@article {pmid38041553,
year = {2023},
author = {Schmitz, M and Querques, I},
title = {DNA on the move: mechanisms, functions and applications of transposable elements.},
journal = {FEBS open bio},
volume = {},
number = {},
pages = {},
doi = {10.1002/2211-5463.13743},
pmid = {38041553},
issn = {2211-5463},
abstract = {Transposons are mobile genetic elements that have invaded all domains of life by moving between and within their host genomes. Due to their mobility (or transposition), transposons facilitate horizontal gene transfer in bacteria and foster the evolution of new molecular functions in prokaryotes and eukaryotes. As transposition can lead to detrimental genomic rearrangements, organisms have evolved a multitude of molecular strategies to control transposons, including genome defence mechanisms provided by CRISPR-Cas systems. Apart from their biological impacts on genomes, DNA transposons have been leveraged as efficient gene insertion vectors in basic research, transgenesis and gene therapy. However, the close to random insertion profile of transposon-based tools limits their programmability and safety. Despite recent advances brought by the development of CRISPR-associated genome editing nucleases, a strategy for efficient insertion of large, multi-kilobase transgenes at user-defined genomic sites is currently challenging. The discovery and experimental characterization of bacterial CRISPR-associated transposons (CASTs) led to the attractive hypothesis that these systems could be repurposed as programmable, site-specific gene integration technologies. Here, we provide a broad overview of the molecular mechanisms underpinning DNA transposition and of its biological and technological impact. The second focus of the article is to describe recent mechanistic and functional analyses of CAST transposition. Finally, current challenges and desired future advances of CAST-based genome engineering applications are briefly discussed.},
}

@article {pmid38039844,
year = {2023},
author = {Harada, R and Inagaki, Y},
title = {Gleaning Euglenozoa-specific DNA polymerases in public single-cell transcriptome data.},
journal = {Protist},
volume = {174},
number = {6},
pages = {125997},
doi = {10.1016/j.protis.2023.125997},
pmid = {38039844},
issn = {1618-0941},
abstract = {Multiple genes encoding family A DNA polymerases (famA DNAPs), which are evolutionary relatives of DNA polymerase I (PolI) in bacteria and phages, have been found in eukaryotic genomes, and many of these proteins are used mainly in organelles. Among members of the phylum Euglenozoa, distinct types of famA DNAP, PolIA, PolIBCD+, POP, and eugPolA, have been found. It is intriguing how the suite of famA DNAPs had been established during the evolution of Euglenozoa, but the DNAP data have not been sampled from the taxa that sufficiently represent the diversity of this phylum. In particular, little sequence data were available for basal branching species in Euglenozoa until recently. Thanks to the single-cell transcriptome data from symbiontids and phagotrophic euglenids, we have an opportunity to cover the "hole" in the repertory of famA DNAPs in the deep branches in Euglenozoa. The current study identified 16 new famA DNAP sequences in the transcriptome data from 33 phagotrophic euglenids and two symbiontids, respectively. Based on the new famA DNAP sequences, the updated diversity and evolution of famA DNAPs in Euglenozoa are discussed.},
}

@article {pmid38031909,
year = {2023},
author = {Kröger, C and Lerminiaux, NA and Ershova, AS and MacKenzie, KD and Kirzinger, MW and Märtlbauer, E and Perry, BJ and Cameron, ADS and Schauer, K},
title = {Plasmid-encoded lactose metabolism and mobilized colistin resistance (mcr-9) genes in Salmonella enterica serovars isolated from dairy facilities in the 1980s.},
journal = {Microbial genomics},
volume = {9},
number = {11},
pages = {},
doi = {10.1099/mgen.0.001149},
pmid = {38031909},
issn = {2057-5858},
mesh = {*Colistin/pharmacology ; *Salmonella enterica/genetics ; Lactose ; Serogroup ; Drug Resistance, Bacterial/genetics ; Plasmids/genetics ; },
abstract = {Horizontal gene transfer by plasmids can confer metabolic capabilities that expand a host cell's niche. Yet, it is less understood whether the coalescence of specialized catabolic functions, antibiotic resistances and metal resistances on plasmids provides synergistic benefits. In this study, we report whole-genome assembly and phenotypic analysis of five Salmonella enterica strains isolated in the 1980s from milk powder in Munich, Germany. All strains exhibited the unusual phenotype of lactose-fermentation and encoded either of two variants of the lac operon. Surprisingly, all strains encoded the mobilized colistin resistance gene 9 (mcr-9), long before the first report of this gene in the literature. In two cases, the mcr-9 gene and the lac locus were linked within a large gene island that formed an IncHI2A-type plasmid in one strain but was chromosomally integrated in the other strain. In two other strains, the mcr-9 gene was found on a large IncHI1B/IncP-type plasmid, whereas the lac locus was encoded on a separate chromosomally integrated plasmidic island. The mcr-9 sequences were identical and genomic contexts could not explain the wide range of colistin resistances exhibited by the Salmonella strains. Nucleotide variants did explain phenotypic differences in motility and exopolysaccharide production. The observed linkage of mcr-9 to lactose metabolism, an array of heavy-metal detoxification systems, and other antibiotic resistance genes may reflect a coalescence of specialized phenotypes that improve the spread of colistin resistance in dairy facilities, much earlier than previously suspected.},
}

*Colistin/pharmacology
*Salmonella enterica/genetics
Lactose
Serogroup
Drug Resistance, Bacterial/genetics
Plasmids/genetics

@article {pmid38013098,
year = {2023},
author = {Fang, GY and Liu, XQ and Jiang, YJ and Mu, XJ and Huang, BW},
title = {Horizontal gene transfer in activated sludge enhances microbial antimicrobial resistance and virulence.},
journal = {The Science of the total environment},
volume = {912},
number = {},
pages = {168908},
doi = {10.1016/j.scitotenv.2023.168908},
pmid = {38013098},
issn = {1879-1026},
abstract = {Activated sludge (AS) plays a vital role in removing organic pollutants and nutrients from wastewater. However, the risks posed by horizontal gene transfer (HGT) between bacteria in AS are still unclear. Here, a total of 478 high-quality non-redundant metagenome-assembled genomes (MAGs) were obtained. >50 % and 5 % of MAGs were involved in at least one HGT and recent HGT, respectively. Most of the transfers (82.4 %) of antimicrobial resistance genes (ARGs) occurred among the classes of Alphaproteobacteria and Gammaproteobacteria. The bacteria involved in the transfers of virulence factor genes (VFGs) mainly include Alphaproteobacteria (42.3 %), Bacteroidia (19.2 %), and Gammaproteobacteria (11.5 %). Moreover, the number of ARGs and VFGs in the classes of Alphaproteobacteria and Gammaproteobacteria was higher than that in other bacteria (P < 0.001). Mobile genetic elements were important contributors to ARGs and VFGs in AS bacteria. These results have implications for the management of antimicrobial resistance and virulence in activated sludge microorganisms.},
}

@article {pmid38012331,
year = {2023},
author = {Zhu, H and Yu, J and Fu, Y and Mao, X and Yang, H},
title = {Two-Omics Probe on the Potential of Pseudomonas sp. GDMCC 1.1703 Under Phenol Stress.},
journal = {Current microbiology},
volume = {81},
number = {1},
pages = {21},
pmid = {38012331},
issn = {1432-0991},
support = {2019YFC1803801//Key Technologies Research and Development Program/ ; 2019YFC1803800//Key Technology Research and Development Program of Shandong/ ; },
abstract = {Pseudomonas sp. harbors genetic diversity and readily adapts to environmental challenges, conferring upon it the ability to remediate. It is important to genetically determine the effects of bacterial application. The two-omics integration approach may shed more light on Pseudomonas isolates, filling the knowledge gap between genetic potential and dynamic function. In the present study, a strain from the Xi River was isolated using benzene-selective enrichment medium and phylogenetically identified as Pseudomonas sp. GDMCC 1.1703 by 16S rRNA gene sequencing. Its phenol degradability was optimally assessed at a rate of 45.7% (by statistics P < 0.05) in 12 h with a 200 mg/L concentration. Genomics and transcriptomics analyses were successively used to identify the genes and pathways responsible for phenol degradation. At least 42 genes were genomically identified to be involved in xenobiotic biodegradation. The degradative genes clustered into operons were hypothesized to have evolved through horizontal gene transfer. On the basis of genomic authentication, transcriptome analysis dynamically revealed that phenol degradation and responsive mechanisms were both upregulated as defense between the Ctrl (control) and PS (phenol-stressed) groups. Quantitative reverse transcription-PCR not only validated the key genes identified via RNA sequencing but also consistently confirmed the realistic intracellular expression. The approach of omics integration, which is effective in exploring the potential of isolates, will hopefully become an established method for determining the remediation potential of a candidate for development.},
}

@article {pmid38007474,
year = {2023},
author = {Liu, Y and Brinkhoff, T and Berger, M and Poehlein, A and Voget, S and Paoli, L and Sunagawa, S and Amann, R and Simon, M},
title = {Metagenome-assembled genomes reveal greatly expanded taxonomic and functional diversification of the abundant marine Roseobacter RCA cluster.},
journal = {Microbiome},
volume = {11},
number = {1},
pages = {265},
pmid = {38007474},
issn = {2049-2618},
support = {TRR51//Deutsche Forschungsgemeinschaft/ ; TRR51//Deutsche Forschungsgemeinschaft/ ; TRR51//Deutsche Forschungsgemeinschaft/ ; TRR51//Deutsche Forschungsgemeinschaft/ ; TRR51//Deutsche Forschungsgemeinschaft/ ; 205321_184955//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; 205321_184955//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; 51NF40_180575//National Center of Competence in Research Quantum Science and Technology/ ; },
mesh = {*Roseobacter/genetics ; Seawater/microbiology ; Metagenome ; Phylogeny ; Oceans and Seas ; Metagenomics ; },
abstract = {BACKGROUND: The RCA (Roseobacter clade affiliated) cluster belongs to the family Roseobacteracea and represents a major Roseobacter lineage in temperate to polar oceans. Despite its prevalence and abundance, only a few genomes and one described species, Planktomarina temperata, exist. To gain more insights into our limited understanding of this cluster and its taxonomic and functional diversity and biogeography, we screened metagenomic datasets from the global oceans and reconstructed metagenome-assembled genomes (MAG) affiliated to this cluster.

RESULTS: The total of 82 MAGs, plus five genomes of isolates, reveal an unexpected diversity and novel insights into the genomic features, the functional diversity, and greatly refined biogeographic patterns of the RCA cluster. This cluster is subdivided into three genera: Planktomarina, Pseudoplanktomarina, and the most deeply branching Candidatus Paraplanktomarina. Six of the eight Planktomarina species have larger genome sizes (2.44-3.12 Mbp) and higher G + C contents (46.36-53.70%) than the four Pseudoplanktomarina species (2.26-2.72 Mbp, 42.22-43.72 G + C%). Cand. Paraplanktomarina is represented only by one species with a genome size of 2.40 Mbp and a G + C content of 45.85%. Three novel species of the genera Planktomarina and Pseudoplanktomarina are validly described according to the SeqCode nomenclature for prokaryotic genomes. Aerobic anoxygenic photosynthesis (AAP) is encoded in three Planktomarina species. Unexpectedly, proteorhodopsin (PR) is encoded in the other Planktomarina and all Pseudoplanktomarina species, suggesting that this light-driven proton pump is the most important mode of acquiring complementary energy of the RCA cluster. The Pseudoplanktomarina species exhibit differences in functional traits compared to Planktomarina species and adaptations to more resource-limited conditions. An assessment of the global biogeography of the different species greatly expands the range of occurrence and shows that the different species exhibit distinct biogeographic patterns. They partially reflect the genomic features of the species.

CONCLUSIONS: Our detailed MAG-based analyses shed new light on the diversification, environmental adaptation, and global biogeography of a major lineage of pelagic bacteria. The taxonomic delineation and validation by the SeqCode nomenclature of prominent genera and species of the RCA cluster may be a promising way for a refined taxonomic identification of major prokaryotic lineages and sublineages in marine and other prokaryotic communities assessed by metagenomics approaches. Video Abstract.},
}

*Roseobacter/genetics
Seawater/microbiology
Metagenome
Phylogeny
Oceans and Seas
Metagenomics

@article {pmid38007076,
year = {2023},
author = {Zhang, Z and Bo, L and Wang, S and Li, C and Zhang, X and Xue, B and Yang, X and He, X and Shen, Z and Qiu, Z and Zhao, C and Wang, J},
title = {Multidrug-resistant plasmid RP4 inhibits the nitrogen removal capacity of ammonia-oxidizing archaea, ammonia-oxidizing bacteria, and comammox in activated sludge.},
journal = {Environmental research},
volume = {},
number = {},
pages = {117739},
doi = {10.1016/j.envres.2023.117739},
pmid = {38007076},
issn = {1096-0953},
abstract = {In wastewater treatment plants (WWTPs), ammonia oxidation is primarily carried out by three types of ammonia oxidation microorganisms (AOMs): ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and comammox (CMX). Antibiotic resistance genes (ARGs), which pose an important public health concern, have been identified at every stage of wastewater treatment. However, few studies have focused on the impact of ARGs on ammonia removal performance. Therefore, our study sought to investigate the effect of the representative multidrug-resistant plasmid RP4 on the functional microorganisms involved in ammonia oxidation. Using an inhibitor-based method, we first evaluated the contributions of AOA, AOB, and CMX to ammonia oxidation in activated sludge, which were determined to be 13.7%, 41.1%, and 39.1%, respectively. The inhibitory effects of C2H2, C8H14, and 3,4-dimethylpyrazole phosphate (DMPP) were then validated by qPCR. After adding donor strains to the sludge, fluorescence in situ hybridization (FISH) imaging analysis demonstrated the co-localization of RP4 plasmids and all three AOMs, thus confirming the horizontal gene transfer (HGT) of the RP4 plasmid among these microorganisms. Significant inhibitory effects of the RP4 plasmid on the ammonia nitrogen consumption of AOA, AOB, and CMX were also observed, with inhibition rates of 39.7%, 36.2%, and 49.7%, respectively. Moreover, amoA expression in AOB and CMX was variably inhibited by the RP4 plasmid, whereas AOA amoA expression was not inhibited. These results demonstrate the adverse environmental effects of the RP4 plasmid and provide indirect evidence supporting plasmid-mediated conjugation transfer from bacteria to archaea.},
}

@article {pmid38006896,
year = {2023},
author = {Yang, QE and Ma, X and Zeng, L and Wang, Q and Li, M and Teng, L and He, M and Liu, C and Zhao, M and Wang, M and Hui, D and Madsen, JS and Liao, H and Walsh, TR and Zhou, S},
title = {Interphylum dissemination of NDM-5-positive plasmids in hospital wastewater from Fuzhou, China: a single-centre, culture-independent, plasmid transmission study.},
journal = {The Lancet. Microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/S2666-5247(23)00227-6},
pmid = {38006896},
issn = {2666-5247},
abstract = {BACKGROUND: The global spread of plasmid-borne carbapenem resistance is an ongoing public health challenge; however, the nature of such horizontal gene transfer events among complex bacterial communities remains poorly understood. We examined the in-situ transfer of the globally dominant New Delhi metallo-β-lactamase (NDM)-5-positive IncX3 plasmid (denoted pX3_NDM-5) in hospital wastewater to simulate a real-world, One Health antimicrobial resistance context.

METHODS: For this transmission study, we tagged pX3_NDM-5 with the green fluorescent protein gene, gfp, using a CRISPR-based method and transferred the plasmid to a donor Escherichia coli strain. Bacteria were extracted from a hospital wastewater treatment plant (Fujian Provincial Maternity and Children's Hospital, Fuzhou, China) as the bacterial recipient community. We mixed this recipient community with the E coli donor strain carrying the gfp-tagged plasmid, both with and without sodium hypochlorite (NaClO) as an environmental stressor, and conducted several culture-based and culture-independent conjugation assays. The conjugation events were observed microscopically and quantified by fluorescence-activated cell sorting. We analysed the taxonomic composition of the sorted transconjugal pool by 16S rRNA gene amplicon sequencing and assessed the stability of the plasmid in the isolated transconjugants and its ability to transfer back to E coli.

FINDINGS: We show that the plasmid pX3_NDM-5 has a broad host range and can transfer across various bacterial phyla, including between Gram-negative and Gram-positive bacteria. Although environmental stress with NaClO did not affect the overall plasmid transfer frequency, it reduced the breadth of the transconjugant pool. The taxonomic composition of the transconjugal pool was distinct from that of the recipient communities, and environmental stress modulated the permissiveness of some operational taxonomic units towards the acquisition of pX3_NDM-5. Notably, pX3_NDM-5 transconjugants included the Gram-positive pathogen Enterococcus faecalis, and the plasmid could subsequently be reconjugated back to E coli. These findings suggest that E faecalis could act as a natural shuttle vector for the wide dissemination of pX3_NDM-5 plasmids.

INTERPRETATION: Our culture-independent conjugation model simulates natural environmental conditions and challenges the established theory that Gram-negative and Gram-positive bacteria rarely exchange clinically important plasmids. The data show that plasmids disseminate more widely across genera and phyla than previously thought. These findings have substantial implications when considering the spread of antimicrobial resistance across One Health sectors.

FUNDING: The Laboratory of Lingnan Modern Agriculture Project, the National Natural Science Foundation of China, the Natural Science Foundation of Fujian Province of China, and the Outstanding Young Research Talents Program of Fujian Agriculture and Forestry University.},
}

@article {pmid38006562,
year = {2024},
author = {Serbus, LR},
title = {A Light in the Dark: Uncovering Wolbachia-Host Interactions Using Fluorescence Imaging.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2739},
number = {},
pages = {349-373},
pmid = {38006562},
issn = {1940-6029},
abstract = {The success of microbial endosymbionts, which reside naturally within a eukaryotic "host" organism, requires effective microbial interaction with, and manipulation of, the host cells. Fluorescence microscopy has played a key role in elucidating the molecular mechanisms of endosymbiosis. For 30 years, fluorescence analyses have been a cornerstone in studies of endosymbiotic Wolbachia bacteria, focused on host colonization, maternal transmission, reproductive parasitism, horizontal gene transfer, viral suppression, and metabolic interactions in arthropods and nematodes. Fluorescence-based studies stand to continue informing Wolbachia-host interactions in increasingly detailed and innovative ways.},
}

@article {pmid38006561,
year = {2024},
author = {Bordenstein, SR},
title = {Isolation of Phage WO Particles from Wolbachia-Infected Arthropods.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2739},
number = {},
pages = {337-348},
pmid = {38006561},
issn = {1940-6029},
abstract = {Nearly all arthropod-associated Wolbachia contain intact and/or genomic remnants of phage WO, temperate bacteriophages that facilitate horizontal gene transfer, genomic rearrangement of the bacterial chromosome, and symbiotic interactions between Wolbachia and their arthropod hosts. Integrated prophage WO genomes produce active, lytic particles; but the lack of a cell-free culturing system for Wolbachia render them difficult to purify and study. This chapter describes polyethylene glycol (PEG) precipitation of phage particles from Wolbachia-infected arthropods, followed by confirmation of phage WO isolation and purification using electron microscopy and PCR.},
}

@article {pmid38005943,
year = {2023},
author = {Loney, RE and Delesalle, VA and Chaudry, BE and Czerpak, M and Guffey, AA and Goubet-McCall, L and McCarty, M and Strine, MS and Tanke, NT and Vill, AC and Krukonis, GP},
title = {A Novel Subcluster of Closely Related Bacillus Phages with Distinct Tail Fiber/Lysin Gene Combinations.},
journal = {Viruses},
volume = {15},
number = {11},
pages = {},
pmid = {38005943},
issn = {1999-4915},
support = {52007540/HHMI/Howard Hughes Medical Institute/United States ; },
abstract = {Bacteriophages (phages) are the most numerous entities on Earth, but we have only scratched the surface of describing phage diversity. We isolated seven Bacillus subtilis phages from desert soil in the southwest United States and then sequenced and characterized their genomes. Comparative analyses revealed high nucleotide and amino acid similarity between these seven phages, which constitute a novel subcluster. Interestingly, the tail fiber and lysin genes of these phages seem to come from different origins and carry out slightly different functions. These genes were likely acquired by this subcluster of phages via horizontal gene transfer. In conjunction with host range assays, our data suggest that these phages are adapting to hosts with different cell walls.},
}

@article {pmid38005684,
year = {2023},
author = {Khafizova, GV and Sierro, N and Ivanov, NV and Sokornova, SV and Polev, DE and Matveeva, TV},
title = {Nicotiana noctiflora Hook. Genome Contains Two Cellular T-DNAs with Functional Genes.},
journal = {Plants (Basel, Switzerland)},
volume = {12},
number = {22},
pages = {},
doi = {10.3390/plants12223787},
pmid = {38005684},
issn = {2223-7747},
support = {21-14-00050//Russian Science Foundation/ ; },
abstract = {Agrobacterium (Rhizobium)-mediated transformation leads to the formation of crown galls or hairy roots on infected plants. These effects develop due to the activity of T-DNA genes, gathered on a big plasmid, acquired from agrobacteria during horizontal gene transfer. However, a lot of plant species are known to contain such sequences, called cellular T-DNAs (cT-DNAs), and maintain normal phenotypes. Some of the genes remain intact, which leads to the conclusion of their functional role in plants. In this study, we present a comprehensive analysis of the cT-DNAs in the Nicotiana noctiflora Hook. genome, including gene expression and opine identification. Deep sequencing of the Nicotiana noctiflora genome revealed the presence of two different cT-DNAs, NnT-DNA1 and NnT-DNA2, which contain the intact genes iaaM, iaaH, acs, orf13, orf13a, and orf14. According to the expression analysis results, all these genes are most active in roots in comparison with other organs, which is consistent with data on cT-DNA gene expression in other plant species. We also used genetic engineering approaches and HPTLC and HPLC-MS methods to investigate the product of the acs gene (agrocinopine synthase), which turned out to be similar to agrocinopine A. Overall, this study expands our knowledge of cT-DNAs in plants and brings us closer to understanding their possible functions. Further research of cT-DNAs in different species and their functional implications could contribute to advancements in plant genetics and potentially unveil novel traits with practical applications in agriculture and other fields.},
}

