterized by vastly different encounter rates between cells, based on mechanisms ranging from simple diffusion to fluid flow. However, how the environment affects the conjugation rate by setting the encounter rate has been largely neglected, mostly because existing experimental setups do not allow for direct control over cell encounters. Here, we describe the results of conjugation experiments in Escherichia coli in which we systematically varied the magnitude of shear flow using a cone-and-plate rheometer to control the encounter rate. We found that the conjugation rate increases with shear until it peaks at an optimal shear rate ([Formula: see text]), reaching a conjugation rate fivefold higher than the baseline set by diffusion-driven encounters. This optimum marks the transition from a regime in which shear promotes conjugation by increasing the rate of cell-cell encounters to a regime in which shear disrupts conjugation. Regions of high fluid shear are widespread in aquatic systems, in the gut of host organisms, and in soil, and our results indicate that these regions could be hot spots of bacterial conjugation in the environment.},
}

*Escherichia coli/genetics/physiology
*Conjugation, Genetic
Plasmids/genetics

@article {pmid40763289,
year = {2025},
author = {AbdulHak, A and Zedan, HH and El-Mahallawy, HA and Sayed, AA and Mohamed, HO and Zafer, MM},
title = {The genomic configurations driving antimicrobial resistance and virulence in colistin resistant Pseudomonas aeruginosa from an Egyptian Tertiary Oncology Hospital.},
journal = {PLOS global public health},
volume = {5},
number = {8},
pages = {e0004976},
pmid = {40763289},
issn = {2767-3375},
abstract = {Pseudomonas aeruginosa, recognized by the World Health Organization as a critical priority pathogen, exhibits significant genomic plasticity and a high potential for developing resistance to multiple antimicrobials. This study provides comprehensive genomic insights into colistin-resistant P. aeruginosa isolates obtained from cancer patients. Phenotypic assays were conducted to evaluate antibiotic susceptibility, biofilm formation, efflux pump activity, swarming motility, and pigment production. Whole genome sequencing of the collected isolates was performed using Oxford-Nanopore technology to examine sequence types, resistome profiles, virulence-associated genes, and mobile genetic elements. Our findings reveled that out of 52 isolates, 10 (19.2%) were resistant to colistin. Ceftolozane/tazobactam demonstrated full efficacy against 60% of colistin resistant P. aeruginosa isolates. Within this colistin resistant subset, high-risk clones ST308 and ST773 emerged as dominant, both harboring blaNDM-1 and exhibiting extensive resistance profiles, including resistance to colistin and, in some cases, ceftolozane/tazobactam. The first detection of ST1143 and ST1693 in Egypt carrying blaOXA-1028 and blaOXA-904, respectively was documented, neither of which had been previously reported in the country. The accessory genome, accounting for up to 34.6% of the total genome, highlights the remarkable genomic plasticity of P. aeruginosa, and its capacity for horizontal acquisition of resistance and virulence genes via mobile genetic elements, such as integrative and conjugative elements (ICEs). Virulome analysis revealed the presence of the exoU gene in high-risk clones, a marker closely linked to hypervirulence in infection models, whereas other sequence types were associated with less virulent factors, such as exoS. Despite phenotypic variability in biofilm formation, pigment production, and motility, the underlying genetic determinants of these traits were highly conserved. Mutational analysis revealed mutations in the regulatory system PhoPQ as the primary mechanism of colistin resistance, with no mcr genes detected. In conclusion, the substantial genomic plasticity of P. aeruginosa, reflected by an extensive accessory genome facilitates horizontal gene transfer (HGT), and significantly influences antimicrobial resistance and virulence. Colistin resistance was predominantly mediated by chromosomal mutations. Virulome and resistome analyses underscores the high pathogenicity and resistance potential of high-risk clones ST773 and ST308. The detection of horizontally acquired elements, such as integrative and conjugative elements (ICEs) carrying resistance genes such as blaNDM-1, underscores their role in disseminating resistance determinants. These findings emphasize the need urgent for targeted antimicrobial stewardship and surveillance strategies within Egyptian healthcare settings.},
}