@article {pmid38004737,
year = {2023},
author = {Cai, T and Tang, H and Du, X and Wang, W and Tang, K and Wang, X and Liu, D and Wang, P},
title = {Genomic Island-Encoded Diguanylate Cyclase from Vibrio alginolyticus Regulates Biofilm Formation and Motility in Pseudoalteromonas.},
journal = {Microorganisms},
volume = {11},
number = {11},
pages = {},
doi = {10.3390/microorganisms11112725},
pmid = {38004737},
issn = {2076-2607},
support = {42188102, 91951203 and 32070175//the National Science Foundation of China/ ; 2022YFC3103600//the National Key R&D Program of China/ ; 2021345//the Youth Innovation Promotion Association CAS/ ; 2019BT02Y262//the Local Innovative and Research Teams Project of Guangdong Pearl River Talents Program/ ; GJTD-2020-12//the K. C. Wong Education Foundation/ ; 2021B1212050023//the Science and Technology Planning Project of Guangdong Province of China/ ; },
abstract = {Many bacteria use the second messenger c-di-GMP to regulate exopolysaccharide production, biofilm formation, motility, virulence, and other phenotypes. The c-di-GMP level is controlled by the complex network of diguanylate cyclases (DGCs) and phosphodiesterases (PDEs) that synthesize and degrade c-di-GMP. In addition to chromosomally encoded DGCs, increasing numbers of DGCs were found to be located on mobile genetic elements. Whether these mobile genetic element-encoded DGCs can modulate the physiological phenotypes in recipient bacteria after horizontal gene transfer should be investigated. In our previous study, a genomic island encoding three DGC proteins (Dgc137, Dgc139, and Dgc140) was characterized in Vibrio alginolyticus isolated from the gastric cavity of the coral Galaxea fascicularis. Here, the effect of the three DGCs in four Pseudoalteromonas strains isolated from coral Galaxea fascicularis and other marine environments was explored. The results showed that when dgc137 is present rather than the three DGC genes, it obviously modulates biofilm formation and bacterial motility in these Pseudoalteromonas strains. Our findings implied that mobile genetic element-encoded DGC could regulate the physiological status of neighboring bacteria in a microbial community by modulating the c-di-GMP level after horizontal gene transfer.},
}

@article {pmid38004480,
year = {2023},
author = {Muteeb, G and Rehman, MT and Shahwan, M and Aatif, M},
title = {Origin of Antibiotics and Antibiotic Resistance, and Their Impacts on Drug Development: A Narrative Review.},
journal = {Pharmaceuticals (Basel, Switzerland)},
volume = {16},
number = {11},
pages = {},
doi = {10.3390/ph16111615},
pmid = {38004480},
issn = {1424-8247},
support = {xxx//King Faisal University/ ; },
abstract = {Antibiotics have revolutionized medicine, saving countless lives since their discovery in the early 20th century. However, the origin of antibiotics is now overshadowed by the alarming rise in antibiotic resistance. This global crisis stems from the relentless adaptability of microorganisms, driven by misuse and overuse of antibiotics. This article explores the origin of antibiotics and the subsequent emergence of antibiotic resistance. It delves into the mechanisms employed by bacteria to develop resistance, highlighting the dire consequences of drug resistance, including compromised patient care, increased mortality rates, and escalating healthcare costs. The article elucidates the latest strategies against drug-resistant microorganisms, encompassing innovative approaches such as phage therapy, CRISPR-Cas9 technology, and the exploration of natural compounds. Moreover, it examines the profound impact of antibiotic resistance on drug development, rendering the pursuit of new antibiotics economically challenging. The limitations and challenges in developing novel antibiotics are discussed, along with hurdles in the regulatory process that hinder progress in this critical field. Proposals for modifying the regulatory process to facilitate antibiotic development are presented. The withdrawal of major pharmaceutical firms from antibiotic research is examined, along with potential strategies to re-engage their interest. The article also outlines initiatives to overcome economic challenges and incentivize antibiotic development, emphasizing international collaborations and partnerships. Finally, the article sheds light on government-led initiatives against antibiotic resistance, with a specific focus on the Middle East. It discusses the proactive measures taken by governments in the region, such as Saudi Arabia and the United Arab Emirates, to combat this global threat. In the face of antibiotic resistance, a multifaceted approach is imperative. This article provides valuable insights into the complex landscape of antibiotic development, regulatory challenges, and collaborative efforts required to ensure a future where antibiotics remain effective tools in safeguarding public health.},
}

@article {pmid38002987,
year = {2023},
author = {Wang, B and Finazzo, M and Artsimovitch, I},
title = {Machine Learning Suggests That Small Size Helps Broaden Plasmid Host Range.},
journal = {Genes},
volume = {14},
number = {11},
pages = {},
doi = {10.3390/genes14112044},
pmid = {38002987},
issn = {2073-4425},
support = {GM067153//National Institute of Health/ ; },
abstract = {Plasmids mediate gene exchange across taxonomic barriers through conjugation, shaping bacterial evolution for billions of years. While plasmid mobility can be harnessed for genetic engineering and drug-delivery applications, rapid plasmid-mediated spread of resistance genes has rendered most clinical antibiotics useless. To solve this urgent and growing problem, we must understand how plasmids spread across bacterial communities. Here, we applied machine-learning models to identify features that are important for extending the plasmid host range. We assembled an up-to-date dataset of more than thirty thousand bacterial plasmids, separated them into 1125 clusters, and assigned each cluster a distribution possibility score, taking into account the host distribution of each taxonomic rank and the sampling bias of the existing sequencing data. Using this score and an optimized plasmid feature pool, we built a model stack consisting of DecisionTreeRegressor, EvoTreeRegressor, and LGBMRegressor as base models and LinearRegressor as a meta-learner. Our mathematical modeling revealed that sequence brevity is the most important determinant for plasmid spread, followed by P-loop NTPases, mobility factors, and β-lactamases. Ours and other recent results suggest that small plasmids may broaden their range by evading host defenses and using alternative modes of transfer instead of autonomous conjugation.},
}

@article {pmid38000736,
year = {2023},
author = {Yao, N and Li, W and Hu, L and Fang, N},
title = {Do mould inhibitors alter the microbial community structure and antibiotic resistance gene profiles on textiles?.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {168808},
doi = {10.1016/j.scitotenv.2023.168808},
pmid = {38000736},
issn = {1879-1026},
abstract = {Mould inhibitors are closely associated with human health and have been extensively applied to textiles to prevent mould and insect infestations. However, the impact of these mould inhibitors on the microbial community structure on textiles and antibiotic resistance gene (ARG) profiles remains largely unexplored. In this study, testing techniques, including high-throughput quantitative PCR and Illumina sequencing, were employed to analyse the effects of three types of mould inhibitors -para-dichlorobenzene (PDCB), naphthalene, and natural camphor balls-on the composition of microbial communities and ARG profiles. The microbial mechanisms underlying these effects were also investigated. The experiments revealed that PDCB reduced the diversity of bacterial communities on textiles, whereas naphthalene and natural camphor balls exerted relatively minor effects. In contrast with bacterial diversity, PDCB enhanced the diversity of fungal communities on textiles, but significantly reduced their abundance. Naphthalene had the least impact on fungal communities; however, it notably increased the relative abundance of Basidiomycota. All three types of mould inhibitors substantially altered ARG profiles. Potential mechanisms responsible for the alterations in ARG profiles include microbial community succession and horizontal gene transfer mediated by mobile genetic elements. PDCB prominently increased the abundance of ARGs, mainly attributable to the relative enrichment of potential hosts (including certain γ-Proteobacteria and Bacillales) for specific ARGs. Thus, this study has important implications for the selection of mould inhibitors, as well as the assessment of microbial safety in textiles.},
}

@article {pmid37999346,
year = {2023},
author = {Marinacci, B and Krzyżek, P and Pellegrini, B and Turacchio, G and Grande, R},
title = {Latest Update on Outer Membrane Vesicles and Their Role in Horizontal Gene Transfer: A Mini-Review.},
journal = {Membranes},
volume = {13},
number = {11},
pages = {},
pmid = {37999346},
issn = {2077-0375},
abstract = {Outer membrane vesicles (OMVs) are spherical, lipid-based nano-structures, which are released by Gram-negative bacteria in both in vitro and in vivo conditions. The size and composition of OMVs depend on not only the producer bacterial species but also cells belonging to the same strain. The mechanism of vesicles' biogenesis has a key role in determining their cargo and the pattern of macromolecules exposed on their surface. Thus, the content of proteins, lipids, nucleic acids, and other biomolecules defines the properties of OMVs and their beneficial or harmful effects on human health. Many studies have provided evidence that OMVs can be involved in a plethora of biological processes, including cell-to-cell communication and bacteria-host interactions. Moreover, there is a growing body of literature supporting their role in horizontal gene transfer (HGT). During this process, OMVs can facilitate the spreading of genes involved in metabolic pathways, virulence, and antibiotic resistance, guaranteeing bacterial proliferation and survival. For this reason, a deeper understanding of this new mechanism of genetic transfer could improve the development of more efficient strategies to counteract infections sustained by Gram-negative bacteria. In line with this, the main aim of this mini-review is to summarize the latest evidence concerning the involvement of OMVs in HGT.},
}

@article {pmid37995998,
year = {2023},
author = {Huang, B and Lv, X and Zheng, H and Yu, H and Zhang, Y and Zhang, C and Wang, J},
title = {Microbial organic fertilizer prepared by co-composting of Trichoderma dregs mitigates dissemination of resistance, virulence genes, and bacterial pathogens in soil and rhizosphere.},
journal = {Environmental research},
volume = {},
number = {},
pages = {117718},
doi = {10.1016/j.envres.2023.117718},
pmid = {37995998},
issn = {1096-0953},
abstract = {The use of manure, mycelium dregs and other waste as organic fertilizer is the main source of antibiotic resistance genes (ARGs) and pathogens in farmland. Composting of waste may effectively remove ARGs and pathogens. However, the profiles and drivers of changes in metal resistance genes (MRGs), biocide resistance genes (BRGs), and virulence genes (VGs) in soil-crop rhizosphere systems after compost application remain largely unknown. Here, we prepared two kinds of microbial organic fertilizers (MOF) by using Trichoderma dregs (TDs) and organic fertilizer mixing method (MOF1) and TDs co-composting method (MOF2). The effects of different types and doses of MOF on resistance genes, VGs and pathogens in soil-rhizosphere system and their potential mechanisms were studied. The results showed that co-composting of TDs promoted the decomposition of organic carbon and decreased the absolute abundance of ARGs and mobile genetic elements (MGEs) by 53.4-65.0%. MOF1 application significantly increased the abundance and diversity of soil ARGs, BRGs, and VGs, while low and medium doses of MOF2 significantly decreased their abundance and diversity in soil and rhizosphere. Patterns of positive co-occurrence between MGEs and VGs/MRGs/BRGs/ARGs were observed through statistical analysis and gene arrangements. ARGs/MRGs reductions in MOF2 soil were directly driven by weakened horizontal gene transfer triggered by MGEs. Furthermore, MOF2 reduced soil BRGs/VGs levels by shifting bacterial communities (e.g., reduced bacterial host) or improving soil property. Our study provided new insights into the rational use of waste to minimize the spread of resistomes and VGs in soil.},
}

@article {pmid37988660,
year = {2023},
author = {Zhang, M and Tong, X and Wang, W and Wang, J and Qu, W},
title = {Agarose biodegradation by deep-sea bacterium Vibrio natriegens WPAGA4 with the agarases through horizontal gene transfer.},
journal = {Journal of basic microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1002/jobm.202300521},
pmid = {37988660},
issn = {1521-4028},
support = {2022C02040//"Pioneer" and "Leading Goose" R&D Program of Zhejiang/ ; },
abstract = {This study aimed to reveal the importance of horizontal gene transfer (HGT) for the agarose-degrading ability and the related degradation pathway of a deep-sea bacterium Vibrio natriegens WPAGA4, which was rarely reported in former works. A total of four agarases belonged to the GH50 family, including Aga3418, Aga3419, Aga3420, and Aga3472, were annotated and expressed in Escherichia coli cells. The agarose degradation products of Aga3418, Aga3420, and Aga3472 were neoagarobiose, while those of Aga3419 were neoagarobiose and neoagarotetraose. The RT-qPCR analysis showed that the expression level ratio of Aga3418, Aga3419, Aga3420, and Aga3472 was stable at about 1:1:1.5:2.5 during the degradation, which indicated the optimal expression level ratio of the agarases for agarose degradation by V. natriegens WPAGA4. Based on the genomic information, three of four agarases and other agarose-degrading related genes were in a genome island with a G + C content that was obviously lower than that of the whole genome of V. natriegens WPAGA4, indicating that these agarose-degrading genes were required through HGT. Our results demonstrated that the expression level ratio instead of the expression level itself of agarase genes was crucial for agarose degradation by V. natriegens WPAGA4, and HGT occurred in the deep-sea environment, thereby promoting the deep-sea carbon cycle and providing a reference for studying the evolution and transfer pathways of agar-related genes.},
}

@article {pmid37987191,
year = {2023},
author = {Garbisu, C and Alkorta, I},
title = {A case for the importance of following antibiotic resistant bacteria throughout the soil food web.},
journal = {BioEssays : news and reviews in molecular, cellular and developmental biology},
volume = {45},
number = {12},
pages = {e2300153},
doi = {10.1002/bies.202300153},
pmid = {37987191},
issn = {1521-1878},
support = {PID2020-116495RB-I00//MCIN/AEI/10.13039/501100011033/ ; IT1578-22//Basque Government/ ; //JRL Environmental Antibiotic Resistance/ ; },
abstract = {It is necessary to complement next-generation sequencing data on the soil resistome with theoretical knowledge provided by ecological studies regarding the spread of antibiotic resistant bacteria (ARB) in the abiotic and, especially, biotic fraction of the soil ecosystem. Particularly, when ARB enter agricultural soils as a consequence of the application of animal manure as fertilizer, from a microbial ecology perspective, it is important to know their fate along the soil food web, that is, throughout that complex network of feeding interactions among members of the soil biota that has crucial effects on species richness and ecosystem productivity and stability. It is critical to study how the ARB that enter the soil through the application of manure can reach other taxonomical groups (e.g., fungi, protists, nematodes, arthropods, earthworms), paying special attention to their presence in the gut microbiomes of mesofauna-macrofauna and to the possibilities for horizontal gene transfer of antibiotic resistant genes.},
}

@article {pmid37983489,
year = {2023},
author = {Simmons, M and Horbelt, N and Sverko, T and Scoppola, E and Jackson, DJ and Harrington, MJ},
title = {Invasive mussels fashion silk-like byssus via mechanical processing of massive horizontally acquired coiled coils.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {48},
pages = {e2311901120},
doi = {10.1073/pnas.2311901120},
pmid = {37983489},
issn = {1091-6490},
support = {RGPIN-2018-05243//Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; CRC Tier 2 950-231953//Canada Research Chairs (Chaires de recherche du Canada)/ ; 528314512//Deutsche Forschungsgemeinschaft (DFG)/ ; },
abstract = {Zebra and quagga mussels (Dreissena spp.) are invasive freshwater biofoulers that perpetrate devastating economic and ecological impact. Their success depends on their ability to anchor onto substrates with protein-based fibers known as byssal threads. Yet, compared to other mussel lineages, little is understood about the proteins comprising their fibers or their evolutionary history. Here, we investigated the hierarchical protein structure of Dreissenid byssal threads and the process by which they are fabricated. Unique among bivalves, we found that threads possess a predominantly β-sheet crystalline structure reminiscent of spider silk. Further analysis revealed unexpectedly that the Dreissenid thread protein precursors are mechanoresponsive α-helical proteins that are mechanically processed into β-crystallites during thread formation. Proteomic analysis of the byssus secretory organ and byssus fibers revealed a family of ultrahigh molecular weight (354 to 467 kDa) asparagine-rich (19 to 20%) protein precursors predicted to form α-helical coiled coils. Moreover, several independent lines of evidence indicate that the ancestral predecessor of these proteins was likely acquired via horizontal gene transfer. This chance evolutionary event that transpired at least 12 Mya has endowed Dreissenids with a distinctive and effective fiber formation mechanism, contributing significantly to their success as invasive species and possibly, inspiring new materials design.},
}

@article {pmid37982820,
year = {2023},
author = {Cheatle Jarvela, AM and Wexler, JR},
title = {Advances in genome sequencing reveal changes in gene content that contribute to arthropod macroevolution.},
journal = {Development genes and evolution},
volume = {},
number = {},
pages = {},
pmid = {37982820},
issn = {1432-041X},
abstract = {Current sequencing technology allows for the relatively affordable generation of highly contiguous genomes. Technological advances have made it possible for researchers to investigate the consequences of diverse sorts of genomic variants, such as gene gain and loss. With the extraordinary number of high-quality genomes now available, we take stock of how these genomic variants impact phenotypic evolution. We take care to point out that the identification of genomic variants of interest is only the first step in understanding their impact. Painstaking lab or fieldwork is still required to establish causal relationships between genomic variants and phenotypic evolution. We focus mostly on arthropod research, as this phylum has an impressive degree of phenotypic diversity and is also the subject of much evolutionary genetics research. This article is intended to both highlight recent advances in the field and also to be a primer for learning about evolutionary genetics and genomics.},
}

@article {pmid37982629,
year = {2023},
author = {Tian, D and Zhao, M and Zheng, S and Jiang, X and Zhang, B},
title = {Involvement of Tn3 transposon in formation and transmission of hypervirulent and carbapenem-resistant Klebsiella pneumoniae.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0303823},
doi = {10.1128/spectrum.03038-23},
pmid = {37982629},
issn = {2165-0497},
abstract = {Carbapenem-resistant Klebsiella pneumoniae (CRKP) is resistant to most common antibiotics, becoming the most important and prevalent nosocomial opportunity pathogen. Besides, K. pneumoniae can also cause severe community-acquired infections, such as primary liver abscess and endophthalmitis. These pathogens are commonly referred to as hvKp. CRKP and hvKp have evolved separately, each occupying its own clonal lineage and exhibiting a variety of properties. Our study provides important insights into the evolutionary events related to the arousal of virulence and drug resistance in K. pneumoniae through plasmid transmission, mediated by Tn3 transposon. Our study also provides evidence that multiple mechanisms contribute to the successful transfer of non-conjugative virulence plasmid, and the involvement of transposons enhances the efficiency. A good knowledge of its transmission mechanisms is fundamental to finding effective strategies to combat these threatening pathogens. Transposons are widely present in bacteria, spreading resistance and virulence genes between the environment and humans. Therefore, emerging transposon-mediated hypervirulent and carbapenem-resistant pathogens should be highly valued.},
}

@article {pmid37981687,
year = {2023},
author = {Chen, X and Wang, Z and Zhang, C and Hu, J and Lu, Y and Zhou, H and Mei, Y and Cong, Y and Guo, F and Wang, Y and He, K and Liu, Y and Li, F},
title = {Unraveling the complex evolutionary history of lepidopteran chromosomes through ancestral chromosome reconstruction and novel chromosome nomenclature.},
journal = {BMC biology},
volume = {21},
number = {1},
pages = {265},
pmid = {37981687},
issn = {1741-7007},
support = {2019FY100400//National Science & Technology Fundamental Resources Investigation Program of China/ ; 2022YFD1401600//Key Technologies Research and Development Program/ ; LZ23C140002//Natural Science Foundation of Zhejiang Province/ ; LY22C140005//Natural Science Foundation of Zhejiang Province/ ; 32202366//National science foundation of China/ ; 32102271//National science foundation of China/ ; },
abstract = {BACKGROUND: Lepidoptera is one of the most species-rich animal groups, with substantial karyotype variations among species due to chromosomal rearrangements. Knowledge of the evolutionary patterns of lepidopteran chromosomes still needs to be improved.

RESULTS: Here, we used chromosome-level genome assemblies of 185 lepidopteran insects to reconstruct an ancestral reference genome and proposed a new chromosome nomenclature. Thus, we renamed over 5000 extant chromosomes with this system, revealing the historical events of chromosomal rearrangements and their features. Additionally, our findings indicate that, compared with autosomes, the Z chromosome in Lepidoptera underwent a fast loss of conserved genes, rapid acquisition of lineage-specific genes, and a low rate of gene duplication. Moreover, we presented evidence that all available 67 W chromosomes originated from a common ancestor chromosome, with four neo-W chromosomes identified, including one generated by fusion with an autosome and three derived through horizontal gene transfer. We also detected nearly 4000 inter-chromosomal gene movement events. Notably, Geminin is transferred from the autosome to the Z chromosome. When located on the autosome, Geminin shows female-biased expression, but on the Z chromosome, it exhibits male-biased expression. This contributes to the sexual dimorphism of body size in silkworms.

CONCLUSIONS: Our study sheds light on the complex evolutionary history of lepidopteran chromosomes based on ancestral chromosome reconstruction and novel chromosome nomenclature.},
}

@article {pmid37980566,
year = {2023},
author = {Lee, IPA and Eldakar, OT and Gogarten, JP and Andam, CP},
title = {Protocol for an agent-based model of recombination in bacteria playing a public goods game.},
journal = {STAR protocols},
volume = {4},
number = {4},
pages = {102733},
doi = {10.1016/j.xpro.2023.102733},
pmid = {37980566},
issn = {2666-1667},
abstract = {Agent-based models are composed of individual agents coded for traits, such as cooperation and cheating, that interact in a virtual world based on defined rules. Here, we describe the use of an agent-based model of homologous recombination in bacteria playing a public goods game. We describe steps for software installation, setting model parameters, running and testing models, and visualization and statistical analysis. This protocol is useful in analyses of horizontal gene transfer, bacterial sociobiology, and game theory. For complete details on the use and execution of this protocol, please refer to Lee et al.[1].},
}

@article {pmid37980337,
year = {2023},
author = {Yenew, B and Ghodousi, A and Diriba, G and Tesfaye, E and Cabibbe, AM and Amare, M and Moga, S and Alemu, A and Dagne, B and Sinshaw, W and Mollalign, H and Meaza, A and Tadesse, M and Gamtesa, DF and Abebaw, Y and Seid, G and Zerihun, B and Getu, M and Chiacchiaretta, M and Gaudin, C and Marceau, M and Didelot, X and Tolera, G and Abdella, S and Kebede, A and Getahun, M and Mehammed, Z and Supply, P and Cirillo, DM},
title = {A smooth tubercle bacillus from Ethiopia phylogenetically close to the Mycobacterium tuberculosis complex.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {7519},
pmid = {37980337},
issn = {2041-1723},
abstract = {The Mycobacterium tuberculosis complex (MTBC) includes several human- and animal-adapted pathogens. It is thought to have originated in East Africa from a recombinogenic Mycobacterium canettii-like ancestral pool. Here, we describe the discovery of a clinical tuberculosis strain isolated in Ethiopia that shares archetypal phenotypic and genomic features of M. canettii strains, but represents a phylogenetic branch much closer to the MTBC clade than to the M. canettii strains. Analysis of genomic traces of horizontal gene transfer in this isolate and previously identified M. canettii strains indicates a persistent albeit decreased recombinogenic lifestyle near the emergence of the MTBC. Our findings support that the MTBC emergence from its putative free-living M. canettii-like progenitor is evolutionarily very recent, and suggest the existence of a continuum of further extant derivatives from ancestral stages, close to the root of the MTBC, along the Great Rift Valley.},
}

@article {pmid37976849,
year = {2023},
author = {Li, YJ and Yuan, Y and Tan, WB and Xi, BD and Wang, H and Hui, KL and Chen, JB and Zhang, YF and Wang, LF and Li, RF},
title = {Antibiotic resistance genes and heavy metals in landfill: A review.},
journal = {Journal of hazardous materials},
volume = {464},
number = {},
pages = {132395},
doi = {10.1016/j.jhazmat.2023.132395},
pmid = {37976849},
issn = {1873-3336},
abstract = {Landfill is reservoir containing antibiotic resistance genes (ARGs) that pose a threat to human life and health. Heavy metals impose lasting effects on ARGs. This review investigated and analyzed the distribution, composition, and abundance of heavy metals and ARGs in landfill. The abundance ranges of ARGs detected in refuse and leachate were similar. The composition of ARG varied with sampling depth in refuse. ARG in leachate varies with the distribution of ARG in the refuse. The ARG of sulI was associated with 11 metals (Co, Pb, Mn, Zn, Cu, Cr, Ni, Sb, As, Cd, and Al). The effects of the total metal concentration on ARG abundance were masked by many factors. Low heavy metal concentrations showed positive effects on ARG diffusion; conversely, high heavy metal concentrations showed negative effects. Organic matter had a selective pressure effect on microorganisms and could provide energy for the diffusion of ARGs. Complexes of heavy metals and organic matter were common in landfill. Therefore, the hypothesis was proposed that organic matter and heavy metals have combined effects on the horizontal gene transfer (HGT) of ARGs during landfill stabilization. This work provides a new basis to better understand the HGT of ARGs in landfill.},
}

@article {pmid37976735,
year = {2023},
author = {Gao, Y and Liu, J and Fang, Y and Xu, X and Wang, F and Tang, Y and Yin, D and Cookson, AL and Zhu, W and Mao, S and Zhong, R},
title = {Straw-based compost cultivation disproportionally contributes to the environmental persistence of antibiotic resistance from raw cattle manure to organic vegetables.},
journal = {Microbiological research},
volume = {278},
number = {},
pages = {127540},
doi = {10.1016/j.micres.2023.127540},
pmid = {37976735},
issn = {1618-0623},
abstract = {Cattle manure, is a reservoir of antimicrobial resistance genes, but the mechanisms by which they migrate from farm to table remain obscure. Here, we chose Agaricus bisporus as a model vegetable to examine such migration and characterized the resistome in 112 metagenomes covering samples from raw manure, composting substrates, rhizosphere, and surfaces of mushrooms. A total of 1864 resistance genes, representing 113 unique mechanisms of resistance, were identified. Monensin treatment on beef specifically enriched fecal resistance genes within Moraxellaceae, but this effect did not persist in downstream mushrooms. Interestingly, we found that resistance genes were significantly more enriched on mushroom surfaces when cultivated with corn-based compost compared to rice and wheat, likely a result of the disproportional propagation of Pseudomonadaceae and varied ability of lateral gene transfer. Importantly, our sequence alignment together with genome-centric analysis observed that 89 resistance genes, mainly conferring resistance to drug and biocide (20.22%) and mercury (19.10%), were shared across all types of samples, indicating an efficient transmission of resistance in food production. Moreover, co-occurrence of genes conferring resistance to different compounds frequently occurred in parallel with microbial migration. Together, we present the influences of antibiotic treatment and straw-based composting on resistome along the mushroom production chain (from manure to straw-based compost, rhizosphere of compost cultivated mushroom and surface of mushroom) and highlighted the risks of resistance genes migration.},
}

@article {pmid37975503,
year = {2023},
author = {Irby, I and Brown, SP},
title = {The social lives of viruses and other mobile genetic elements: a commentary on Leeks et al. 2023.},
journal = {Journal of evolutionary biology},
volume = {36},
number = {11},
pages = {1582-1586},
doi = {10.1111/jeb.14239},
pmid = {37975503},
issn = {1420-9101},
support = {5R21AI156817-02/NH/NIH HHS/United States ; },
abstract = {Illustration of life-histories of phages and plasmids through horizontal and vertical transmission (see Figure 1 for more information).},
}

@article {pmid37974331,
year = {2023},
author = {Zhang, Y and Ding, N and Li, Y and Ouyang, M and Fu, P and Peng, Y and Tan, Y},
title = {Transcription factor FOXM1 specifies chromatin DNA to extracellular vesicles.},
journal = {Autophagy},
volume = {},
number = {},
pages = {},
doi = {10.1080/15548627.2023.2284523},
pmid = {37974331},
issn = {1554-8635},
abstract = {Extracellular vesicle DNAs (evDNAs) hold significant diagnostic value for various diseases and facilitate transcellular transfer of genetic material. Our study identifies transcription factor FOXM1 as a mediator for directing chromatin genes or DNA fragments (termed FOXM1-chDNAs) to extracellular vesicles (EVs). FOXM1 binds to MAP1LC3/LC3 in the nucleus, and FOXM1-chDNAs, such as the DUX4 gene and telomere DNA, are designated by FOXM1 binding and translocated to the cytoplasm before being released to EVs through the secretory autophagy during lysosome inhibition (SALI) process involving LC3. Disrupting FOXM1 expression or the SALI process impairs FOXM1-chDNAs incorporation into EVs. FOXM1-chDNAs can be transmitted to recipient cells via EVs and expressed in recipient cells when they carry functional genes. This finding provides an example of how chromatin DNA fragments are specified to EVs by transcription factor FOXM1, revealing its contribution to the formation of evDNAs from nuclear chromatin. It provides a basis for further exploration of the roles of evDNAs in biological processes, such as horizontal gene transfer.},
}

@article {pmid37974017,
year = {2023},
author = {Thepmanee, O and Munkongwongsiri, N and Prachumwat, A and Saksmerprome, V and Jitrakorn, S and Sritunyalucksana, K and Vanichviriyakit, R and Chanarat, S and Jaroenlak, P and Itsathitphaisarn, O},
title = {Molecular and cellular characterization of four putative nucleotide transporters from the shrimp microsporidian Enterocytozoon hepatopenaei (EHP).},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {20008},
pmid = {37974017},
issn = {2045-2322},
support = {BRF1-054/2565//The National Science Research and Innovation Fund (NSRF)/ ; BRF1-054/2565//The National Science Research and Innovation Fund (NSRF)/ ; PRP6505030760//The Agricultural Research Development Agency/ ; PRP6505030760//The Agricultural Research Development Agency/ ; B05F640137//The Program Management Unit for Human Resources & Institutional Development, Research and Innovation/ ; RGNS 65-013//Chulalongkorn University/ ; },
abstract = {Microsporidia are obligate intracellular parasites that lost several enzymes required in energy production. The expansion of transporter families in these organisms enables them to hijack ATP from hosts. In this study, nucleotide transporters of the microsporidian Enterocytozoon hepatopenaei (EHP), which causes slow growth in economically valuable Penaeus shrimp, were characterized. Analysis of the EHP genome suggested the presence of four putative nucleotide transporter genes, namely EhNTT1, EhNTT2, EhNTT3, and EhNTT4. Sequence alignment revealed four charged amino acids that are conserved in previously characterized nucleotide transporters. Phylogenetic analysis suggested that EhNTT1, 3, and 4 were derived from one horizontal gene transfer event, which was independent from that of EhNTT2. Localization of EhNTT1 and EhNTT2 using immunofluorescence analysis revealed positive signals within the envelope of developing plasmodia and on mature spores. Knockdown of EhNTT2 by double administration of sequence specific double-stranded RNA resulted in a significant reduction in EHP copy numbers, suggesting that EhNTT2 is crucial for EHP replication in shrimp. Taken together, the insight into the roles of NTTs in microsporidian proliferation can provide the biological basis for the development of alternative control strategies for microsporidian infection in shrimp.},
}

@article {pmid37973843,
year = {2023},
author = {Allard, N and Collette, A and Paquette, J and Rodrigue, S and Côté, JP},
title = {Systematic investigation of recipient cell genetic requirements reveals important surface receptors for conjugative transfer of IncI2 plasmids.},
journal = {Communications biology},
volume = {6},
number = {1},
pages = {1172},
pmid = {37973843},
issn = {2399-3642},
support = {5014521//Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (Conseil de Recherches en Sciences Naturelles et en Génie du Canada)/ ; 571440//Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (Conseil de Recherches en Sciences Naturelles et en Génie du Canada)/ ; 314063//Fonds de Recherche du Québec - Nature et Technologies (Quebec Fund for Research in Nature and Technology)/ ; },
abstract = {Bacterial conjugation is a major horizontal gene transfer mechanism. While the functions encoded by many conjugative plasmids have been intensively studied, the contribution of recipient chromosome-encoded genes remains largely unknown. Here, we analyzed the genetic requirement of recipient cells for conjugation of IncI2 plasmid TP114, which was recently shown to transfer at high rates in the gut microbiota. We performed transfer assays with ~4,000 single-gene deletion mutants of Escherichia coli. When conjugation occurs on a solid medium, we observed that recipient genes impairing transfer rates were not associated with a specific cellular function. Conversely, transfer assays performed in broth were largely dependent on the lipopolysaccharide biosynthesis pathway. We further identified specific structures in lipopolysaccharides used as recipient cell surface receptors by PilV adhesins associated with the type IVb accessory pilus of TP114. Our strategy is applicable to study other mobile genetic elements and understand important host cell factors for their dissemination.},
}

@article {pmid37972772,
year = {2023},
author = {Xin, R and Zhang, Y and Zhang, K and Yang, Y and Ma, Y and Niu, Z},
title = {Investigation of the antimicrobial susceptibility patterns of marine cyanobacteria in Bohai Bay: Cyanobacteria may be important hosts of antibiotic resistance genes in marine environment.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {168516},
doi = {10.1016/j.scitotenv.2023.168516},
pmid = {37972772},
issn = {1879-1026},
abstract = {Marine cyanobacteria, as widely distributed and photosynthetically autotrophic bacteria in the ocean, may contribute to the global dissemination of antibiotic resistance genes (ARGs) and develop a different antimicrobial susceptibility pattern from heterotrophic bacteria and cyanobacteria from freshwater environments. However, studies on antimicrobial susceptibility and the carriage of ARGs in marine cyanobacteria are still very limited. In this study, the antibiotic resistance characteristics of cyanobacteria in nearshore waters were examined through field monitoring and laboratory investigations, which included PCR detection and ARG transformation. The results showed a positive correlation between marine cyanobacteria and some ARGs in the nearshore waters of Bohai Bay. Moreover, most screened cyanobacteria showed high minimum inhibitory concentration (MIC) values for polymyxins, tetracyclines, kanamycin, and sulfonamides, moderate MIC values for streptomycin, chloramphenicol, rifampicin, and norfloxacin, and low MIC values for roxithromycin and cephalosporins. The blaTEM, blaKPC, sul1, sul2, strA, tetA, tetB, tetC, tetM, mdfA, and intI1 genes were detected in the screened marine cyanobacteria. The highest detection rates were observed for blaTEM (93.3 %), sul1 (56.6 %), sul2 (90 %), and strA (73.3 %). The detection rate of tetA (33.3 %) was the highest among the tetracycline resistance genes, and mdfA, a multidrug-resistant pump gene with resistance to tetracycline, also showed a high detection level (23.3 %). Overall, most of the screened marine cyanobacteria were found to tolerate multiple antibiotics in seawater, and the condition of the ARGs carriage was serious. Furthermore, the screened marine Synechocystis sp. C12-2 demonstrated the ability to accept ARGs on the RP4 plasmid through natural transformation and showed reduced sensitivity to ampicillin, suggesting the possibility that some marine cyanobacteria could acquire ARGs from the environment through horizontal gene transfer. Thus, marine cyanobacteria may play an important role in the propagation of marine ARGs.},
}

@article {pmid37971327,
year = {2023},
author = {Förster, M and Rathmann, I and Yüksel, M and Power, JJ and Maier, B},
title = {Genome-wide transformation reveals extensive exchange across closely related Bacillus species.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkad1074},
pmid = {37971327},
issn = {1362-4962},
support = {CRC 1310//Deutsche Forschungsgemeinschaft/ ; //University of Cologne/ ; },
abstract = {Bacterial transformation is an important mode of horizontal gene transfer that helps spread genetic material across species boundaries. Yet, the factors that pose barriers to genome-wide cross-species gene transfer are poorly characterized. Here, we develop a replacement accumulation assay to study the effects of genomic distance on transfer dynamics. Using Bacillus subtilis as recipient and various species of the genus Bacillus as donors, we find that the rate of orthologous replacement decreases exponentially with the divergence of their core genomes. We reveal that at least 96% of the B. subtilis core genes are accessible to replacement by alleles from Bacillus spizizenii. For the more distantly related Bacillus atrophaeus, gene replacement events cluster at genomic locations with high sequence identity and preferentially replace ribosomal genes. Orthologous replacement also creates mosaic patterns between donor and recipient genomes, rearranges the genome architecture, and governs gain and loss of accessory genes. We conclude that cross-species gene transfer is dominated by orthologous replacement of core genes which occurs nearly unrestricted between closely related species. At a lower rate, the exchange of accessory genes gives rise to more complex genome dynamics.},
}

@article {pmid37971255,
year = {2023},
author = {Martínez-Alvarez, L and Ramond, J-B and Vikram, S and León-Sobrino, C and Maggs-Kölling, G and Cowan, DA},
title = {With a pinch of salt: metagenomic insights into Namib Desert salt pan microbial mats and halites reveal functionally adapted and competitive communities.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0062923},
doi = {10.1128/aem.00629-23},
pmid = {37971255},
issn = {1098-5336},
abstract = {The hyperarid Namib Desert is one of the oldest deserts on Earth. It contains multiple clusters of playas which are saline-rich springs surrounded by halite evaporites. Playas are of great ecological importance, and their indigenous (poly)extremophilic microorganisms are potentially involved in the precipitation of minerals such as carbonates and sulfates and have been of great biotechnological importance. While there has been a considerable amount of microbial ecology research performed on various Namib Desert edaphic microbiomes, little is known about the microbial communities inhabiting its multiple playas. In this work, we provide a comprehensive taxonomic and functional potential characterization of the microbial, including viral, communities of sediment mats and halites from two distant salt pans of the Namib Desert, contributing toward a better understanding of the ecology of this biome.},
}

@article {pmid37971242,
year = {2023},
author = {Lerminiaux, N and Mitchell, R and Bartoszko, J and Davis, I and Ellis, C and Fakharuddin, K and Hota, SS and Katz, K and Kibsey, P and Leis, JA and Longtin, Y and McGeer, A and Minion, J and Mulvey, M and Musto, S and Rajda, E and Smith, SW and Srigley, JA and Suh, KN and Thampi, N and Tomlinson, J and Wong, T and Mataseje, L and , },
title = {Plasmid genomic epidemiology of blaKPC carbapenemase-producing Enterobacterales in Canada, 2010-2021.},
journal = {Antimicrobial agents and chemotherapy},
volume = {},
number = {},
pages = {e0086023},
doi = {10.1128/aac.00860-23},
pmid = {37971242},
issn = {1098-6596},
abstract = {Carbapenems are considered last-resort antibiotics for the treatment of infections caused by multidrug-resistant Enterobacterales, but carbapenem resistance due to acquisition of carbapenemase genes is a growing threat that has been reported worldwide. Klebsiella pneumoniae carbapenemase (blaKPC) is the most common type of carbapenemase in Canada and elsewhere; it can hydrolyze penicillins, cephalosporins, aztreonam, and carbapenems and is frequently found on mobile plasmids in the Tn4401 transposon. This means that alongside clonal expansion, blaKPC can disseminate through plasmid- and transposon-mediated horizontal gene transfer. We applied whole genome sequencing to characterize the molecular epidemiology of 829 blaKPC carbapenemase-producing isolates collected by the Canadian Nosocomial Infection Surveillance Program from 2010 to 2021. Using a combination of short-read and long-read sequencing, we obtained 202 complete and circular blaKPC-encoding plasmids. Using MOB-suite, 10 major plasmid clusters were identified from this data set which represented 87% (175/202) of the Canadian blaKPC-encoding plasmids. We further estimated the genomic location of incomplete blaKPC-encoding contigs and predicted a plasmid cluster for 95% (603/635) of these. We identified different patterns of carbapenemase mobilization across Canada related to different plasmid clusters, including clonal transmission of IncF-type plasmids (108/829, 13%) in K. pneumoniae clonal complex 258 and novel repE(pEh60-7) plasmids (44/829, 5%) in Enterobacter hormaechei ST316, and horizontal transmission of IncL/M (142/829, 17%) and IncN-type plasmids (149/829, 18%) across multiple genera. Our findings highlight the diversity of blaKPC genomic loci and indicate that multiple, distinct plasmid clusters have contributed to blaKPC spread and persistence in Canada.},
}

@article {pmid37968548,
year = {2023},
author = {Naidoo, Y and Pierneef, RE and Cowan, DA and Valverde, A},
title = {Characterization of the soil resistome and mobilome in Namib Desert soils.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {},
number = {},
pages = {},
pmid = {37968548},
issn = {1618-1905},
abstract = {The study of the soil resistome is important in understanding the evolution of antibiotic resistance and its dissemination between the clinic and the environment. However, very little is known about the soil resistome, especially of those from deserts. Here, we characterize the bacterial communities, using targeted sequencing of the 16S rRNA genes, and both the resistome and the mobilome in Namib Desert soils, using shotgun metagenomics. We detected a variety of antibiotic resistance genes (ARGs) that conferred resistance to antibiotics such as elfamycin, rifampicin, and fluoroquinolones, metal/biocide resistance genes (MRGs/BRGs) conferring resistance to metals such as arsenic and copper, and mobile genetic elements (MGEs) such as the ColE1-like plasmid. The presence of metal/biocide resistance genes in close proximity to ARGs indicated a potential for co-selection of resistance to antibiotics and metals/biocides. The co-existence of MGEs and horizontally acquired ARGs most likely contributed to a decoupling between bacterial community composition and ARG profiles. Overall, this study indicates that soil bacterial communities in Namib Desert soils host a diversity of resistance elements and that horizontal gene transfer, rather than host phylogeny, plays an essential role in their dynamics.},
}

@article {pmid37966605,
year = {2024},
author = {Chu Yuan Kee, MJ and Chen, J},
title = {Phage Transduction of Staphylococcus aureus.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2738},
number = {},
pages = {263-275},
pmid = {37966605},
issn = {1940-6029},
abstract = {Bacteriophage transduction is the major mechanism of horizontal gene transfer (HGT) among many bacteria. In Staphylococcus aureus, the phage-mediated acquisition of mobile genetic elements (MGEs) that encode virulence and antibiotic resistance genes largely contribute to its evolutionary adaptation and genetic plasticity. In molecular biology, generalized transduction is routinely used as a technique to manipulate and construct bacterial strains. Here, we describe optimized protocols for generalized transduction, applicable for the transfer of plasmid or chromosomal deoxyribonucleic acid (DNA) from donor to recipient S. aureus strains.},
}

@article {pmid37966239,
year = {2023},
author = {Maccario, L and Silva, AF and Nesme, J and Amador, CI and Sørensen, SJ and Cooper, VS and Røder, HL},
title = {Draft genomes of seven isolates from Danish wastewater facilities belonging to Pseudomonas, Bacillus, Pseudochrobactrum, Brevundimonas, and Pandoraea.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0052923},
doi = {10.1128/MRA.00529-23},
pmid = {37966239},
issn = {2576-098X},
abstract = {We report here seven draft genomes of bacterial strains from two Danish wastewater facilities, two of which might be characterized as a new group within the Pseudomonas and Pseudochrobactrum genera, respectively. These genomes will provide useful references for understanding bacterial interactions and horizontal gene transfer within bacterial communities.},
}