@article {pmid40762257,
year = {2025},
author = {Homsombat, T and Yoshii, K and Fukada, Y and Koiwai, K and Hirono, I and Kondo, H},
title = {Comparative Genomics of Edwardsiella piscicida in the Japanese Flounder (Paralichthys olivaceus): Discovery and Implications of a Novel Genomic Island.},
journal = {Journal of fish diseases},
volume = {},
number = {},
pages = {e70035},
doi = {10.1111/jfd.70035},
pmid = {40762257},
issn = {1365-2761},
support = {JPMJSA1806//Science and Technology Research Partnership for Sustainable Development/ ; },
abstract = {Edwardsiella piscicida is a significant pathogen that poses a particular threat to Japanese flounder (Paralichthys olivaceus) aquaculture in Japan and other countries. The damage is caused by the pathogen's ability to evade host immune defences and establish intracellular infections, intensified by its genomic plasticity and capacity for horizontal gene transfer. To investigate evolutionary adaptations between one older (2019) and four recent (2023) E. piscicida strains from the same geographical locations, we performed comparative genomic analysis of five isolates using high-quality hybrid genome assemblies and compared them with 27 Edwardsiella reference genomes. Pangenome analysis identified distinct novel genomic islands (GIs) specific to the 2023 strains. These GIs (~100 kb in size) shared 85 gene clusters encoding multiple antibiotic resistance genes, phage defence systems, mobilisation genes, and mercury resistance. In addition, they encoded integrases, transposases, and conjugative transfer genes, suggesting they function as integrative and conjugative elements (ICEs), a type of mobile genetic element. Phenotypic characterisation showed the 2023 strains carrying novel GI increased antibiotic resistance, but no significant difference in virulence in Japanese flounder infection trials. These findings highlight the recent genomic diversification of E. piscicida in aquaculture and the importance of monitoring emerging GIs driving antibiotic resistance and environmental persistence.},
}

@article {pmid40759899,
year = {2025},
author = {Zhao, Y and Li, L and Huang, Y and Xu, X and Liu, Z and Li, S and Zhu, L and Hu, B and Zhang, T},
title = {Global soil antibiotic resistance genes are associated with increasing risk and connectivity to human resistome.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {7141},
pmid = {40759899},
issn = {2041-1723},
support = {22193062//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Humans ; *Soil Microbiology ; Gene Transfer, Horizontal ; Escherichia coli/genetics/drug effects/isolation & purification ; Phylogeny ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Microbial/genetics ; *Genes, Bacterial ; Metagenomics ; Genome, Bacterial ; Soil/chemistry ; *Drug Resistance, Bacterial/genetics ; Feces/microbiology ; Metagenome ; },
abstract = {Soil is a reservoir of antibiotic resistance genes (ARGs), and understanding its connection to human antibiotic resistome is crucial for the One Health framework. Rank I ARGs appear key to deciphering this relationship, but their global distribution and attribution in soil remain unclear. To fill this gap, we analyze 3965 metagenomic data (12 habitats, including soil, feces, sewage) and 8388 genomes of Escherichia coli isolates. Results show that soil ARG risk has increased over time (from 2008 to 2021). We introduce a "connectivity" metric that evaluates cross-habitat ARGs connectivity through sequence similarity and phylogenetic analysis, and reveal higher genetic overlap with clinical E. coli genomes (1985-2023) over time suggesting an increasing link between soil and human resistome. A comparison of 45 million genome pairs suggests that cross-habitat horizontal gene transfer (HGT) is crucial for the connectivity of ARGs between humans and soil. Finally, we compile clinical antibiotic resistance datasets (covering 126 countries from 1998 to 2022) and find significant correlations between soil ARG risk, potential HGT events and clinical antibiotic resistance (R[2] = 0.40-0.89, p < 0.001). Overall, our work provides insights into the ARGs connectivity between soil and humans, and could help identify strategies to prevent dissemination of antibiotic resistance.},
}