@article {pmid37965050,
year = {2023},
author = {Kormos, A and Dimopoulos, G and Bier, E and Lanzaro, GC and Marshall, JM and James, AA},
title = {Conceptual risk assessment of mosquito population modification gene-drive systems to control malaria transmission: preliminary hazards list workshops.},
journal = {Frontiers in bioengineering and biotechnology},
volume = {11},
number = {},
pages = {1261123},
pmid = {37965050},
issn = {2296-4185},
abstract = {The field-testing and eventual adoption of genetically-engineered mosquitoes (GEMs) to control vector-borne pathogen transmission will require them meeting safety criteria specified by regulatory authorities in regions where the technology is being considered for use and other locales that might be impacted. Preliminary risk considerations by researchers and developers may be useful for planning the baseline data collection and field research used to address the anticipated safety concerns. Part of this process is to identify potential hazards (defined as the inherent ability of an entity to cause harm) and their harms, and then chart the pathways to harm and evaluate their probability as part of a risk assessment. The University of California Malaria Initiative (UCMI) participated in a series of workshops held to identify potential hazards specific to mosquito population modification strains carrying gene-drive systems coupled to anti-parasite effector genes and their use in a hypothetical island field trial. The hazards identified were placed within the broader context of previous efforts discussed in the scientific literature. Five risk areas were considered i) pathogens, infections and diseases, and the impacts of GEMs on human and animal health, ii) invasiveness and persistence of GEMs, and interactions of GEMs with target organisms, iii) interactions of GEMs with non-target organisms including horizontal gene transfer, iv) impacts of techniques used for the management of GEMs and v) evolutionary and stability considerations. A preliminary hazards list (PHL) was developed and is made available here. This PHL is useful for internal project risk evaluation and is available to regulators at prospective field sites. UCMI project scientists affirm that the subsequent processes associated with the comprehensive risk assessment for the application of this technology should be driven by the stakeholders at the proposed field site and areas that could be affected by this intervention strategy.},
}

@article {pmid37963249,
year = {2023},
author = {Goldlust, K and Ducret, A and Halte, M and Dedieu-Berne, A and Erhardt, M and Lesterlin, C},
title = {The F pilus serves as a conduit for the DNA during conjugation between physically distant bacteria.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {47},
pages = {e2310842120},
doi = {10.1073/pnas.2310842120},
pmid = {37963249},
issn = {1091-6490},
support = {FRM-EQU202103012587//Fondation pour la Recherche Médicale (FRM)/ ; ANR-18-CE35-0008//Agence Nationale de la Recherche (ANR)/ ; ANR-22-CE12-0032//Agence Nationale de la Recherche (ANR)/ ; no. 113_MC_GH_MEL-BER_Erhardt_HU//Berlin University Alliance (BUA)/ ; },
abstract = {Horizontal transfer of F-like plasmids by bacterial conjugation is responsible for disseminating antibiotic resistance and virulence determinants among pathogenic Enterobacteriaceae species, a growing health concern worldwide. Central to this process is the conjugative F pilus, a long extracellular filamentous polymer that extends from the surface of plasmid donor cells, allowing it to probe the environment and make contact with the recipient cell. It is well established that the F pilus can retract to bring mating pair cells in tight contact before DNA transfer. However, whether DNA transfer can occur through the extended pilus has been a subject of active debate. In this study, we use live-cell microscopy to show that while most transfer events occur between cells in direct contact, the F pilus can indeed serve as a conduit for the DNA during transfer between physically distant cells. Our findings enable us to propose a unique model for conjugation that revises our understanding of the DNA transfer mechanism and the dissemination of drug resistance and virulence genes within complex bacterial communities.},
}

@article {pmid37959048,
year = {2023},
author = {Qin, Y and Huang, W and Yang, J and Zhao, Y and Zhao, M and Xu, H and Zhang, M},
title = {The Antibiotic Resistome and Its Association with Bacterial Communities in Raw Camel Milk from Altay Xinjiang.},
journal = {Foods (Basel, Switzerland)},
volume = {12},
number = {21},
pages = {},
doi = {10.3390/foods12213928},
pmid = {37959048},
issn = {2304-8158},
support = {2022D01C404//Natural Science Foundation of Xinjiang/ ; 2019Q002//Natural Science Foundation of Xinjiang/ ; 2022D01D42//Natural Science Foundation of Xinjiang/ ; },
abstract = {Raw camel milk is generally contaminated with varied microbiota, including antibiotic-resistant bacteria (ARB), that can act as a potential pathway for the spread of antibiotic resistance genes (ARGs). In this study, high-throughput quantitative PCR and 16S rRNA gene-based Illumine sequencing data were used to establish a comprehensive understanding of the antibiotic resistome and its relationship with the bacterial community in Bactrian camel milk from Xinjiang. A total of 136 ARGs and up to 1.33 × 10[8] total ARG copies per gram were identified, which predominantly encode resistance to β-lactamas and multidrugs. The ARGs' profiles were mainly explained by interactions between the bacteria community and physicochemical indicators (77.9%). Network analysis suggested that most ARGs exhibited co-occurrence with Corynebacterium, Leuconostoc and MGEs. Overall, raw camel milk serves as a reservoir for ARGs, which may aggravate the spread of ARGs through vertical and horizontal gene transfer in the food chain.},
}

@article {pmid37955258,
year = {2023},
author = {Gong, P and Liu, H and Yu, T and Jiang, C and Gou, E and Guan, J and Chen, H and Kang, H},
title = {Evaluation of resistance risk in soil due to antibiotics during application of penicillin V fermentation residue.},
journal = {Environmental technology},
volume = {},
number = {},
pages = {1-33},
doi = {10.1080/09593330.2023.2283807},
pmid = {37955258},
issn = {1479-487X},
abstract = {The soil application of hydrothermally treated penicillin V fermentation residue (PFR) is attractive but challenged, due to the concern of the resistance risk in soil related to residual antibiotics. In this study, a lab-scale incubation experiment was conducted to investigate the influence of penicillin V on antibiotic resistance genes (ARGs) in PFR-amended soil via qPCR. The introduced penicillin V in soil could not be persistent, and its degradation occurred mainly within 2 days. The higher number of soil ARGs was detected under 108 mg/kg of penicillin V than lower contents (≤54 mg/kg). Additionally, the relative abundance of ARGs was higher in soil spiked with penicillin V than that in blank soil, and the great increase in the relative abundance of soil ARGs occurred earlier under 108 mg/kg of penicillin V than lower contents. The horizontal gene transfer might contribute to the shift of ARGs in PFR-amended soil. The results indicated that the residual penicillin V could cause the proliferation of soil ARGs and should be completely removed by hydrothermal treatment before soil application. The results of this study provide a comprehensive understanding of the resistance risk posed by penicillin V during the application of hydrothermally pretreated PFR.},
}

@article {pmid37953666,
year = {2023},
author = {Pandey, T and Kalluraya, CA and Wang, B and Xu, T and Huang, X and Guang, S and Daugherty, MD and Ma, DK},
title = {Acquired stress resilience through bacteria-to-nematode interdomain horizontal gene transfer.},
journal = {The EMBO journal},
volume = {},
number = {},
pages = {e114835},
doi = {10.15252/embj.2023114835},
pmid = {37953666},
issn = {1460-2075},
support = {P40 OD010440/CD/ODCDC CDC HHS/United States ; },
abstract = {Natural selection drives the acquisition of organismal resilience traits to protect against adverse environments. Horizontal gene transfer (HGT) is an important evolutionary mechanism for the acquisition of novel traits, including metazoan acquisitions in immunity, metabolic, and reproduction function via interdomain HGT (iHGT) from bacteria. Here, we report that the nematode gene rml-3 has been acquired by iHGT from bacteria and that it enables exoskeleton resilience and protection against environmental toxins in Caenorhabditis elegans. Phylogenetic analysis reveals that diverse nematode RML-3 proteins form a single monophyletic clade most similar to bacterial enzymes that biosynthesize L-rhamnose, a cell-wall polysaccharide component. C. elegans rml-3 is highly expressed during larval development and upregulated in developing seam cells upon heat stress and during the stress-resistant dauer stage. rml-3 deficiency impairs cuticle integrity, barrier functions, and nematode stress resilience, phenotypes that can be rescued by exogenous L-rhamnose. We propose that interdomain HGT of an ancient bacterial rml-3 homolog has enabled L-rhamnose biosynthesis in nematodes, facilitating cuticle integrity and organismal resilience to environmental stressors during evolution. These findings highlight a remarkable contribution of iHGT on metazoan evolution conferred by the domestication of a bacterial gene.},
}

@article {pmid37952399,
year = {2023},
author = {Salter, C and Westrick, JA and Chaganti, SR and Birbeck, JA and Peraino, NJ and Weisener, CG},
title = {Elucidating microbial mechanisms of microcystin-LR degradation in Lake Erie beach sand through metabolomics and metatranscriptomics.},
journal = {Water research},
volume = {247},
number = {},
pages = {120816},
doi = {10.1016/j.watres.2023.120816},
pmid = {37952399},
issn = {1879-2448},
abstract = {As one of five Laurentian Great Lakes, Lake Erie ranks among the top freshwater drinking sources and ecosystems globally. Historical and current agriculture mismanagement and climate change sustains the environmental landscape for late summer cyanobacterial harmful algal blooms, and consequently, cyanotoxins such as microcystin (MC). Microcystin microbial degradation is a promising mitigation strategy, however the mechanisms controlling the breakdown of MCs in Lake Erie are not well understood. Pelee Island, Ontario, Canada is located in the western basin of Lake Erie and the bacterial community in the sand has demonstrated the capacity of metabolizing the toxin. Through a multi-omic approach, the metabolic, functional and taxonomical signatures of the Pelee Island microbial community during MC-LR degradation was investigated over a 48-hour period to comprehensively study the degradation mechanism. Cleavage of bonds surrounding nitrogen atoms and the upregulation of nitrogen deamination (dadA, alanine dehydrogenase, leucine dehydrogenase) and assimilation genes (glnA, gltB) suggests a targeted isolation of nitrogen by the microbial community for energy production. Methylotrophic pathways RuMP and H4MPT control assimilation and dissimilation of carbon, respectively and differential abundance of Methylophilales indicates an interconnected role through electron exchange of denitrification and methylotrophic pathways. The detected metabolites did not resolve a clear breakdown pathway, but rather the diversity of products in combination with taxonomic and functional results supports that a variety of strategies are applied, such as epoxidation, hydroxylation, and aromatic degradation. Annual repeated exposure to the toxin may have allowed the community to adaptatively establish a novel pathway through functional plasticity and horizontal gene transfer. The culmination of these results reveals the complexity of the Pelee Island sand community and supports a dynamic and cooperative metabolism between microbial species to achieve MC degradation.},
}

@article {pmid37951253,
year = {2023},
author = {Kang, Y and Zhao, S and Cheng, H and Xu, W and You, R and Hu, J},
title = {The distribution profiles of tetracycline resistance genes in rice: Comparisons using four genotypes.},
journal = {The Science of the total environment},
volume = {908},
number = {},
pages = {168359},
doi = {10.1016/j.scitotenv.2023.168359},
pmid = {37951253},
issn = {1879-1026},
abstract = {The potential transmission of antibiotic resistance genes (ARGs) from the rhizosphere to plants and humans poses a significant concern. This study aims to investigate the distribution of tetracycline resistance genes (TRGs) in rice using four genotypes and identify the primary source of TRGs in grains. Quantitative polymerase chain reaction (qPCR) was employed to determine the abundance of seven TRGs and intI1 in four rice varieties and three partitions during the jointing and heading stages, respectively. The analysis of the bacterial community was conducted to elucidate the underlying mechanism of the profiles of TRGs. It was observed that tetZ was predominantly present in the rhizosphere and endoroot, whereas tetX became dominant in grains. The relative abundances of TRGs and intI1 exhibited significant variations across both the variety and partition. However, no significant differences were observed in grains, where the abundances of TRGs were several orders of magnitude lower compared to those in the rhizosphere. Nevertheless, the potential risk of the dissemination of TRGs to humans, particularly those carried by potential pathogens in grains, warrants attention. The increased likelihood of TRGs accumulation in the rhizosphere and endoroot of hybrid rice varieties, as opposed to japonica varieties, may be attributed to the heightened metabolic activities of their roots. The significant associations observed between intI1 and TRGs, coupled with the substantial alterations in potential hosts for intI1 across various treatments, indicate that intI1-mediated horizontal gene transfer plays a role in the diverse range of bacterial hosts for TRGs. The study also revealed that rhizosphere bacteria during the jointing stage serve as the primary contributors of TRGs in grains through the endoroot junction. The findings indicate that Japonica rice varieties exhibit superior control over TRGs compared to hybrid varieties, emphasizing the need for early interventions throughout the entire growth period of rice.},
}

@article {pmid37944236,
year = {2023},
author = {Xiao, T and Chen, R and Cai, C and Yuan, S and Dai, X and Dong, B and Xu, Z},
title = {Abatement of antibiotics and resistance genes during catalytic ozonation enhanced sludge dewatering process: Synchronized in volume and hazardousness reduction.},
journal = {Journal of hazardous materials},
volume = {463},
number = {},
pages = {132912},
doi = {10.1016/j.jhazmat.2023.132912},
pmid = {37944236},
issn = {1873-3336},
abstract = {Based on the efficiency of the catalytic ozonation techniques (HDWS+O3 and MnFe2O4 @SBC+O3) in enhancing the sludge dewaterability, the effectiveness in synchronized abatement antibiotics and antibiotic resistance genes (ARGs) was conducted to determine. The results revealed that catalytic ozonation conditioning altered the distribution of target antibiotics (tetracycline (TC), oxytetracycline (OTC), norfloxacin (NOR), ofloxacin (OFL)) in the dewatered filtrate, the dewatered sludge cake and the extra-microcolony/cellular polymers (EMPS/ECPS) layers, achieving the redistribution from solid-phase adsorption to liquid-phase dissolution. The total degradation rate was over 90% for TC and OTC, 72-78% for NOR and OFL; the abatement efficiency of eleven ARGs reached 1.47-3.01 log and 1.64-3.59 log, respectively, and more than four eARGs were eliminated. The effective abatement of the absolute abundance of Mobile genetic elements (MGEs) (0.91-1.89 log) demonstrated that catalytic ozonation conditioning could also significantly inhibit horizontal gene transfer (HGT). The abundance of resistant bacteria was greatly reduced and the signal transduction of the typical ARGs host bacteria was inhibited. The highly reactive oxidation species (ROS) generated were responsible for the abatement of antibiotics and ARGs. These findings provided new insights into the sludge conditioning for ideal and synchronized reduction in volume and hazardousness by catalytic ozonation processes in sludge treatment.},
}

@article {pmid37940998,
year = {2023},
author = {Schaller, D and Hartmann, T and Lafond, M and Stadler, PF and Wieseke, N and Hellmuth, M},
title = {Relative timing information and orthology in evolutionary scenarios.},
journal = {Algorithms for molecular biology : AMB},
volume = {18},
number = {1},
pages = {16},
pmid = {37940998},
issn = {1748-7188},
support = {RGPIN-2019-05817//Natural Sciences and Engineering Research Council of Canada/ ; 214087123//Deutsche Forschungsgemeinschaft/ ; },
abstract = {BACKGROUND: Evolutionary scenarios describing the evolution of a family of genes within a collection of species comprise the mapping of the vertices of a gene tree T to vertices and edges of a species tree S. The relative timing of the last common ancestors of two extant genes (leaves of T) and the last common ancestors of the two species (leaves of S) in which they reside is indicative of horizontal gene transfers (HGT) and ancient duplications. Orthologous gene pairs, on the other hand, require that their last common ancestors coincides with a corresponding speciation event. The relative timing information of gene and species divergences is captured by three colored graphs that have the extant genes as vertices and the species in which the genes are found as vertex colors: the equal-divergence-time (EDT) graph, the later-divergence-time (LDT) graph and the prior-divergence-time (PDT) graph, which together form an edge partition of the complete graph.

RESULTS: Here we give a complete characterization in terms of informative and forbidden triples that can be read off the three graphs and provide a polynomial time algorithm for constructing an evolutionary scenario that explains the graphs, provided such a scenario exists. While both LDT and PDT graphs are cographs, this is not true for the EDT graph in general. We show that every EDT graph is perfect. While the information about LDT and PDT graphs is necessary to recognize EDT graphs in polynomial-time for general scenarios, this extra information can be dropped in the HGT-free case. However, recognition of EDT graphs without knowledge of putative LDT and PDT graphs is NP-complete for general scenarios. In contrast, PDT graphs can be recognized in polynomial-time. We finally connect the EDT graph to the alternative definitions of orthology that have been proposed for scenarios with horizontal gene transfer. With one exception, the corresponding graphs are shown to be colored cographs.},
}

@article {pmid37938748,
year = {2023},
author = {Zeldes, B and Poehlein, A and Jain, S and Baum, C and Daniel, R and Müller, V and Basen, M},
title = {DNA uptake from a laboratory environment drives unexpected adaptation of a thermophile to a minor medium component.},
journal = {ISME communications},
volume = {3},
number = {1},
pages = {2},
pmid = {37938748},
issn = {2730-6151},
support = {BA 5757/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 031B0857A//Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)/ ; 031B0857C//Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)/ ; 031B0857B//Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)/ ; },
abstract = {DNA uptake is widespread among microorganisms and considered a strategy for rapid adaptation to new conditions. While both DNA uptake and adaptation are referred to in the context of natural environments, they are often studied in laboratories under defined conditions. For example, a strain of the thermophile Thermoanaerobacter kivui had been adapted to growth on high concentrations of carbon monoxide (CO). Unusual phenotypes of the CO-adapted strain prompted us to examine it more closely, revealing a horizontal gene transfer (HGT) event from another thermophile, Thermoanaerobacter sp. strain X514, being cultured in the same laboratory. The transferred genes conferred on T. kivui the ability to utilize trehalose, a trace component of the yeast-extract added to the media during CO-adaptation. This same HGT event simultaneously deleted a native operon for thiamine biosynthesis, which likely explains why the CO-adapted strain grows poorly without added vitamins. Attempts to replicate this HGT by providing T. kivui with genomic DNA from Thermoanaerobacter sp. strain X514 revealed that it is easily reproducible in the lab. This subtle form of "genome contamination" is difficult to detect, since the genome remains predominantly T. kivui, and no living cells from the original contamination remain. Unexpected HGT between two microorganisms as well as simultaneous adaptation to several conditions may occur often and unrecognized in laboratory environments, requiring caution and careful monitoring of phenotype and genotype of microorganisms that are naturally-competent for DNA uptake.},
}

@article {pmid37935916,
year = {2023},
author = {An, T and Cai, Y and Li, G and Li, S and Wong, PK and Guo, J and Zhao, H},
title = {Prevalence and transmission risk of colistin and multidrug resistance in long-distance coastal aquaculture.},
journal = {ISME communications},
volume = {3},
number = {1},
pages = {115},
pmid = {37935916},
issn = {2730-6151},
support = {U1901210//National Natural Science Foundation of China (National Science Foundation of China)/ ; 41425015//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42122056//École Nationale d'Ingénieurs de Saint-Etienne (National Engineering School of Saint-Étienne)/ ; },
abstract = {Due to the wide use of antibiotics, intensive aquaculture farms have been recognized as a significant reservoir of antibiotic resistomes. Although the prevalence of colistin resistance genes and multidrug-resistant bacteria (MDRB) has been documented, empirical evidence for the transmission of colistin and multidrug resistance between bacterial communities in aquaculture farms through horizontal gene transfer (HGT) is lacking. Here, we report the prevalence and transmission risk of colistin and multidrug resistance in 27 aquaculture water samples from 9 aquaculture zones from over 5000 km of subtropical coastlines in southern China. The colistin resistance gene mcr-1, mobile genetic element (MGE) intl1 and 13 typical antibiotic resistance genes (ARGs) were prevalent in all the aquaculture water samples. Most types of antibiotic (especially colistin) resistance are transmissible in bacterial communities based on evidence from laboratory conjugation and transformation experiments. Diverse MDRB were detected in most of the aquaculture water samples, and a strain with high-level colistin resistance, named Ralstonia pickettii MCR, was isolated. The risk of horizontal transfer of the colistin resistance of R. pickettii MCR through conjugation and transformation was low, but the colistin resistance could be steadily transmitted to offspring through vertical transfer. The findings have important implications for the future regulation of antibiotic use in aquaculture farms globally to address the growing threat posed by antibiotic resistance to human health.},
}

@article {pmid37938682,
year = {2022},
author = {Orevi, T and Sørensen, SJ and Kashtan, N},
title = {Droplet size and surface hydrophobicity enhance bacterial plasmid transfer rates in microscopic surface wetness.},
journal = {ISME communications},
volume = {2},
number = {1},
pages = {72},
pmid = {37938682},
issn = {2730-6151},
support = {#220020475//James S. McDonnell Foundation (McDonnell Foundation)/ ; #1396/19//Israel Science Foundation (ISF)/ ; NNF200C0062223//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; },
abstract = {Conjugal plasmids constitute a major engine for horizontal gene transfer in bacteria, and are key drivers of the spread of antibiotic resistance, virulence, and metabolic functions. Bacteria in terrestrial habitats often inhabit surfaces that are not constantly water-saturated, where microscopic surface wetness (MSW), comprised of thin liquid films and microdroplets, permanently or intermittently occurs. How physical properties of microdroplets, and of the surfaces they reside on, affect plasmid transfer rates is not well understood. Here, building on microscopy-based microdroplet experiments, we examined the relation between droplet properties (size and spread) and plasmid transfer rates at single-cell and individual droplet resolution, using Pseudomonas putida as a model species. We show that transfer rates increase with droplet size, due to higher densities of cells on the surface in larger droplets, resulting from lower ratio between the area of the liquid-solid interface and droplet volumes. We further show that surface hydrophobicity promotes transfer rates via the same mechanism. Our results provide new insights into how physical properties of surfaces and MSW affect plasmid transfer rates, and more generally, microbial interactions mediated by cell-to-cell contact, with important implications for our understanding of the ecology and evolution of bacteria in unsaturated environments.},
}

@article {pmid37938745,
year = {2022},
author = {Kujawska, M and Raulo, A and Millar, M and Warren, F and Baltrūnaitė, L and Knowles, SCL and Hall, LJ},
title = {Bifidobacterium castoris strains isolated from wild mice show evidence of frequent host switching and diverse carbohydrate metabolism potential.},
journal = {ISME communications},
volume = {2},
number = {1},
pages = {20},
pmid = {37938745},
issn = {2730-6151},
support = {100/974/C/13/Z//Wellcome Trust (Wellcome)/ ; BB/M011216/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; BB/R012490/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; BBS/E/F/000PR10353//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; BBS/E/F/000PR10356//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; BB/J004529/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; BB/M011216/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; BB/M011216/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; NE/L011867/1//NERC Environmental Bioinformatics Centre (NEBC)/ ; },
abstract = {Members of the gut microbiota genus Bifidobacterium are widely distributed human and animal symbionts believed to exert beneficial effects on their hosts. However, in-depth genomic analyses of animal-associated species and strains are somewhat lacking, particularly in wild animal populations. Here, to examine patterns of host specificity and carbohydrate metabolism capacity, we sequenced whole genomes of Bifidobacterium isolated from wild-caught small mammals from two European countries (UK and Lithuania). Members of Bifidobacterium castoris, Bifidobacterium animalis and Bifodobacterium pseudolongum were detected in wild mice (Apodemus sylvaticus, Apodemus agrarius and Apodemus flavicollis), but not voles or shrews. B. castoris constituted the most commonly recovered Bifidobacterium (78% of all isolates), with the majority of strains only detected in a single population, although populations frequently harboured multiple co-circulating strains. Phylogenetic analysis revealed that the mouse-associated B. castoris clades were not specific to a particular location or host species, and their distribution across the host phylogeny was consistent with regular host shifts rather than host-microbe codiversification. Functional analysis, including in vitro growth assays, suggested that mouse-derived B. castoris strains encoded an extensive arsenal of carbohydrate-active enzymes, including putative novel glycosyl hydrolases such as chitosanases, along with genes encoding putative exopolysaccharides, some of which may have been acquired via horizontal gene transfer. Overall, these results provide a rare genome-level analysis of host specificity and genomic capacity among important gut symbionts of wild animals, and reveal that Bifidobacterium has a labile relationship with its host over evolutionary time scales.},
}

@article {pmid37934408,
year = {2023},
author = {Martinez-Varela, A and Casas, G and Berrojalbiz, N and Lundin, D and Piña, B and Dachs, J and Vila-Costa, M},
title = {Metatranscriptomic responses and microbial degradation of background polycyclic aromatic hydrocarbons in the coastal Mediterranean and Antarctica.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {37934408},
issn = {1614-7499},
support = {CTM2015-70535-P//Ministerio de Ciencia e Innovación/ ; CTM2015-65691-R//Ministerio de Ciencia e Innovación/ ; CEX2018-000794-S//Ministerio de Ciencia e Innovación/ ; 2017SGR800//Agència de Gestió d'Ajuts Universitaris i de Recerca/ ; },
abstract = {Although microbial degradation is a key sink of polycyclic aromatic hydrocarbons (PAH) in surface seawaters, there is a dearth of field-based evidences of regional divergences in biodegradation and the effects of PAHs on site-specific microbial communities. We compared the magnitude of PAH degradation and its impacts in short-term incubations of coastal Mediterranean and the Maritime Antarctica microbiomes with environmentally relevant concentrations of PAHs. Mediterranean bacteria readily degraded the less hydrophobic PAHs, with rates averaging 4.72 ± 0.5 ng L h[-1]. Metatranscriptomic responses showed significant enrichments of genes associated to horizontal gene transfer, stress response, and PAH degradation, mainly harbored by Alphaproteobacteria. Community composition changed and increased relative abundances of Bacteroidota and Flavobacteriales. In Antarctic waters, there was no degradation of PAH, and minimal metatranscriptome responses were observed. These results provide evidence for factors such as geographic region, community composition, and pre-exposure history to predict PAH biodegradation in seawater.},
}

@article {pmid37931146,
year = {2023},
author = {Kosterlitz, O and Grassi, N and Werner, B and McGee, RS and Top, EM and Kerr, B},
title = {Evolutionary "crowdsourcing": alignment of fitness landscapes allows for cross-species adaptation of a horizontally transferred gene.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msad237},
pmid = {37931146},
issn = {1537-1719},
abstract = {Genes that undergo horizontal gene transfer (HGT) evolve in different genomic backgrounds. Despite the ubiquity of cross-species HGT, the effects of switching hosts on gene evolution remains understudied. Here, we present a framework to examine the evolutionary consequences of host switching and apply this framework to an antibiotic resistance gene commonly found on conjugative plasmids. Specifically, we determined the adaptive landscape of this gene for a small set of mutationally connected genotypes in three enteric species. We uncovered that the landscape topographies were largely aligned with minimal host-dependent mutational effects. By simulating gene evolution over the experimentally gauged landscapes, we found that the adaptive evolution of the mobile gene in one species translated to adaptation in another. By simulating gene evolution over artificial landscapes, we found that sufficient alignment between landscapes ensures such "adaptive equivalency" across species. Thus, given adequate landscape alignment within a bacterial community, vehicles of HGT such as plasmids may enable a distributed form of genetic evolution across community members, where species can 'crowdsource' adaptation.},
}

@article {pmid37930866,
year = {2023},
author = {Camargo, AP and Call, L and Roux, S and Nayfach, S and Huntemann, M and Palaniappan, K and Ratner, A and Chu, K and Mukherjeep, S and Reddy, T and Chen, IA and Ivanova, NN and Eloe-Fadrosh, EA and Woyke, T and Baltrus, DA and Castañeda-Barba, S and de la Cruz, F and Funnell, BE and Hall, JPJ and Mukhopadhyay, A and Rocha, EPC and Stalder, T and Top, E and Kyrpides, NC},
title = {IMG/PR: a database of plasmids from genomes and metagenomes with rich annotations and metadata.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkad964},
pmid = {37930866},
issn = {1362-4962},
support = {//U.S. Department of Energy/ ; //Joint Genome Institute/ ; DE-AC02-05CH11231//DOE Office of Science User Facilities/ ; 17-SC-20-SC//Exascale Computing Project/ ; //U.S. Department of Energy Office of Science/ ; //National Nuclear Security Administration/ ; MR/W02666X/1//MRC Career Development Award/ ; //Office of Science of the US Department of Science/ ; },
abstract = {Plasmids are mobile genetic elements found in many clades of Archaea and Bacteria. They drive horizontal gene transfer, impacting ecological and evolutionary processes within microbial communities, and hold substantial importance in human health and biotechnology. To support plasmid research and provide scientists with data of an unprecedented diversity of plasmid sequences, we introduce the IMG/PR database, a new resource encompassing 699 973 plasmid sequences derived from genomes, metagenomes and metatranscriptomes. IMG/PR is the first database to provide data of plasmid that were systematically identified from diverse microbiome samples. IMG/PR plasmids are associated with rich metadata that includes geographical and ecosystem information, host taxonomy, similarity to other plasmids, functional annotation, presence of genes involved in conjugation and antibiotic resistance. The database offers diverse methods for exploring its extensive plasmid collection, enabling users to navigate plasmids through metadata-centric queries, plasmid comparisons and BLAST searches. The web interface for IMG/PR is accessible at https://img.jgi.doe.gov/pr. Plasmid metadata and sequences can be downloaded from https://genome.jgi.doe.gov/portal/IMG_PR.},
}

@article {pmid37928655,
year = {2023},
author = {Wang, Z and Zhang, N and Li, C and Shao, L},
title = {Diversity of antibiotic resistance genes in soils with four different fertilization treatments.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1291599},
pmid = {37928655},
issn = {1664-302X},
abstract = {Although the enrichment of resistance genes in soil has been explored in recent years, there are still some key questions to be addressed regarding the variation of ARG composition in soil with different fertilization treatments, such as the core ARGs in soil after different fertilization treatments, the correlation between ARGs and bacterial taxa, etc. For soils after different fertilization treatments, the distribution and combination of ARG in three typical fertilization methods (organic fertilizer alone, chemical fertilizer alone, and conventional fertilizer) and non-fertilized soils were investigated in this study using high-throughput fluorescence quantitative PCR (HT-qPCR) technique. The application of organic fertilizers significantly increased the abundance and quantity of ARGs and their subtypes in the soil compared to the non-fertilized soil, where sul1 was the ARGs specific to organic fertilizers alone and in higher abundance. The conventional fertilizer application also showed significant enrichment of ARGs, which indicated that manure addition often had a more decisive effect on ARGs in soil than chemical fertilizers, and three bacteria, Pseudonocardia, Irregularibacter, and Castllaniella, were the key bacteria affecting ARG changes in soil after fertilization. In addition, nutrient factors and heavy metals also affect the distribution of ARGs in soil and are positively correlated. This paper reveals the possible reasons for the increase in the number of total soil ARGs and their relative abundance under different fertilization treatments, which has positive implications for controlling the transmission of ARGs through the soil-human pathway.},
}

@article {pmid37923145,
year = {2023},
author = {Geoffroy, F and Uecker, H},
title = {Limits to evolutionary rescue by conjugative plasmids.},
journal = {Theoretical population biology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tpb.2023.10.001},
pmid = {37923145},
issn = {1096-0325},
abstract = {Plasmids may carry genes coding for beneficial traits and thus contribute to adaptation of bacterial populations to environmental stress. Conjugative plasmids can horizontally transfer between cells, which a priori facilitates the spread of adaptive alleles. However, if the potential recipient cell is already colonized by another incompatible plasmid, successful transfer may be prevented. Competition between plasmids can thus limit horizontal transfer. Previous modeling has indeed shown that evolutionary rescue by a conjugative plasmid is hampered by incompatible resident plasmids in the population. If the rescue plasmid is a mutant variant of the resident plasmid, both plasmids transfer at the same rates. A high conjugation rate then has two, potentially opposing, effects - a direct positive effect on spread of the rescue plasmid and an increase in the fraction of resident plasmid cells. This raises the question whether a high conjugation rate always benefits evolutionary rescue. In this article, we systematically analyse three models of increasing complexity to disentangle the benefits and limits of increasing horizontal gene transfer in the presence of plasmid competition and plasmid costs. We find that the net effect can be positive or negative and that the optimal transfer rate is thus not always the highest one. These results can contribute to our understanding of the many facets of plasmid-driven adaptation and the wide range of transfer rates observed in nature.},
}

@article {pmid37923139,
year = {2023},
author = {Arriaza, RH and Abiskaroon, B and Patel, M and Daneshian, L and Kluza, A and Snoeck, S and Watkins, MB and Hopkins, J and Van Leeuwen, T and Grbic, M and Grbic, V and Borowski, T and Chruszcz, M},
title = {Structural and functional studies reveal the molecular basis of substrate promiscuity of a glycosyltransferase originating from a major agricultural pest.},
journal = {The Journal of biological chemistry},
volume = {},
number = {},
pages = {105421},
doi = {10.1016/j.jbc.2023.105421},
pmid = {37923139},
issn = {1083-351X},
abstract = {The two-spotted spider mite, Tetranychus urticae, is a major cosmopolitan pest that feeds on more than 1,100 plant species. Its genome contains an unprecedentedly large number of genes involved in detoxifying and transporting xenobiotics, including 80 genes that code for uridine diphosphate (UDP) glycosyltransferases (UGTs). These enzymes were acquired via horizontal gene transfer (HGT) from bacteria after loss in the Chelicerata lineage. UGTs are well-known for their role in phase II metabolism, however, their contribution to host adaptation and acaricide resistance in arthropods, such as T. urticae, is not yet resolved. TuUGT202A2 (Tetur22g00270) has been linked to the ability of this pest to adapt to tomato plants. Moreover, it was shown that this enzyme can glycosylate a wide range of flavonoids. To understand this relationship at the molecular level, structural, functional, and computational studies were performed. Structural studies provided specific snapshots of the enzyme in different catalytically relevant stages. The crystal structure of TuUGT202A2 in complex with UDP-glucose was obtained and site directed-mutagenesis paired with molecular dynamic simulations revealed a novel lid-like mechanism involved in the binding of the activated sugar donor. Two additional TuUGT202A2 crystal complexes, UDP-(S)-naringenin and UDP-naringin, demonstrated that this enzyme has a highly plastic and open-ended acceptor binding site. Overall, this work reveals the molecular basis of substrate promiscuity of TuUGT202A2 and provides novel insights into the structural mechanism of UGTs catalysis.},
}

@article {pmid37924893,
year = {2023},
author = {Stevenson, EM and Buckling, A and Cole, M and Lindeque, PK and Murray, AK},
title = {Selection for antimicrobial resistance in the plastisphere.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {168234},
doi = {10.1016/j.scitotenv.2023.168234},
pmid = {37924893},
issn = {1879-1026},
abstract = {Microplastics and antimicrobials are widespread contaminants that threaten global systems and frequently co-exist in the presence of human or animal pathogens. Whilst the impact of each of these contaminants has been studied in isolation, the influence of this co-occurrence in driving antimicrobial resistance (AMR)[1] in microplastic-adhered microbial communities, known as 'the Plastisphere', is not well understood. This review proposes the mechanisms by which interactions between antimicrobials and microplastics may drive selection for AMR in the Plastisphere. These include: 1) increased rates of horizontal gene transfer in the Plastisphere compared with free-living counterparts and natural substrate controls due to the proximity of cells, co-occurrence of environmental microplastics with AMR selective compounds and the sequestering of extracellular antibiotic resistance genes in the biofilm matrix. 2) An elevated AMR selection pressure in the Plastisphere due to the adsorbing of AMR selective or co-selective compounds to microplastics at concentrations greater than those found in surrounding mediums and potentially those adsorbed to comparator particles. 3) AMR selection pressure may be further elevated in the Plastisphere due to the incorporation of antimicrobial or AMR co-selective chemicals in the plastic matrix during manufacture. Implications for both ecological functioning and environmental risk assessments are discussed, alongside recommendations for further research.},
}

@article {pmid37917352,
year = {2023},
author = {Rekadwad, BN and Shouche, YS and Jangid, K},
title = {Investigation of tRNA-based relatedness within the Planctomycetes-Verrucomicrobia-Chlamydiae (PVC) superphylum: a comparative analysis.},
journal = {Archives of microbiology},
volume = {205},
number = {12},
pages = {366},
pmid = {37917352},
issn = {1432-072X},
support = {PDFSS-2013-14-ST-MAH-4350//University Grants Commission/ ; },
abstract = {The PVC superphylum is a diverse group of prokaryotes that require stringent growth conditions. RNA is a fascinating molecule to find evolutionary relatedness according to the RNA World Hypothesis. We conducted tRNA gene analysis to find evolutionary relationships in the PVC phyla. The analysis of genomic data (P = 9, V = 4, C = 8) revealed that the number of tRNA genes varied from 28 to 90 in Planctomycetes and Chlamydia, respectively. Verrucomicrobia has whole genomes and the longest scaffold (3 + 1), with tRNA genes ranging from 49 to 53 in whole genomes and 4 in the longest scaffold. Most tRNAs in the E. coli genome clustered with homologs, but approximately 43% clustered with tRNAs encoding different amino acids. Planctomyces, Akkermansia, Isosphaera, and Chlamydia were similar to E. coli tRNAs. In a phylum, tRNAs coding for different amino acids clustered at a range of 8 to 10%. Further analysis of these tRNAs showed sequence similarity with Cyanobacteria, Proteobacteria, Viridiplantae, Ascomycota and Basidiomycota (Eukaryota). This indicates the possibility of horizontal gene transfer or, otherwise, a different origin of tRNA in PVC bacteria. Hence, this work proves its importance for determining evolutionary relatedness and potentially identifying bacteria using tRNA. Thus, the analysis of these tRNAs indicates that primitive RNA may have served as the genetic material of LUCA before being replaced by DNA. A quantitative analysis is required to test these possibilities that relate the evolutionary significance of tRNA to the origin of life.},
}

@article {pmid37909761,
year = {2023},
author = {Xedzro, C and Shimamoto, T and Yu, L and Zuo, H and Sugawara, Y and Sugai, M and Shimamoto, T},
title = {Emergence of colistin-resistant Enterobacter cloacae and Raoultella ornithinolytica carrying the phosphoethanolamine transferase gene, mcr-9, derived from vegetables in Japan.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0106323},
doi = {10.1128/spectrum.01063-23},
pmid = {37909761},
issn = {2165-0497},
abstract = {Colistin, a last-line antimicrobial agent, is recommended for the treatment of severe infections caused by multidrug-resistant (MDR) microorganisms. However, reports on plasmid-mediated mobilized colistin resistance (mcr) genes have prompted the importance of routine colistin resistance surveillance. Herein, we report the emergence of Enterobacter cloacae CST17-2 and Raoultella ornithinolytica CST129-1 carrying an mcr-9.1 gene in vegetables from Japan. A total of 308 colistin-resistant isolates were retrieved from 200 fresh vegetables in Hiroshima Prefecture, Japan. PCR detection of mcr-1 to mcr-9 was conducted. While none of the isolates detected positive for mcr-1 to mcr-8 genes, we found two (0.65%) positive strains, E. cloacae CST17-2 and R. ornithinolytica CST129-1, that harbored mcr-9.1 allele. These isolates were subjected to phenotypic susceptibility testing, whole-genome sequencing (WGS), PCR-based replicon typing, and conjugation experiment. We found that both isolates had high colistin resistance [minimum inhibitory concentration (MIC) 16 or >64 µg/mL] and showed MDR phenotypes. WGS of both isolates revealed mcr-9 on a plasmid of the IncHI2/HI2A backbone. The mcr-9-bearing plasmid, pCST17-2_1, was self-transferable, although the pCST129-1_1 plasmid was not. Despite being colistin-resistant, the so-called two-component regulatory operon, qseBC, which induces polymyxin resistance, was absent from the genetic arrangements downstream of mcr-9 in R. ornithinolytica CST129-1. Nonetheless, a conjugation experiment demonstrated that mcr-9 in a Raoultella-type background is capable of mediating colistin resistance. In silico genomic analysis and comparison revealed distinct genetic structures surrounding mcr-9, especially in the downstream vicinities. The E. cloacae CST17-2 strain is of sequence-type ST738, a sequence type that has emerged in mcr-9.1-containing E. cloacae. Remarkably, we report the first mcr-9-carrying colistin-resistant Enterobacteriaceae isolated from Japanese vegetables, which is a grave public health concern. Our findings highlight the importance of strict epidemiological monitoring to track and/or prevent further dissemination of mcr homologs across the vegetable industry.IMPORTANCEPlasmid-mediated mobile colistin-resistance genes have been recognized as a global threat because they jeopardize the efficacy of colistin in therapeutic practice. Here, we described the genetic features of two mcr-9.1-carrying Gram-negative bacteria with a colistin-resistant phenotype derived from vegetables in Japan. The colistin-resistant mcr-9.1, which has never been detected in vegetables, was located on a large plasmid in Enterobacter cloacae CST17-2 and Raoultella ornithinolytica CST129-1, suggesting a high chance of horizontal gene transfer. To the best of our knowledge, this is the first report of mcr-9 in R. ornithinolytica. This study indicates that fresh vegetables might be a potential source for the transmission of mcr-9 genes encoding resistance to frontline (colistin) and clinically relevant antimicrobials. The study also provides additional consideration for colistin use and the relevance of routine surveillance in epidemiological perspective to curb the continuous spread of mcr alleles.},
}

@article {pmid37909043,
year = {2023},
author = {Subramanian, S and Bergland Drarvik, SM and Tinney, KR and Parent, KN},
title = {Cryo-EM structure of a Shigella podophage reveals a hybrid tail and novel decoration proteins.},
journal = {Structure (London, England : 1993)},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.str.2023.10.007},
pmid = {37909043},
issn = {1878-4186},
abstract = {There is a paucity of high-resolution structures of phages infecting Shigella, a human pathogen and a serious threat to global health. HRP29 is a Shigella podophage belonging to the Autographivirinae family, and has very low sequence identity to other known phages. Here, we resolved the structure of the entire HRP29 virion by cryo-EM. Phage HRP29 has a highly unusual tail that is a fusion of a T7-like tail tube and P22-like tailspikes mediated by interactions from a novel tailspike adaptor protein. Understanding phage tail structures is critical as they mediate hosts interactions. Furthermore, we show that the HRP29 capsid is stabilized by two novel, and essential decoration proteins, gp47 and gp48. Only one high resolution structure is currently available for Shigella podophages. The presence of a hybrid tail and an adapter protein suggests that it may be a product of horizontal gene transfer, and may be prevalent in other phages.},
}

@article {pmid37907163,
year = {2023},
author = {Su, X and Qian, F and Bao, Y},
title = {The effect of bulk-biochar and nano-biochar amendment on the removal of antibiotic resistance genes in microplastic contaminated soil.},
journal = {Environmental research},
volume = {},
number = {},
pages = {117488},
doi = {10.1016/j.envres.2023.117488},
pmid = {37907163},
issn = {1096-0953},
abstract = {Biochar amendment has significant benefits in removing antibiotic resistance genes (ARGs) in the soil. Nevertheless, there is little information on ARGs removal in microplastic contaminated soil. Herein, a 42-day soil microcosm experiment were carried out to study how two coconut shell biochars (bulk- and nano-size) eliminate soil ARGs with/without microplastic presence. The results showed that microplastic increased significantly the numbers and abundances of ARGs in soil at 14d of cultivation. And, two biochars amendment effectively inhibited soil ARGs spread whether or not microplastic was present, especially for nano-biochar which had more effective removal compared to bulk-biochar. However, microplastic weakened soil ARGs removal after applying same biochar. Two biochars removed ARGs through decreasing horizontal gene transfer (HGT) of ARGs, potential host-bacteria abundances, some bacteria crowding the eco-niche of hosts and promoting soil properties. The adverse effect of microplastic on ARGs removal was mainly caused by weakening mobile genetic elements (MGEs) removal, and by changing soil properties. Structural equation modeling (SEM) analysis indicated that biochar's effect on ARGs profile was changed by its size and microplastic presence through altering MGEs abundances. These results highlight that biochar amendment is still an effective method for ARGs removal in microplastic contaminated soil.},
}