Humans
*Soil Microbiology
Gene Transfer, Horizontal
Escherichia coli/genetics/drug effects/isolation & purification
Phylogeny
Anti-Bacterial Agents/pharmacology
*Drug Resistance, Microbial/genetics
*Genes, Bacterial
Metagenomics
Genome, Bacterial
Soil/chemistry
*Drug Resistance, Bacterial/genetics
Feces/microbiology
Metagenome

@article {pmid40759277,
year = {2025},
author = {Guo, Z and Ma, H and Liu, Y and Xie, J and Liu, X and Chang, Y and Wang, Z and Cui, P},
title = {Metagenomic analysis reveals Northwest Pacific Ocean as a reservoir and evolutionary hub of antibiotic resistance genes.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {384},
number = {},
pages = {126938},
doi = {10.1016/j.envpol.2025.126938},
pmid = {40759277},
issn = {1873-6424},
abstract = {Antibiotic resistance genes (ARGs) were identified as a novel type of environmental contaminants. Ocean is thought to be one of the ultimate environments where ARGs gathered. Marine ecosystems represent vast reservoirs of ARGs, yet their dynamics in open-ocean environments remain poorly characterized. Through large-scale metagenomic profiling of the Kuroshio Extension, a hydrographically dynamic region in the Northwest Pacific, we identified a striking enrichment of ARGs (1.81 × 10[-3] ratio) at a frontal zone site (S30). The ARG abundance at this site exceeded coastal levels by 90-fold. Notably, multidrug resistance genes dominated this hotspot, with efflux pumps contributing 62 % of the resistance mechanisms, a pattern distinct from the target-alteration strategies prevalent in other regions. The site exhibited unique microbial consortia, including pathogenic Acinetobacter (30.2 % abundance) carrying clinically critical determinants (msbA, adeJ). Co-occurrence networks revealed horizontal transfer risks, linking clinical pathogen and nature carrier to multiple ARGs. Crucially, we discovered three novel plasmid-borne resistance genes circulating in >15 % of microbial populations, demonstrating open-ocean ARG diversification independent of direct anthropogenic inputs. These findings redefine oceanic frontiers as crucibles of resistance evolution, demanding urgent integration into global antimicrobial stewardship strategies.},
}

@article {pmid40758767,
year = {2025},
author = {Lerminiaux, N and Fakharuddin, K and Longtin, Y and McGill, E and Mitchell, R and Mataseje, L and On Behalf Of The Canadian Nosocomial Infection Surveillance Program, },
title = {Plasmid genomic epidemiology of bla NDM carbapenemase-producing Enterobacterales in Canada from 2010 to 2023.},
journal = {Microbial genomics},
volume = {11},
number = {8},
pages = {},
pmid = {40758767},
issn = {2057-5858},
mesh = {*beta-Lactamases/genetics ; Canada/epidemiology ; Humans ; *Plasmids/genetics ; *Enterobacteriaceae Infections/epidemiology/microbiology ; Whole Genome Sequencing ; *Bacterial Proteins/genetics ; *Enterobacteriaceae/genetics/enzymology/isolation & purification ; Cross Infection/epidemiology/microbiology ; Genome, Bacterial ; Gene Transfer, Horizontal ; },
abstract = {Carbapenems are broad-spectrum antibiotics that are losing effectiveness against infections caused by multidrug-resistant Enterobacterales that have acquired carbapenemase genes. The New Delhi metallo-β-lactamase (bla NDM) is one of the most common carbapenemases in Canada and around the globe. These genes are frequently found on conjugative plasmids, which can disseminate through horizontal gene transfer. We applied whole-genome sequencing to characterize 1,032 bla NDM carbapenemase-producing Enterobacterales isolates collected by the Canadian Nosocomial Infection Surveillance Program from 2010 to 2023. Using a combination of short-read and long-read sequencing, we obtained 226 complete and circular bla NDM-encoding plasmids. Unlike other carbapenemases in Canada, we found that bla NDM plasmids were very diverse; there was a lack of dominant clusters identified using MOB-suite, and clustering methods were not able to accurately predict plasmid clusters for short-read-only data. The majority of bla NDM plasmids were IncF-type (69.0%, 156/226). Both bla NDM and bla OXA-48-type carbapenemase genes were found in 11.4% (118/1,032) of isolates, and we identified several instances of both carbapenemase genes co-harboured on the same plasmid replicon (n=9). Our findings highlight that plasmid transfer has not played a major role in bla NDM transmission across Canada and that long-read sequencing is essential for resolving bla NDM plasmid structure and cluster membership.},
}