@article {pmid37902330,
year = {2023},
author = {Benigno, V and Carraro, N and Sarton-Lohéac, G and Romano-Bertrand, S and Blanc, DS and van der Meer, JR},
title = {Diversity and evolution of an abundant ICEclc family of integrative and conjugative elements in Pseudomonas aeruginosa.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0051723},
doi = {10.1128/msphere.00517-23},
pmid = {37902330},
issn = {2379-5042},
abstract = {Integrative and conjugative elements (ICEs) are widespread autonomous mobile DNA elements, containing the genes necessary for their excision, conjugative transfer, and insertion into a new host cell. ICEs can carry additional genes that are non-essential for their transfer but can confer adaptive phenotypes to the host. Our aim here was to better characterize the presence, distribution, and variation of ICEs related to the well-described ICEclc among Pseudomonas aeruginosa clinical isolates within a geographically restrained environment to understand the factors contributing to their evolution. We examined a total of 181 P. aeruginosa genome sequences obtained from patient or hospital environment isolates, most of which were obtained from a single hospital during 20 years of sampling. More than 90% of the isolates carried one or more ICEclc-like elements, with different degrees of conservation to the known ICEclc lifestyle and transfer genes. ICE clones closely matched their host clonal phylogeny, but not exclusively, indicating that both clonal evolution and ICE horizontal transfer are occurring in the hospital environment. ICEs from this singular hospital environment were mainly associated to three clone types found worldwide, suggesting an enrichment of local clones. Variable gene regions among the clinical P. aeruginosa ICEclc-type elements were notably enriched for heavy metal resistance genes, toxin-anti-toxin systems, potential efflux systems and multidrug resistance proteins, a metalloprotease and for a variety of regulatory systems, but not for specific recognizable antibiotic-resistance cassettes. Clonal persistence suggests adaptive benefits of these functional categories, and micro-patterns of gene gain and loss indicate ongoing ICE evolution within the P. aeruginosa hosts. IMPORTANCE Microbial populations swiftly adapt to changing environments through horizontal gene transfer. While the mechanisms of gene transfer are well known, the impact of environmental conditions on the selection of transferred gene functions remains less clear. We investigated ICEs, specifically the ICEclc-type, in Pseudomonas aeruginosa clinical isolates. Our findings revealed co-evolution between ICEs and their hosts, with ICE transfers occurring within strains. Gene functions carried by ICEs are positively selected, including potential virulence factors and heavy metal resistance. Comparison to publicly available P. aeruginosa genomes unveiled widespread antibiotic-resistance determinants within ICEclc clades. Thus, the ubiquitous ICEclc family significantly contributes to P. aeruginosa's adaptation and fitness in diverse environments.},
}

@article {pmid37901845,
year = {2023},
author = {Li, L and Zhang, H and Meng, D and Yin, H},
title = {Transcriptomics of Lactobacillus paracasei: metabolism patterns and cellular responses under high-density culture conditions.},
journal = {Frontiers in bioengineering and biotechnology},
volume = {11},
number = {},
pages = {1274020},
pmid = {37901845},
issn = {2296-4185},
abstract = {Lactobacillus paracasei has significant potential for development and application in the environmental field, particularly in addressing malodor pollution. This study aims to investigate the cellular response of L. paracasei B1 under high-density culture conditions. The selected strain has previously shown effective deodorizing and bacteriostatic abilities. Transcriptomics techniques are employed to dissect the nutrient metabolism pattern of L. paracasei B1 and its response mechanism under environmental stress. The study characterizes the functions of key differentially expressed genes during growth before and after optimizing the culture conditions. The optimization of fermentation culture conditions provides a suitable growth environment for L. paracasei B1, inducing an enhancement of its phosphotransferase system for sugar source uptake and maintaining high levels of glycolysis and pyruvate metabolism. Consequently, the strain is able to grow and multiply rapidly. Under acid stress conditions, glycolysis and pyruvate metabolism are inhibited, and L. paracasei B1 generates additional energy through aerobic respiration to meet the energy demand. The two-component system and quorum sensing play roles in the response and regulation of L. paracasei B1 to adverse environments. The strain mitigates oxygen stress damage through glutathione metabolism, cysteine and methionine metabolism, base excision repair, and purine and pyrimidine metabolism. Additionally, the strain enhances lysine synthesis, the alanine, aspartate, and glutamate metabolic pathways, and relies on the ABC transport system to accumulate amino acid-compatible solutes to counteract acid stress and osmotic stress during pH regulation. These findings establish a theoretical basis for the further development and application of L. paracasei B1 for its productive properties.},
}

@article {pmid37900760,
year = {2023},
author = {Yan, XM and Zhou, SS and Liu, H and Zhao, SW and Tian, XC and Shi, TL and Bao, YT and Li, ZC and Jia, KH and Nie, S and Guo, JF and Kong, L and Porth, IM and Mao, JF},
title = {Unraveling the evolutionary dynamics of the TPS gene family in land plants.},
journal = {Frontiers in plant science},
volume = {14},
number = {},
pages = {1273648},
pmid = {37900760},
issn = {1664-462X},
abstract = {Terpenes and terpenoids are key natural compounds for plant defense, development, and composition of plant oil. The synthesis and accumulation of a myriad of volatile terpenoid compounds in these plants may dramatically alter the quality and flavor of the oils, which provide great commercial utilization value for oil-producing plants. Terpene synthases (TPSs) are important enzymes responsible for terpenic diversity. Investigating the differentiation of the TPS gene family could provide valuable theoretical support for the genetic improvement of oil-producing plants. While the origin and function of TPS genes have been extensively studied, the exact origin of the initial gene fusion event - it occurred in plants or microbes - remains uncertain. Furthermore, a comprehensive exploration of the TPS gene differentiation is still pending. Here, phylogenetic analysis revealed that the fusion of the TPS gene likely occurred in the ancestor of land plants, following the acquisition of individual C- and N- terminal domains. Potential mutual transfer of TPS genes was observed among microbes and plants. Gene synteny analysis disclosed a differential divergence pattern between TPS-c and TPS-e/f subfamilies involved in primary metabolism and those (TPS-a/b/d/g/h subfamilies) crucial for secondary metabolites. Biosynthetic gene clusters (BGCs) analysis suggested a correlation between lineage divergence and potential natural selection in structuring terpene diversities. This study provides fresh perspectives on the origin and evolution of the TPS gene family.},
}

@article {pmid37898203,
year = {2023},
author = {Jian, J and Wu, Z and Silva-Núñez, A and Li, X and Zheng, X and Luo, B and Liu, Y and Fang, X and Workman, CT and Larsen, TO and Hansen, PJ and Sonnenschein, EC},
title = {Long-read genome sequencing provides novel insights into the harmful algal bloom species Prymnesium parvum.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {168042},
doi = {10.1016/j.scitotenv.2023.168042},
pmid = {37898203},
issn = {1879-1026},
abstract = {Prymnesium parvum is a toxin-producing haptophyte that causes harmful algal blooms worldwide, which are often associated with massive fish-kills and subsequent economic losses. In here, we present nuclear and plastid genome assemblies using PacBio HiFi long reads and DNBseq short reads for the two P. parvum strains UTEX 2797 and CCMP 3037, representing producers of type A prymnesins. Our results show that the P. parvum strains have a moderate haptophyte genome size of 97.56 and 107.32 Mb. The genome assemblies present one of highest contiguous assembled contig sequences to date consisting of 463 and 362 contigs with a contig N50 of 596.99 kb and 968.39 kb for strain UTEX 2797 and CCMP 3037, respectively. The assembled contigs of UTEX 2797 and CCMP 3037 were anchored to 34 scaffolds, with a scaffold N50 of 5.35 Mb and 3.61 Mb, respectively, accounting for 93.2 % and 97.9 % of the total length. Each plastid genome comprises a circular contig. A total of 20,578 and 19,426 protein-coding genes were annotated for UTEX 2797 and CCMP 3037. The expanded gene family analysis showed that starch and sucrose metabolism, sulfur metabolism, energy metabolism and ABC transporters are involved in the evolution of P. parvum. Polyketide synthase (PKSs) genes responsible for the production of secondary metabolites such as prymnesins displayed different expression patterns under nutrient limitation. Repeat expanded and horizontal gene transfer may be two contributing factors to the high number of PKS genes found in this species. The two high quality P. parvum genomes will serve as valuable resources for ecological, genetic, and toxicological studies of haptophytes that can be used to monitor and potentially manage harmful blooms of ichthyotoxic P. parvum in the future.},
}

@article {pmid37873201,
year = {2023},
author = {Attah, V and Milner, DS and Fang, Y and Yan, X and Leonard, G and Heitman, J and Talbot, NJ and Richards, TA},
title = {Duplication and neofunctionalization of a horizontally-transferred xyloglucanase as a facet of the red queen co-evolutionary dynamic.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {37873201},
support = {R01 AI039115/AI/NIAID NIH HHS/United States ; },
abstract = {UNLABELLED: Oomycetes are heterotrophic protists that share phenotypic similarities with fungi, including the ability to cause plant diseases, but branch in a separate and distant region of the eukaryotic tree of life. It has been suggested that multiple horizontal gene transfers (HGTs) from fungi-to-oomycetes contributed to the evolution of plant-pathogenic traits. These HGTs are predicted to include secreted proteins that degrade plant cell walls. This is a key trait in the pathology of many oomycetes, as the plant cell wall represents a primary barrier to pathogen invasion and a rich source of carbohydrates. Many of the HGT gene families identified have undergone multiple rounds of duplication. Using a combination of phylogenomic analysis and functional assays, we investigate the diversification of a horizontally-transferred xyloglucanase gene family in the model oomycete species Phytophthora sojae. Our analyses detect 11 genes retained in P. sojae among a complex pattern of gene duplications and losses. Using a phenotype assay, based on heterologous expression in yeast, we show that eight of these paralogs have xyloglucanase function, including variants with distinct protein characteristics, such as a long-disordered C-terminal extension that can increase xyloglucanase activity. The functional xyloglucanase variants analysed subtend an ancestral node close to the fungi-oomycetes gene transfer, suggesting the horizontally-transferred gene was a bona fide xyloglucanase. Expression of xyloglucanase paralogs in Nicotiana benthamiana triggers distinct patterns of reactive oxygen species (ROS) generation, demonstrating that enzyme variants differentially stimulate pattern-triggered immunity in plants. Mass spectrometry of detectable enzymatic products demonstrates that some paralogs catalyze production of variant breakdown profiles, suggesting that secretion of multiple xyloglucanase variants increases efficiency of xyloglucan breakdown, as well as potentially diversifying the range of Damage-Associated Molecular Patterns (DAMPs) released during pathogen attack. We suggest that such patterns of protein neofunctionalization, and variant host responses, represent an aspect of the Red Queen host-pathogen co-evolutionary dynamic.

SIGNIFICANCE STATEMENT: The oomycetes are a diverse group of eukaryotic microbes that include some of the most devastating pathogens of plants. Oomycetes perceive, invade, and colonize plants in similar ways to fungi, in part because they acquired the genes to attack and feed on plants from fungi. These genes are predicted to be useful to oomycete plant pathogens because they have undergone multiple rounds of gene duplication. One key enzyme for attacking plant cell wall structures is called xyloglucanase. Xyloglucanase in the oomycetes has undergone multiple rounds of gene duplication, leading to variants including an enzyme with a C-terminal extension that increases activity. Some xyloglucanase variants trigger unique patterns of reactive oxygen species (ROS) in planta, and generate different profiles of cell wall breakdown products - such outcomes could act to mystify and increase the workload of the plant immune system, allowing successful pathogens to proliferate.},
}

@article {pmid37894729,
year = {2023},
author = {Bravo, A and Moreno-Blanco, A and Espinosa, M},
title = {One Earth: The Equilibrium between the Human and the Bacterial Worlds.},
journal = {International journal of molecular sciences},
volume = {24},
number = {20},
pages = {},
pmid = {37894729},
issn = {1422-0067},
support = {PID2019-104553RB-C21//Spanish Ministry of Science and Innovation (MCIN/AEI/10.13039/501100011033)/ ; },
abstract = {Misuse and abuse of antibiotics on humans, cattle, and crops have led to the selection of multi-resistant pathogenic bacteria, the most feared 'superbugs'. Infections caused by superbugs are progressively difficult to treat, with a subsequent increase in lethality: the toll on human lives is predicted to reach 10 million by 2050. Here we review three concepts linked to the growing resistance to antibiotics, namely (i) the Resistome, which refers to the collection of bacterial genes that confer resistance to antibiotics, (ii) the Mobilome, which includes all the mobile genetic elements that participate in the spreading of antibiotic resistance among bacteria by horizontal gene transfer processes, and (iii) the Nichome, which refers to the set of genes that are expressed when bacteria try to colonize new niches. We also discuss the strategies that can be used to tackle bacterial infections and propose an entente cordiale with the bacterial world so that instead of war and destruction of the 'fierce enemy' we can achieve a peaceful coexistence (the One Earth concept) between the human and the bacterial worlds. This, in turn, will contribute to microbial biodiversity, which is crucial in a globally changing climate due to anthropogenic activities.},
}

@article {pmid37894082,
year = {2023},
author = {Anton, BP and Roberts, RJ},
title = {A Survey of Archaeal Restriction-Modification Systems.},
journal = {Microorganisms},
volume = {11},
number = {10},
pages = {},
doi = {10.3390/microorganisms11102424},
pmid = {37894082},
issn = {2076-2607},
abstract = {When compared with bacteria, relatively little is known about the restriction-modification (RM) systems of archaea, particularly those in taxa outside of the haloarchaea. To improve our understanding of archaeal RM systems, we surveyed REBASE, the restriction enzyme database, to catalog what is known about the genes and activities present in the 519 completely sequenced archaeal genomes currently deposited there. For 49 (9.4%) of these genomes, we also have methylome data from Single-Molecule Real-Time (SMRT) sequencing that reveal the target recognition sites of the active m[6]A and m[4]C DNA methyltransferases (MTases). The gene-finding pipeline employed by REBASE is trained primarily on bacterial examples and so will look for similar genes in archaea. Nonetheless, the organizational structure and protein sequence of RM systems from archaea are highly similar to those of bacteria, with both groups acquiring systems from a shared genetic pool through horizontal gene transfer. As in bacteria, we observe numerous examples of "persistent" DNA MTases conserved within archaeal taxa at different levels. We experimentally validated two homologous members of one of the largest "persistent" MTase groups, revealing that methylation of C(m[5]C)WGG sites may play a key epigenetic role in Crenarchaea. Throughout the archaea, genes encoding m[6]A, m[4]C, and m[5]C DNA MTases, respectively, occur in approximately the ratio 4:2:1.},
}

@article {pmid37888586,
year = {2023},
author = {Ortega-Balleza, JL and Guerrero, A and Castro-Escarpulli, G and Martínez-Vázquez, AV and Cruz-Hernández, MA and Luna-Santillana, EJ and Acosta-Cruz, E and Rodríguez-Sánchez, IP and Rivera, G and Bocanegra-García, V},
title = {Genomic Analysis of Multidrug-Resistant Escherichia coli Strains Isolated in Tamaulipas, Mexico.},
journal = {Tropical medicine and infectious disease},
volume = {8},
number = {10},
pages = {},
pmid = {37888586},
issn = {2414-6366},
abstract = {The global spread of antimicrobial resistance genes (ARGs) is a major public health concern. Mobile genetic elements (MGEs) are the main drivers of this spread by horizontal gene transfer (HGT). Escherichia coli is widespread in various environments and serves as an indicator for monitoring antimicrobial resistance (AMR). Therefore, the objective of this work was to evaluate the whole genome of multidrug-resistant E. coli strains isolated from human clinical, animal, and environmental sources. Four E. coli strains previously isolated from human urine (n = 2), retail meat (n = 1), and water from the Rio Grande River (n = 1) collected in northern Tamaulipas, Mexico, were analyzed. E. coli strains were evaluated for antimicrobial susceptibility, followed by whole genome sequencing and bioinformatic analysis. Several ARGs were detected, including blaCTX-M-15, blaOXA-1, blaTEM-1B, blaCMY-2, qnrB, catB3, sul2, and sul3. Additionally, plasmid replicons (IncFIA, IncFIB, IncFII, IncY, IncR, and Col) and intact prophages were also found. Insertion sequences (ISs) were structurally linked with resistance and virulence genes. Finally, these findings indicate that E. coli strains have a large repertoire of resistance determinants, highlighting a high pathogenic potential and the need to monitor them.},
}

@article {pmid37887056,
year = {2023},
author = {Sandmann, G},
title = {Genes and Pathway Reactions Related to Carotenoid Biosynthesis in Purple Bacteria.},
journal = {Biology},
volume = {12},
number = {10},
pages = {},
doi = {10.3390/biology12101346},
pmid = {37887056},
issn = {2079-7737},
abstract = {In purple bacteria, the genes of the carotenoid pathways are part of photosynthesis gene clusters which were distributed among different species by horizontal gene transfer. Their close organisation facilitated the first-time cloning of carotenogenic genes and promoted the molecular investigation of spheroidene and spirilloxanthin biosynthesis. This review highlights the cloning of the spheroidene and spirilloxanthin pathway genes and presents the current knowledge on the enzymes involved in the carotenoid biosynthesis of purple sulphur and non-sulphur bacteria. Mostly, spheroidene or spirilloxanthin biosynthesis exists in purple non-sulphur bacteria but both pathways operate simultaneously in Rubrivivax gelatinosus. In the following years, genes from other bacteria including purple sulphur bacteria with an okenone pathway were cloned. The individual steps were investigated by kinetic studies with heterologously expressed pathway genes which supported the establishment of the reaction mechanisms. In particular, the substrate and product specificities revealed the sequential order of the speroidene and spiriloxanthin pathways as well as their interactions. Information on the enzymes involved revealed that the phytoene desaturase determines the type of pathway by the formation of different products. By selection of mutants with amino acid exchanges in the putative substrate-binding site, the neurosporene-forming phytoene desaturase could be changed into a lycopene-producing enzyme and vice versa. Concerning the oxygen groups in neurosporene and lycopene, the tertiary alcohol group at C1 is formed from water and not by oxygenation, and the C2 or C4 keto groups are inserted differently by an oxygen-dependent or oxygen-independent ketolation reaction, respectively.},
}

@article {pmid37886666,
year = {2023},
author = {Arbé-Carton, K and Rey-Sogo, A and Santos-Fernández, N and Altube, O and Garbisu, C and Arana, L and Alkorta, I},
title = {Development of a high-throughput platform to measure plasmid transfer frequency.},
journal = {Frontiers in cellular and infection microbiology},
volume = {13},
number = {},
pages = {1269732},
pmid = {37886666},
issn = {2235-2988},
abstract = {Antibiotic resistance represents one of the greatest threats to global health. The spread of antibiotic resistance genes among bacteria occurs mostly through horizontal gene transfer via conjugation mediated by plasmids. This process implies a direct contact between a donor and a recipient bacterium which acquires the antibiotic resistance genes encoded by the plasmid and, concomitantly, the capacity to transfer the acquired plasmid to a new recipient. Classical assays for the measurement of plasmid transfer frequency (i.e., conjugation frequency) are often characterized by a high variability and, hence, they require many biological and technical replicates to reduce such variability and the accompanying uncertainty. In addition, classical conjugation assays are commonly tedious and time-consuming because they typically involve counting colonies on a large number of plates for the quantification of donors, recipients, and transconjugants (i.e., the bacteria that have received the genetic material by conjugation). Due to the magnitude of the antibiotic resistance problem, it is critical to develop reliable and rapid methods for the quantification of plasmid transfer frequency that allow the simultaneous analysis of many samples. Here, we present the development of a high-throughput, reliable, quick, easy, and cost-effective method to simultaneously accomplish and measure multiple conjugation events in 96-well plates, in which the quantification of donors, recipients, and transconjugants is estimated from the time required to reach a specific threshold value (OD600 value) in the bacterial growth curves. Our method successfully discriminates different plasmid transfer frequencies, yielding results that are equivalent to those obtained by a classical conjugation assay.},
}

@article {pmid37884245,
year = {2023},
author = {Zhang, Z and Li, B and Chai, Z and Yang, Z and Zhang, F and Kang, F and Ren, H and Jin, Y and Yue, J},
title = {Evolution of the ability to evade host innate immune defense by Talaromyces marneffei.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {127597},
doi = {10.1016/j.ijbiomac.2023.127597},
pmid = {37884245},
issn = {1879-0003},
abstract = {Talaromyces (Penicillium) marneffei is an intracellular pathogenic fungus. Some strains of this fungus have been misidentified due to the similarity between Talaromyces and Penicillium. T. marneffei has mainly been found to afflict immunocompromised individuals, causing respiratory, skin, and systemic mycosis. Mp1p is a key virulence factor that can help T. marneffei evade clearance by the normally functioning immune system. Understanding how novel functions arise is an intriguing question in many fields of biology. Mp1p has two homologous domains (Mp1p-LBD1 and Mp1p-LBD2). Sequence similarity searches with Mp1p-LBD sequences revealed Mp1p homologs in many other pathogenic fungi. Integrated information on the taxonomic distribution, phylogenetic relationships, and sequence similarity of Mp1p domains revealed that the ancestor of Mp1p-LBDs was acquired through horizontal gene transfer (HGT). Additional evidence revealed that Mp1p homologs have undergone extensive gene duplications in T. marneffei. Mp1p might be a result of gene fusion following gene duplication. Furthermore, we propose a new method for identifying Talaromyces and identify 4 strains with misclassification errors. Our results characterize the evolutionary mechanism of T. marneffei evasion of host innate immune defense and clearly demonstrate the role of gene duplication and HGT in the evolution of host immune escape by T. marneffei.},
}

@article {pmid37883987,
year = {2023},
author = {Parthasarathy, R and Wakefield, D and Santiago, FS and Kaakoush, NO and Tedla, N},
title = {Horizontal gene transfer and endogenous retroviruses as mechanisms for molecular mimicry.},
journal = {The Lancet. Microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/S2666-5247(23)00316-6},
pmid = {37883987},
issn = {2666-5247},
}

@article {pmid37882558,
year = {2023},
author = {Marti, H and Biggel, M and Shima, K and Onorini, D and Rupp, J and Charette, SJ and Borel, N},
title = {Chlamydia suis displays high transformation capacity with complete cloning vector integration into the chromosomal rrn-nqrF plasticity zone.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0237823},
doi = {10.1128/spectrum.02378-23},
pmid = {37882558},
issn = {2165-0497},
abstract = {Chlamydia, comprising several human and zoonotic pathogens, is a genus of the conserved bacterial phylum Chlamydiota. Their obligate intracellular niche serves as a barrier for natural genetic exchange via horizontal gene transfer (HGT), and further limits the development and application of genetic tools. To date, the only example for recent inter-phylum HGT among the Chlamydiota is tetracycline resistance in the potentially zoonotic species Chlamydia suis, a close phylogenetic relative of human C. trachomatis, which causes bacterial sexually transmitted infections and ocular trachoma. Tetracycline resistance in porcine C. suis strains has been described worldwide and is always part of a genomic island dividing invasin (inv), located within a chromosomal region between the rRNA operon (rrn) and the nqrF reductase. Here, we aimed to expand the still modest number of available genetic manipulation systems for Chlamydia by generating allele-replacement and integration vectors for C. suis. These vectors comprised homologous C. suis sequences of the chromosomal region of interest, an E. coli origin of replication (ori) and selection markers but lacked the native chlamydial plasmids or its ori. We first recovered allele-replacement mutants using a vector that targets the tryptophan (trp) operon of C. suis. The vector was further successfully maintained as a free plasmid in C. trachomatis without allele replacement, suggesting complex plasmid dynamics in the absence of a chlamydial ori. Moreover, we showed that the hypervariable rrn-nqrF intergenic region of C. suis is highly susceptible to transformation, resulting in complete vector integration upstream of nqrF without interruption of the targeted inv gene.IMPORTANCEThe obligate intracellular Chlamydia genus contains many pathogens with a negative impact on global health and economy. Despite recent progress, there is still a lack of genetic tools limiting our understanding of these complex bacteria. This study provides new insights into genetic manipulation of Chlamydia with the opportunistic porcine pathogen Chlamydia suis, the only chlamydial species naturally harboring an antibiotic resistance gene, originally obtained by horizontal gene transfer. C. suis is transmissible to humans, posing a potential public health concern. We report that C. suis can take up vectors that lack the native plasmid, a requirement for most chlamydial transformation systems described to date. Additionally, we show that C. trachomatis, the most common cause for bacterial sexually transmitted infections and infectious blindness worldwide, can be transformed with C. suis vectors. Finally, the chromosomal region that harbors the resistance gene of C. suis is highly susceptible to complete vector integration.},
}

@article {pmid37880110,
year = {2023},
author = {Tanaka, E and Wajima, T and Ota, R and Uchiya, KI},
title = {The association between transformation ability and antimicrobial resistant potential in Haemophilus influenzae.},
journal = {Biological & pharmaceutical bulletin},
volume = {},
number = {},
pages = {},
doi = {10.1248/bpb.b23-00583},
pmid = {37880110},
issn = {1347-5215},
abstract = {The prevalence of quinolone low-susceptible H. influenzae has increased in Japan. Low quinolone susceptibility is caused by point mutations in target genes; however, it can also be caused by horizontal gene transfer via natural transformation. In this study, we examined whether this horizontal gene transfer could be associated with resistance to not only quinolones but also other antimicrobial agents. Horizontal transfer ability was quantified using the experimental transfer assay method for low quinolone susceptibility. Further, the association between horizontal transfer ability and resistance to β-lactams, the first-choice drugs for H. influenzae infection, was investigated. The transformation efficiency of 50 clinical isolates varied widely, ranging from 10[2] to 10[6] CFU of the colonies obtained by horizontal transfer assay. Efficiency was associated with β-lactam resistance caused by ftsI mutations, indicating that strains with high horizontal transfer ability acquired quinolone low-susceptibility as well as β-lactam resistance more easily. Strains with high transformation efficiency increased the transcript level of comA, suggesting that enhanced com operon was associated with a high DNA uptake ability. Overall, this study revealed that the transformation ability of H. influenzae was associated with multiple antimicrobial resistance. Increase in the number of strains with high horizontal transformation ability has raised concerns regarding the rapid spread of antimicrobial-resistant H. influenzae.},
}

@article {pmid37796811,
year = {2023},
author = {Teixeira, M and Pillay, S and Urhan, A and Abeel, T},
title = {SHIP: identifying antimicrobial resistance gene transfer between plasmids.},
journal = {Bioinformatics (Oxford, England)},
volume = {39},
number = {10},
pages = {},
pmid = {37796811},
issn = {1367-4811},
support = {120192//National Research Foundation of South Africa/ ; },
mesh = {*Anti-Bacterial Agents/pharmacology ; Phylogeny ; *Drug Resistance, Bacterial/genetics ; Plasmids/genetics ; Escherichia coli/genetics ; Integrons/genetics ; Gene Transfer, Horizontal ; },
abstract = {MOTIVATION: Plasmids are carriers for antimicrobial resistance (AMR) genes and can exchange genetic material with other structures, contributing to the spread of AMR. There is no reliable approach to identify the transfer of AMR genes across plasmids. This is mainly due to the absence of a method to assess the phylogenetic distance of plasmids, as they show large DNA sequence variability. Identifying and quantifying such transfer can provide novel insight into the role of small mobile elements and resistant plasmid regions in the spread of AMR.

RESULTS: We developed SHIP, a novel method to quantify plasmid similarity based on the dynamics of plasmid evolution. This allowed us to find conserved fragments containing AMR genes in structurally different and phylogenetically distant plasmids, which is evidence for lateral transfer. Our results show that regions carrying AMR genes are highly mobilizable between plasmids through transposons, integrons, and recombination events, and contribute to the spread of AMR. Identified transferred fragments include a multi-resistant complex class 1 integron in Escherichia coli and Klebsiella pneumoniae, and a region encoding tetracycline resistance transferred through recombination in Enterococcus faecalis.

The code developed in this work is available at https://github.com/AbeelLab/plasmidHGT.},
}

*Anti-Bacterial Agents/pharmacology
Phylogeny
*Drug Resistance, Bacterial/genetics
Plasmids/genetics
Escherichia coli/genetics
Integrons/genetics
Gene Transfer, Horizontal

@article {pmid37875161,
year = {2023},
author = {Ribes-Navarro, A and Kabeya, N and Castro, LFC and Gomes-Dos-Santos, A and Fonseca, MM and Alberts-Hubatsch, H and Hontoria, F and Navarro, JC and Monroig, Ó},
title = {Examination of gammarid transcriptomes reveals a widespread occurrence of key metabolic genes from epibiont bdelloid rotifers in freshwater species.},
journal = {Open biology},
volume = {13},
number = {10},
pages = {230196},
doi = {10.1098/rsob.230196},
pmid = {37875161},
issn = {2046-2441},
abstract = {Previous data revealed the unexpected presence of genes encoding for long-chain polyunsaturated fatty acid (LC-PUFA) biosynthetic enzymes in transcriptomes from freshwater gammarids but not in marine species, even though closely related species were compared. This study aimed to clarify the origin and occurrence of selected LC-PUFA biosynthesis gene markers across all published gammarid transcriptomes. Through systematic searches, we confirmed the widespread occurrence of sequences from seven elongases and desaturases involved in LC-PUFA biosynthesis, in transcriptomes from freshwater gammarids but not marine species, and clarified that such occurrence is independent from the gammarid species and geographical origin. The phylogenetic analysis established that the retrieved elongase and desaturase sequences were closely related to bdelloid rotifers, confirming that multiple transcriptomes from freshwater gammarids contain contaminating rotifers' genetic material. Using the Adineta steineri genome, we investigated the genomic location and exon-intron organization of the elongase and desaturase genes, establishing they are all genome-anchored and, importantly, identifying instances of horizontal gene transfer. Finally, we provide compelling evidence demonstrating Bdelloidea desaturases and elongases enable these organisms to perform all the reactions for de novo biosynthesis of PUFA and, from them, LC-PUFA, an advantageous trait when considering the low abundance of these essential nutrients in freshwater environments.},
}

@article {pmid37875024,
year = {2023},
author = {Wang, X and Qin, J and Xiang, G and Wang, C and Wang, Q and Qin, J and Wang, H and Shen, Z},
title = {Nosocomial dissemination of blaIMP-4 among Klebsiella pneumoniae by horizontal gene transfer and clonal spread: the epidemic IncN plasmids and the emerging high-risk IMP-4-producing ST101 clone.},
journal = {The Journal of antimicrobial chemotherapy},
volume = {},
number = {},
pages = {},
doi = {10.1093/jac/dkad326},
pmid = {37875024},
issn = {1460-2091},
support = {82272374//National Natural Science Foundation of China/ ; 22PJ1409600//Shanghai Pujiang Program/ ; RJTJ22-MS-018//Renji Hospital/ ; },
abstract = {OBJECTIVES: To determine the genomic features of IMP-4-producing Klebsiella pneumoniae isolates recovered from paediatric patients and the transmission dynamics of blaIMP-4.

METHODS: IMP-producing K. pneumoniae isolates were collected from paediatric patients in Shanghai Children's Medical Center from 2013 to 2020. WGS was performed for all isolates, and the complete genomes of three IMP-4-producing isolates were generated. The distribution of blaIMP-4-harbouring plasmids was determined, and a conjugation assay was employed to investigate the horizontal transfer of blaIMP-4-harbouring plasmids.

RESULTS: We collected 21 blaIMP-carrying K. pneumoniae isolates, with IMP-4 (16/21, 76.2%) as the predominant subtype, followed by IMP-8 (n = 3) and IMP-26 (n = 2). IMP-4-producing isolates displayed a diverse population structure and all blaIMP-4 genes were located on plasmids, including IncN (n = 9), IncHI5 (n = 5), IncFII(K) (n = 1) and IncFII(pKP91) (n = 1), although only IncN plasmids were conjugative. Clonal transmission of ST101 strains carrying IncHI5 blaIMP-4-harbouring plasmids was observed, and the acquisition of blaIMP-4 by the international high-risk ST101 clone constituted a novel combination of ST101 clone and carbapenemase genes. Plasmid analysis demonstrated that the conjugal transfer of the IncHI5 blaIMP-4-harbouring plasmid might be blocked by the ST101 bacterial host.

CONCLUSIONS: The horizontal transfer of IncN plasmids and clonal spread of the international high-risk ST101 clone facilitated the nosocomial dissemination of blaIMP-4 among K. pneumoniae. The emerging IMP-4-producing ST101 clone displays diverse combinations of carbapenemase genes, and this clone could be a continually evolving threat and warrants prospective monitoring.},
}

@article {pmid37873187,
year = {2023},
author = {Hamrick, GS and Maddamsetti, R and Son, HI and Wilson, ML and Davis, HM and You, L},
title = {Programming dynamic division of labor using horizontal gene transfer.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2023.10.03.560696},
pmid = {37873187},
abstract = {The metabolic engineering of microbes has broad applications, including in biomanufacturing, bioprocessing, and environmental remediation. The introduction of a complex, multi-step pathway often imposes a substantial metabolic burden on the host cell, restraining the accumulation of productive biomass and limiting pathway efficiency. One strategy to alleviate metabolic burden is division of labor (DOL), in which different subpopulations carry out different parts of the pathway and work together to convert a substrate into a final product. However, the maintenance of different engineered subpopulations is challenging due to competition and convoluted inter-strain population dynamics. Through modeling, we show that dynamic division of labor (DDOL) mediated by horizontal gene transfer (HGT) can overcome these limitations and enable the robust maintenance of burdensome, multi-step pathways. We also use plasmid genomics to uncover evidence that DDOL is a strategy utilized by natural microbial communities. Our work suggests that bioengineers can harness HGT to stabilize synthetic metabolic pathways in microbial communities, enabling the development of robust engineered systems for deployment in a variety of contexts.},
}

@article {pmid37871361,
year = {2023},
author = {Moussa, J and Nassour, E and Tahan, E and El Chaar, M and Jisr, T and Tokajian, S},
title = {Carbapenem resistance determinants and their transmissibility among clinically isolated Enterobacterales in Lebanon.},
journal = {Journal of infection and public health},
volume = {16},
number = {12},
pages = {1947-1953},
doi = {10.1016/j.jiph.2023.10.003},
pmid = {37871361},
issn = {1876-035X},
abstract = {BACKGROUND: The occurrence of carbapenem-resistant bacterial infections has increased significantly over the years with Gram-negative bacteria exhibiting the broadest resistance range. In this study we aimed to investigate the genomic characteristics of clinical carbapenem-resistant Enterobacterales (CRE).

METHODS: Seventeen representative multi-drug resistant (MDR) isolates from a hospital setting showing high level of resistance to carbapenems (ertapenem, meropenem and imipenem) were chosen for further characterization through whole-genome sequencing. Resistance mechanisms and transferability of plasmids carrying carbapenemase-encoding genes were also determined in silico and through conjugative mating assays.

RESULTS: We detected 18 different β-lactamases, including four carbapenemases (blaNDM-1, blaNDM-5, blaNDM-7, blaOXA-48) on plasmids with different Inc groups. The combined results from PBRT and in silico replicon typing revealed 20 different replicons linked to plasmids ranging in size between 80 and 200 kb. The most prevalent Inc groups were IncFIB(K) and IncM. OXA-48, detected on 76-kb IncM1 conjugable plasmid, was the most common carbapenemase. We also detected other conjugative plasmids with different carbapenemases confirming the role of horizontal gene transfer in the dissemination of antimicrobial resistance genes.

CONCLUSION: Our findings verified the continuing spread of carbapenemases in Enterobacterales and revealed the types of mobile elements circulating in a hospital setting and contributing to the spread of resistance determinants. The occurrence and transmission of plasmids carrying carbapenemase-encoding genes call for strengthening active surveillance and prevention efforts to control antimicrobial resistance dissemination in healthcare settings.},
}

@article {pmid37870180,
year = {2023},
author = {Zhang, Q and Xu, N and Lei, C and Chen, B and Wang, T and Ma, Y and Lu, T and Penuelas, J and Gillings, M and Zhu, YG and Fu, Z and Qian, H},
title = {Metagenomic Insight into The Global Dissemination of The Antibiotic Resistome.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e2303925},
doi = {10.1002/advs.202303925},
pmid = {37870180},
issn = {2198-3844},
support = {2022YFD1700400//National Key Research and Development Program of China/ ; 21976161//National Natural Science Foundation of China/ ; 22376187//National Natural Science Foundation of China/ ; 42307158//National Natural Science Foundation of China/ ; LZ23B070001//Natural Science Foundation of Zhejiang Province/ ; TED2021-132627B-I00//Department of Local Government, Sport and cultural industries/ ; },
abstract = {The global crisis in antimicrobial resistance continues to grow. Estimating the risks of antibiotic resistance transmission across habitats is hindered by the lack of data on mobility and habitat-specificity. Metagenomic samples of 6092 are analyzed to delineate the unique core resistomes from human feces and seven other habitats. This is found that most resistance genes (≈85%) are transmitted between external habitats and human feces. This suggests that human feces are broadly representative of the global resistome and are potentially a hub for accumulating and disseminating resistance genes. The analysis found that resistance genes with ancient horizontal gene transfer (HGT) events have a higher efficiency of transfer across habitats, suggesting that HGT may be the main driver for forming unique but partly shared resistomes in all habitats. Importantly, the human fecal resistome is historically different and influenced by HGT and age. The most important routes of cross-transmission of resistance are from the atmosphere, buildings, and animals to humans. These habitats should receive more attention for future prevention of antimicrobial resistance. The study will disentangle transmission routes of resistance genes between humans and other habitats in a One Health framework and can identify strategies for controlling the ongoing dissemination and antibiotic resistance.},
}

@article {pmid37865329,
year = {2023},
author = {Ye, C and Chen, C and Zhang, K and Feng, M and Yu, X},
title = {Solar/periodate inhibits ARGs transformation by degradation of DNA without damaging cell membrane.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {122766},
doi = {10.1016/j.envpol.2023.122766},
pmid = {37865329},
issn = {1873-6424},
abstract = {Antibiotic-resistant bacterial infections are a growing global threat to public health. Chlorine-based water disinfection and some advanced oxidation processes significantly increase the risk of ARGs release and transmission in the aquatic environment. Therefore, it is critical to develop or optimize disinfection methods to reduce the conversion and transmission of ARGs in natural water. This study investigated whether the solar/periodate (PI) system inhibited the natural transmission of ARGs and its mechanism. The results showed that solar/PI systems could effectively inhibit the propagation of ARGs in two simulated natural transformation systems, up to more than 100 times. By characterizing the cellular process of bacteria treated by the solar/PI system, we found that the solar/PI system could directly cause damage to DNA bases and its dual effect with almost no damage to the bacterial cell membrane, which was the main reason why this technology could inhibit natural transformation processes. Specifically, the inhibition effect of solar/PI on bacteria did not result in enhanced membrane permeability under appropriate PI dosage (<200 μM), which greatly reduced the risk of secondary contamination of eARGs released by traditional disinfection. Our findings could help improve existing disinfection strategies to ensure that antibiotic resistance is not spread in the natural water environment.},
}

@article {pmid37856455,
year = {2023},
author = {Aubin, E and Llauro, C and Garrigue, J and Mirouze, M and Panaud, O and El Baidouri, M},
title = {Genome-wide analysis of horizontal transfer in non-model wild species from a natural ecosystem reveals new insights into genetic exchange in plants.},
journal = {PLoS genetics},
volume = {19},
number = {10},
pages = {e1010964},
pmid = {37856455},
issn = {1553-7404},
mesh = {*Ecosystem ; Pilot Projects ; *Genome, Plant/genetics ; Genomics ; Retroelements ; Phylogeny ; Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; },
abstract = {Horizontal transfer (HT) refers to the exchange of genetic material between divergent species by mechanisms other than reproduction. In recent years, several studies have demonstrated HTs in eukaryotes, particularly in the context of parasitic relationships and in model species. However, very little is known about HT in natural ecosystems, especially those involving non-parasitic wild species, and the nature of the ecological relationships that promote these HTs. In this work, we conducted a pilot study investigating HTs by sequencing the genomes of 17 wild non-model species from a natural ecosystem, the Massane forest, located in southern France. To this end, we developed a new computational pipeline called INTERCHANGE that is able to characterize HTs at the whole genome level without prior annotation and directly in the raw sequencing reads. Using this pipeline, we identified 12 HT events, half of which occurred between lianas and trees. We found that mainly low copy number LTR-retrotransposons from the Copia superfamily were transferred between these wild plant species, especially those of the Ivana and Ale lineages. This study revealed a possible new route for HTs between non-parasitic plants and provides new insights into the genomic characteristics of horizontally transferred DNA in plant genomes.},
}

*Ecosystem
Pilot Projects
*Genome, Plant/genetics
Genomics
Retroelements
Phylogeny
Evolution, Molecular
Gene Transfer, Horizontal/genetics

@article {pmid37864197,
year = {2023},
author = {Abante, J and Wang, PL and Salzman, J},
title = {DIVE: a reference-free statistical approach to diversity-generating and mobile genetic element discovery.},
journal = {Genome biology},
volume = {24},
number = {1},
pages = {240},
pmid = {37864197},
issn = {1474-760X},
support = {R35 GM139517/GM/NIGMS NIH HHS/United States ; },
abstract = {Diversity-generating and mobile genetic elements are key to microbial and viral evolution and can result in evolutionary leaps. State-of-the-art algorithms to detect these elements have limitations. Here, we introduce DIVE, a new reference-free approach to overcome these limitations using information contained in sequencing reads alone. We show that DIVE has improved detection power compared to existing reference-based methods using simulations and real data. We use DIVE to rediscover and characterize the activity of known and novel elements and generate new biological hypotheses about the mobilome. Building on DIVE, we develop a reference-free framework capable of de novo discovery of mobile genetic elements.},
}

@article {pmid37863223,
year = {2023},
author = {Jiménez-Volkerink, SN and Jordán, M and Smidt, H and Minguillón, C and Vila, J and Grifoll, M},
title = {Metagenomic insights into the microbial cooperative networks of a benz(a)anthracene-7,12-dione degrading community from a creosote-contaminated soil.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {167832},
doi = {10.1016/j.scitotenv.2023.167832},
pmid = {37863223},
issn = {1879-1026},
abstract = {Genotoxicity of PAH-contaminated soils can eventually increase after bioremediation due to the formation and accumulation of polar transformation products, mainly oxygenated PAHs (oxy-PAHs). Biodegradation of oxy-PAHs has been described in soils, but information on the microorganisms and mechanisms involved is still scarce. Benz(a)anthracene-7,12-dione (BaAQ), a transformation product from benz(a)anthracene frequently detected in soils, presents higher genotoxic potential than its parent PAH. Here, using sand-in-liquid microcosms we identified a specialized BaAQ-degrading subpopulation in a PAH-contaminated soil. A BaAQ-degrading microbial consortium was obtained by enrichment in sand-in-liquid cultures with BaAQ as sole carbon source, and its metagenomic analysis identified members of Sphingobium, Stenotrophomonas, Pusillimonas, Olivibacter, Pseudomonas, Achromobacter, and Hyphomicrobiales as major components. The integration of data from metabolomic and metagenomic functional gene analyses of the consortium revealed that the BaAQ metabolic pathway was initiated by Baeyer-Villiger monooxygenases (BVMOs). The presence of plasmid pANTQ-1 in the metagenomic sequences, identified in a previous multi-omic characterization of a 9,10-anthraquinone-degrading isolate recovered from the same soil, suggested the occurrence of a horizontal gene transfer event. Further metagenomic analysis of the BaAQ-degrading consortium also provided insights into the potential roles and interactions within the consortium members. Several potential auxotrophies were detected, indicating that relevant nutritional interdependencies and syntrophic associations were taking place within the community members, not only to provide suitable carbon and energy sources, but also to supply essential nutrients and cofactors. Our work confirms the essential role that BVMO may play as a detoxification mechanism to mitigate the risk posed by oxy-PAH formation during bioremediation of contaminated soils.},
}