*beta-Lactamases/genetics
Canada/epidemiology
Humans
*Plasmids/genetics
*Enterobacteriaceae Infections/epidemiology/microbiology
Whole Genome Sequencing
*Bacterial Proteins/genetics
*Enterobacteriaceae/genetics/enzymology/isolation & purification
Cross Infection/epidemiology/microbiology
Genome, Bacterial
Gene Transfer, Horizontal

@article {pmid40757871,
year = {2025},
author = {Mohamed, FA and Timmer, B and Hargitai, R and Melegh, S and Meszéna, R and Pál, T and Urbán, P and Herczeg, R and Gyenesei, A and Sonnevend, Á},
title = {Hypervirulent Klebsiella pneumoniae causing bloodstream infections in Hungary.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0003125},
doi = {10.1128/spectrum.00031-25},
pmid = {40757871},
issn = {2165-0497},
abstract = {Hypervirulent Klebsiella pneumoniae (hvKP) can cause severe infections even in healthy individuals. Currently, no data are available on the frequency of hvKP-induced bloodstream infections (BSI) in Hungary. Our investigation revealed that of the 157 K. pneumoniae isolated from BSI in 2020-2022 at a university hospital in Hungary, three (2%) carried the hypervirulence-associated rmpA and iutAiucABCD genes. The complete genomes of these three hvKP isolates were sequenced. They were unrelated and belonged to ST5, ST86, and ST6771, a single-locus variant of ST893, i.e., to internationally known hvKP clones. In the K. pneumoniae ST86 and ST6771 isolates, the rmpA/A2, aerobactin, and salmochelin siderophore genes were located on virulence plasmids highly similar to those of K. pneumoniae ST23 and ST86 isolated in Asia, while the K. pneumoniae ST5 isolate harboured rmpA, iroBCDN, and yersiniabactin locus on a chromosomally integrated ICEKp1 element. Comparison of the core genome MLST of the three Hungarian hvKP isolates to genomes belonging to the same ST/CC deposited in the Bigsdb database of the Pasteur Institute revealed that, although no direct epidemiological link could be established, KP48326 K. pneumoniae ST86, isolated in Pécs, clustered with a Greek isolate (ID-48733). The emergence of K. pneumoniae belonging to known hypervirulent clones in Hungary, albeit sporadic, is alarming and underscores the importance of continued whole-genome-based epidemiological surveillance.IMPORTANCEThis study represents the first investigation of the prevalence of hypervirulent K. pneumoniae (hvKP) in bloodstream infections in Hungary, conducted at the University Hospital of Pécs. Our findings emphasize the need to accurately identify hvKP strains, integrating both phenotypic and genotypic screening. Whole genome sequencing revealed genetic diversity among the Hungarian hvKP isolates, confirming the emergence of globally disseminating hvKP clones-ST86, CC893, and ST5-in Hungary. The localization of hypervirulence-related genes on mobile genetic elements, e.g., on virulence plasmids or on ICEKp1 similar to those found in hvKP isolates from different continents, underscores the significant role of horizontal gene transfer in the spread of hvKP. Overall, the study enhances our understanding of hvKP epidemiology and underscores the importance of continued molecular surveillance and control measures to mitigate the threat of hvKP infections in Hungary.},
}

@article {pmid40752531,
year = {2025},
author = {Liu, Q and Zhuo, R and He, W and Li, C},
title = {The new SCCmec type methicillin-resistant Staphylococcus aureus carried CRISPR-cas system isolated from a pig in China.},
journal = {Microbial pathogenesis},
volume = {207},
number = {},
pages = {107943},
doi = {10.1016/j.micpath.2025.107943},
pmid = {40752531},
issn = {1096-1208},
mesh = {Animals ; *Methicillin-Resistant Staphylococcus aureus/genetics/isolation & purification/drug effects/classification ; Swine/microbiology ; *CRISPR-Cas Systems/genetics ; China ; *Staphylococcal Infections/veterinary/microbiology ; Plasmids/genetics ; Drug Resistance, Multiple, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; *Swine Diseases/microbiology ; Gene Transfer, Horizontal ; Microbial Sensitivity Tests ; },
abstract = {Methicillin-resistant Staphylococcus aureus (MRSA) lineages circulate globally in healthcare, community, and livestock-associated (LA) settings. Nine MRSA isolates were recovered from swine in China, all exhibiting resistance to ampicillin and multidrug resistance phenotypes. Among eight ST9-t899 isolates, SCCmec type XII(9C2) predominated. However, we identified a novel staphylococcal cassette chromosome mec (SCCmec) type, designated XIII (9A), in an LA-MRSA strain (LS45). Structural analysis revealed SCCmec XIII(9A) comprises a CRISPR-Cas system (cas10-csm2-csm3-csm4-csm5-csm6). Functional analysis demonstrated this CRISPR-Cas system provided partial protection against phage infection at low multiplicities of infection (MOIs ≤10[-7]), but conferred no detectable immunity against spacer-matched plasmids, with no significant change in cas10 expression during plasmid challenge. The co-location of this novel SCCmec element and a functional CRISPR-Cas system within an LA-MRSA strain demonstrates that S. aureus can maintain a defense system active against phages while accommodating SCCmec-mediated horizontal gene transfer. These findings provide new insights into the genomic adaptations of MRSA across different hosts.},
}

Animals
*Methicillin-Resistant Staphylococcus aureus/genetics/isolation & purification/drug effects/classification
Swine/microbiology
*CRISPR-Cas Systems/genetics
China
*Staphylococcal Infections/veterinary/microbiology
Plasmids/genetics
Drug Resistance, Multiple, Bacterial/genetics
Anti-Bacterial Agents/pharmacology
*Swine Diseases/microbiology
Gene Transfer, Horizontal
Microbial Sensitivity Tests

@article {pmid40752385,
year = {2025},
author = {Chen, G and Qiu, X and Guo, J and Liu, T and Zha, M and Wu, X and Zheng, X and Sheng, GP and Wang, Y},
title = {Hidden risks: Unrecognized biological toxicity and antibiotic resistance spread in peracetic acid-based advanced wastewater treatment technologies.},
journal = {Water research},
volume = {287},
number = {Pt A},
pages = {124318},
doi = {10.1016/j.watres.2025.124318},
pmid = {40752385},
issn = {1879-2448},
abstract = {The escalating concern over antibiotic resistance in wastewater demands urgent attention. While advanced treatment technologies are anticipated to enhance secondary effluent quality and mitigate this issue, the associated biological toxicity and potential for resistance spread have been largely neglected. Herein, we explored the impact of peracetic acid (PAA)-based processes on antibiotic resistance during advanced secondary effluent treatment. Our findings revealed that PAA effectively inactivated most wastewater bacteria. However, it simultaneously induced environmental biotoxicity and genotoxicity, triggering a 1.5-2-fold increase in extracellular ARGs (eARGs) release and doubling horizontal gene transfer frequency. In contrast, PAA-based advanced oxidation process (PAA-AOP) demonstrated strong efficacy in detoxifying antibiotics and minimizing harm to aquatic organisms. It reduced both intracellular and extracellular ARGs by 2-4 orders of magnitude in real wastewater and significantly inhibited the conjugative transfer and transformation frequency of ARGs (by approximately 10 times), impairing their spread. Moreover, PAA-AOP reduced the abundance of pathogenic bacteria in wastewater transconjugants, thus minimizing direct harm to humans. Additionally, a membrane flow-through system designed with PAA-AOP exhibited excellent catalytic performance and stability in removing antibiotics and ARGs. These findings provide key insights into PAA-based advanced wastewater treatment, making a significant contribution to mitigating biotoxicity and antibiotic resistance in aquatic ecosystems.},
}