@article {pmid37863060,
year = {2023},
author = {Mishina, T and Chiu, MC and Hashiguchi, Y and Oishi, S and Sasaki, A and Okada, R and Uchiyama, H and Sasaki, T and Sakura, M and Takeshima, H and Sato, T},
title = {Massive horizontal gene transfer and the evolution of nematomorph-driven behavioral manipulation of mantids.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2023.09.052},
pmid = {37863060},
issn = {1879-0445},
abstract = {To complete their life cycle, a wide range of parasites must manipulate the behavior of their hosts.[1] This manipulation is a well-known example of the "extended phenotype,[2]" where genes in one organism have phenotypic effects on another organism. Recent studies have explored the parasite genes responsible for such manipulation of host behavior, including the potential molecular mechanisms.[3][,][4] However, little is known about how parasites have acquired the genes involved in manipulating phylogenetically distinct hosts.[4] In a fascinating example of the extended phenotype, nematomorph parasites have evolved the ability to induce their terrestrial insect hosts to enter bodies of water, where the parasite then reproduces. Here, we comprehensively analyzed nematomorphs and their mantid hosts, focusing on the transcriptomic changes associated with host manipulations and sequence similarity between host and parasite genes to test molecular mimicry. The nematomorph's transcriptome changed during host manipulation, whereas no distinct changes were found in mantids. We then discovered numerous possible host-derived genes in nematomorphs, and these genes were frequently up-regulated during host manipulation. Our findings suggest a possible general role of horizontal gene transfer (HGT) in the molecular mechanisms of host manipulation, as well as in the genome evolution of manipulative parasites. The evidence of HGT between multicellular eukaryotes remains scarce but is increasing and, therefore, elucidating its mechanisms will advance our understanding of the enduring influence of HGT on the evolution of the web of life.},
}

@article {pmid37858689,
year = {2023},
author = {Sajjad, W and Ali, B and Niu, H and Ilahi, N and Rafiq, M and Bahadur, A and Banerjee, A and Kang, S},
title = {High prevalence of antibiotic-resistant and metal-tolerant cultivable bacteria in remote glacier environment.},
journal = {Environmental research},
volume = {},
number = {},
pages = {117444},
doi = {10.1016/j.envres.2023.117444},
pmid = {37858689},
issn = {1096-0953},
abstract = {Studies of antibiotic-resistant bacteria (ARB) have mainly originated from anthropic-influenced environments, with limited information from pristine environments. Remote cold environments are major reservoirs of ARB and have been determined in polar regions; however, their abundance in non-polar cold habitats is underexplored. This study evaluated antibiotics and metals resistance profiles, prevalence of antibiotic resistance genes (ARGs) and metals tolerance genes (MTGs) in 38 ARB isolated from the glacier debris and meltwater from Baishui Glacier No 1, China. Molecular identification displayed Proteobacteria (39.3%) predominant in debris, while meltwater was dominated by Actinobacteria (30%) and Proteobacteria (30%). Bacterial isolates exhibited multiple antibiotic resistance index values > 0.2. Gram-negative bacteria displayed higher resistance to antibiotics and metals than Gram-positive. PCR amplification exhibited distinct ARGs in bacteria dominated by β-lactam genes blaCTX-M (21.1-71.1%), blaACC (21.1-60.5%), tetracycline-resistant gene tetA (21.1-60.5%), and sulfonamide-resistant gene sulI (18.4-52.6%). Moreover, different MTGs were reported in bacterial isolates, including mercury-resistant merA (21.1-63.2%), copper-resistant copB (18.4-57.9%), chromium-resistant chrA (15.8-44.7%) and arsenic-resistant arsB (10.5-44.7%). This highlights the co-selection and co-occurrence of MTGs and ARGs in remote glacier environments. Different bacteria shared same ARGs, signifying horizontal gene transfer between species. Strong positive correlation among ARGs and MTGs was reported. Metals tolerance range exhibited that Gram-negative and Gram-positive bacteria clustered distinctly. Gram-negative bacteria were significantly tolerant to metals. Amino acid sequences of blaACC,blaCTX-M,blaSHV,blaampC,qnrA, sulI, tetA and blaTEM revealed variations. This study presents promising ARB, harboring ARGs with variations in amino acid sequences, highlighting the need to assess the transcriptome study of glacier bacteria conferring ARGs and MTGs.},
}

@article {pmid37856515,
year = {2023},
author = {Johansson, MHK and Aarestrup, FM and Petersen, TN},
title = {Importance of mobile genetic elements for dissemination of antimicrobial resistance in metagenomic sewage samples across the world.},
journal = {PloS one},
volume = {18},
number = {10},
pages = {e0293169},
pmid = {37856515},
issn = {1932-6203},
abstract = {We are facing an ever-growing threat from increasing antimicrobial resistance (AMR) in bacteria. To mitigate this, we need a better understanding of the global spread of antimicrobial resistance genes (ARGs). ARGs are often spread among bacteria by horizontal gene transfer facilitated by mobile genetic elements (MGE). Here we use a dataset consisting of 677 metagenomic sequenced sewage samples from 97 countries or regions to study how MGEs are geographically distributed and how they disseminate ARGs worldwide. The ARGs, MGEs, and bacterial abundance were calculated by reference-based read mapping. We found systematic differences in the abundance of MGEs and ARGs, where some elements were prevalent on all continents while others had higher abundance in separate geographic areas. Different MGEs tended to be localized to temperate or tropical climate zones, while different ARGs tended to separate according to continents. This suggests that the climate is an important factor influencing the local flora of MGEs. MGEs were also found to be more geographically confined than ARGs. We identified several integrated MGEs whose abundance correlated with the abundance of ARGs and bacterial genera, indicating the ability to mobilize and disseminate these genes. Some MGEs seemed to be more able to mobilize ARGs and spread to more bacterial species. The host ranges of MGEs seemed to differ between elements, where most were associated with bacteria of the same family. We believe that our method could be used to investigate the population dynamics of MGEs in complex bacterial populations.},
}

@article {pmid37855620,
year = {2023},
author = {Jia, C and Wang, Z and Huang, C and Teng, L and Zhou, H and An, H and Liao, S and Liu, Y and Huang, L and Tang, B and Yue, M},
title = {Mobilome-driven partitions of the resistome in Salmonella.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0088323},
doi = {10.1128/msystems.00883-23},
pmid = {37855620},
issn = {2379-5077},
abstract = {Mobile genetic elements (MGEs) or mobilomes promote the mobilization and dissemination of antimicrobial resistance genes (ARGs), serving as critical drivers for antimicrobial resistance (AMR) accumulation, interaction, and persistence. However, systematic and quantitative evaluations of the role of mobilome in spreading resistome in a bacterial pathogen remain unaddressed, partially due to the lack of closed genomes. Here, we examined MGEs across 1,817 Salmonella isolates with complete genomic sequences from 58 countries between 1911 and 2022. We found the plasmid harboring 69.8% ARGs to be the largest ARG reservoir, correlated with serovar-based evolution in most Salmonella lineages. Prophages, specifically RCS47 and SJ46, play a crucial role in the plasmids' plasticity and the acquisition of ARGs. Furthermore, distinct ARG accumulation, including resistance toward last-resort antibiotics, exhibited an MGE-favored manner. Certain socioeconomic and ecological factors, as additional layers of mediators, are associated with the preferential distribution of MGE-mediated ARGs in Salmonella. Collectively, this study demonstrated an uncharted knowledge of the segmentation of Salmonella resistome driven by mobilome, elucidating dynamic drivers and distinct mediators for resistome development that are of immediate relevance for targeted interventions. IMPORTANCE Antimicrobial resistance (AMR) has become a significant global challenge, with an estimated 10 million deaths annually by 2050. The emergence of AMR is mainly attributed to mobile genetic elements (MGEs or mobilomes), which accelerate wide dissemination among pathogens. The interaction between mobilomes and AMR genes (or resistomes) in Salmonella, a primary cause of diarrheal diseases that results in over 90 million cases annually, remains poorly understood. The available fragmented or incomplete genomes remain a significant limitation in investigating the relationship between AMR and MGEs. Here, we collected the most extensive closed Salmonella genomes (n = 1,817) from various sources across 58 countries. Notably, our results demonstrate that resistome transmission between Salmonella lineages follows a specific pattern of MGEs and is influenced by external drivers, including certain socioeconomic factors. Therefore, targeted interventions are urgently needed to mitigate the catastrophic consequences of Salmonella AMR.},
}

@article {pmid37855599,
year = {2023},
author = {Feng, Z and Wang, L and Guan, Q and Chu, X and Luo, Z-Q},
title = {Acinetobacter baumannii coordinates central metabolism, plasmid dissemination, and virulence by sensing nutrient availability.},
journal = {mBio},
volume = {},
number = {},
pages = {e0227623},
doi = {10.1128/mbio.02276-23},
pmid = {37855599},
issn = {2150-7511},
abstract = {Plasmid conjugation plays an important role in the dissemination of antibiotic-resistance genes. The emergence of multidrug-resistant isolates of Acinetobacter baumannii poses grave challenges in treating infections caused by this notorious nosocomial pathogen. Yet, the composition, functionality, and regulation of conjugative machinery utilized by A. baumannii remain poorly understood. Here, we found that conjugation of the major plasmid pAB3 of A. baumannii is mediated by a type IVB secretion system similar to the Dot/Icm transporter of Legionella pneumophila. Furthermore, the expression of the structural genes of the Dot/Icm-like system is co-regulated with genes involved in central metabolism by the GacS/GacA two-component system in response to various metabolites, including intermediates of the tricarboxylic acid cycle. Loss of GacS/A also severely impaired bacterial virulence. These results establish that A. baumannii coordinates metabolism with plasmid conjugation and virulence by sensing nutrient availability, which may be exploited to develop inhibitory agents for controlling the spread of drug-resistance genes and virulence factors. IMPORTANCE Plasmid conjugation is known to be an energy-expensive process, but our understanding of the molecular linkage between conjugation and metabolism is limited. Our finding reveals that Acinetobacter baumannii utilizes a two-component system to co-regulate metabolism, plasmid transfer, and virulence by sensing reaction intermediates of key metabolic pathways, which suggests that nutrient availability dictates not only bacterial proliferation but also horizontal gene transfer. The identification of Dot/Icm-like proteins as components of a conjugation system involved in the dissemination of antibiotic-resistance genes by A. baumannii has provided important targets for the development of agents capable of inhibiting virulence and the spread of anti-microbial-resistance genes in bacterial communities.},
}

@article {pmid37850911,
year = {2023},
author = {Yee, W-X and Elsener, T and Cehovin, A and Maiden, MCJ and Tang, CM},
title = {Evolution and exchange of plasmids in pathogenic Neisseria.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0044123},
doi = {10.1128/msphere.00441-23},
pmid = {37850911},
issn = {2379-5042},
abstract = {Neisseria gonorrhoeae causes sexually transmitted infection (STI) gonorrhoea and is on the WHO critical list due to increasing antimicrobial resistance (AMR). The bacterium can carry a conjugative plasmid, pConj, which prevents the use of tetracycline or doxycycline for treating gonorrhea, and is responsible for spread of a β-lactamase plasmid, pbla; over 90% of gonococcal isolates also harbor a small cryptic plasmid, pCryp. We systematically analyzed the presence of these plasmids in other Neisseria spp., including Neisseria meningitidis, which causes sepsis/meningitis. pConj is the most frequently found plasmid in the meningococcus and is in many clonal complexes. The plasmid is associated with meningococcal carriage rather than disease, indicating that pConj imposes fitness costs during systemic disease. Phylogenetic analyses reveal that pConj is genetically diverse in N. meningitidis, indicating that it shares a long evolutionary history with the meningococcus and that the plasmid has been transferred at least twice from N. meningitidis to N. gonorrhoeae. Following the first transfer, gonococcal isolates carrying the plasmid underwent clonal expansion and disseminated pConj to other gonococcal lineages. The second introduction was associated with an altered conjugation machinery which reduces conjugation efficiency. Therefore, in contrast to chromosomal resistance which has evolved through introduction of genes from commensals, gonococcal plasmid-mediated resistance has arisen through transfer from another pathogen, N. meningitidis. Further antibiotic pressure from the use of doxycycline for post-exposure prophylaxis against STIs is likely to promote plasmid-mediated AMR in both N. gonorrhoeae and N. meningitidis. IMPORTANCE Horizontal gene transfer (HGT) is a major influence in driving the spread of antimicrobial resistance (AMR) in many bacteria. A conjugative plasmid which is widespread in Neisseria gonorrhoeae, pConj, prevented the use of tetracycline/doxycycline for treating gonococcal infection. Here, we show that pConj evolved in the related pathogen, Neisseria meningitidis, and has been acquired by the gonococcus from the meningococcus on multiple occasions. Following its initial acquisition, pConj spread to different gonococcal lineages; changes in the plasmid's conjugation machinery associated with another transfer event limit spread in the gonococcal populations. Our findings have important implications for the use of doxycycline to prevent bacterial sexually transmitted disease which is likely to exacerbate the spread of AMR through HGT in pathogenic bacteria.},
}

@article {pmid37850800,
year = {2023},
author = {Giengkam, S and Kullapanich, C and Wongsantichon, J and Adcox, HE and Gillespie, JJ and Salje, J},
title = {Orientia tsutsugamushi: comprehensive analysis of the mobilome of a highly fragmented and repetitive genome reveals the capacity for ongoing lateral gene transfer in an obligate intracellular bacterium.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0026823},
doi = {10.1128/msphere.00268-23},
pmid = {37850800},
issn = {2379-5042},
abstract = {The rickettsial human pathogen Orientia tsutsugamushi (Ot) is an obligate intracellular Gram-negative bacterium with one of the most highly fragmented and repetitive genomes of any organism. Around 50% of its ~2.3-Mb genome is composed of repetitive DNA that is derived from the highly proliferated Rickettsiales amplified genetic element (RAGE). RAGE is an integrative and conjugative element (ICE) that is present in a single Ot genome in up to 93 copies, most of which are partially or heavily degraded. In this report, we analyzed RAGEs in eight fully sequenced Ot genomes and manually curated and re-annotated all RAGE-associated genes, including those encoding DNA mobilization proteins, P-type (vir), and F-type (tra) type IV secretion system (T4SS) components, ankyrin repeat- and tetratricopeptide repeat-containing effectors, and other piggybacking cargo. Originally, the heavily degraded Ot RAGEs have led to speculation that they are remnants of historical ICEs that are no longer active. Our analysis, however, identified two Ot genomes harboring one or more intact RAGEs with complete F-T4SS genes essential for mediating ICE DNA transfer. As similar ICEs have been identified in unrelated rickettsial species, we assert that RAGEs may play an ongoing role in lateral gene transfer within the Rickettsiales. We also identified a conserved set of gene transfer agent genes in all Ot genomes. Together these findings indicate that, despite their obligate intracellular lifestyle and host range restricted to mites, rodents, and humans, Ot genomes are highly dynamic and shaped through ongoing invasions by mobile genetic elements and virus-like elements. IMPORTANCE Obligate intracellular bacteria, or those only capable of growth inside other living cells, have limited opportunities for horizontal gene transfer with other microbes due to their isolated replicative niche. The human pathogen Ot, an obligate intracellular bacterium causing scrub typhus, encodes an unusually high copy number of a ~40 gene mobile genetic element that typically facilitates genetic transfer across microbes. This proliferated element is heavily degraded in Ot and previously assumed to be inactive. Here, we conducted a detailed analysis of this element in eight Ot strains and discovered two strains with at least one intact copy. This implies that the element is still capable of moving across Ot populations and suggests that the genome of this bacterium may be even more dynamic than previously appreciated. Our work raises questions about intracellular microbial evolution and sounds an alarm for gene-based efforts focused on diagnosing and combatting scrub typhus.},
}

@article {pmid37849012,
year = {2023},
author = {Wei, Y and Gong, Z and Han, GZ},
title = {Plants acquired mitochondrial linear plasmids horizontally from fungi likely during the conquest of land.},
journal = {Mobile DNA},
volume = {14},
number = {1},
pages = {15},
pmid = {37849012},
issn = {1759-8753},
support = {31922001//National Natural Science Foundation of China/ ; },
abstract = {Mitochondrial linear plasmids have been sporadically reported in fungi and plants. Yet, much remains obscure about the diversity, distribution, and evolution of mitochondrial linear plasmids. Here, through phylogenomic analyses across 7,163 cellular organisms (including 991 plants), we find that mitochondrial linear plasmids are widely present in land plants and fungi. Phylogenetic analyses indicate that plants are likely to have acquired mitochondrial linear plasmids horizontally from fungi before or during the conquest of terrestrial environments by plants. Gene content analyses show that mitochondrial linear plasmids harbor a highly dynamic and promiscuous repertoire of genes. Our study refines the understanding of the origin and evolution of mitochondrial linear plasmids.},
}

@article {pmid37848554,
year = {2023},
author = {Lücking, D and Mercier, C and Alarcón-Schumacher, T and Erdmann, S},
title = {Extracellular vesicles are the main contributor to the non-viral protected extracellular sequence space.},
journal = {ISME communications},
volume = {3},
number = {1},
pages = {112},
pmid = {37848554},
issn = {2730-6151},
support = {Max Planck Research Group Archaeal Virology//Max-Planck-Gesellschaft (Max Planck Society)/ ; Max Planck Research Group Archaeal Virology//Max-Planck-Gesellschaft (Max Planck Society)/ ; Max Planck Research Group Archaeal Virology//Max-Planck-Gesellschaft (Max Planck Society)/ ; Max Planck Research Group Archaeal Virology//Max-Planck-Gesellschaft (Max Planck Society)/ ; },
abstract = {Environmental virus metagenomes, commonly referred to as "viromes", are typically generated by physically separating virus-like particles (VLPs) from the microbial fraction based on their size and mass. However, most methods used to purify VLPs, enrich extracellular vesicles (EVs) and gene transfer agents (GTAs) simultaneously. Consequently, the sequence space traditionally referred to as a "virome" contains host-associated sequences, transported via EVs or GTAs. We therefore propose to call the genetic material isolated from size-fractionated (0.22 µm) and DNase-treated samples protected environmental DNA (peDNA). This sequence space contains viral genomes, DNA transduced by viruses and DNA transported in EVs and GTAs. Since there is no genetic signature for peDNA transported in EVs, GTAs and virus particles, we rely on the successful removal of contaminating remaining cellular and free DNA when analyzing peDNA. Using marine samples collected from the North Sea, we generated a thoroughly purified peDNA dataset and developed a bioinformatic pipeline to determine the potential origin of the purified DNA. This pipeline was applied to our dataset as well as existing global marine "viromes". Through this pipeline, we identified known GTA and EV producers, as well as organisms with actively transducing proviruses as the source of the peDNA, thus confirming the reliability of our approach. Additionally, we identified novel and widespread EV producers, and found quantitative evidence suggesting that EV-mediated gene transfer plays a significant role in driving horizontal gene transfer (HGT) in the world's oceans.},
}

@article {pmid37845226,
year = {2023},
author = {Gonzalez-Serrano, R and Rosselli, R and Roda-Garcia, JJ and Martin-Cuadrado, AB and Rodriguez-Valera, F and Dunne, M},
title = {Distantly related Alteromonas bacteriophages share tail fibers exhibiting properties of transient chaperone caps.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {6517},
pmid = {37845226},
issn = {2041-1723},
support = {PROMETEO/2019/009//Generalitat Valenciana (Regional Government of Valencia)/ ; ACIF/2016/050//Regional Government of Valencia | Conselleria de Sanitat Universal i Salut Pública (Conselleria de Sanitat Universal i Salut Pública de la Generalitat Valenciana)/ ; CRSII5_189957//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; },
abstract = {The host recognition modules encoding the injection machinery and receptor binding proteins (RBPs) of bacteriophages are predisposed to mutation and recombination to maintain infectivity towards co-evolving bacterial hosts. In this study, we reveal how Alteromonas mediterranea schitovirus A5 shares its host recognition module, including tail fiber and cognate chaperone, with phages from distantly related families including Alteromonas myovirus V22. While the V22 chaperone is essential for producing active tail fibers, here we demonstrate production of functional A5 tail fibers regardless of chaperone co-expression. AlphaFold-generated models of tail fiber and chaperone pairs from phages A5, V22, and other Alteromonas phages reveal how amino acid insertions within both A5-like proteins results in a knob domain duplication in the tail fiber and a chaperone β-hairpin "tentacle" extension. These structural modifications are linked to differences in chaperone dependency between the A5 and V22 tail fibers. Structural similarity between the chaperones and intramolecular chaperone domains of other phage RBPs suggests an additional function of these chaperones as transient fiber "caps". Finally, our identification of homologous host recognition modules from morphologically distinct phages implies that horizontal gene transfer and recombination events between unrelated phages may be a more common process than previously thought among Caudoviricetes phages.},
}

@article {pmid37843655,
year = {2023},
author = {Sudhakari, PA and Ramisetty, BCM},
title = {An Eco-evolutionary Model on Surviving Lysogeny Through Grounding and Accumulation of Prophages.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
pmid = {37843655},
issn = {1432-184X},
abstract = {Temperate phages integrate into the bacterial genomes propagating along with the bacterial genomes. Multiple phage elements, representing diverse prophages, are present in most bacterial genomes. The evolutionary events and the ecological dynamics underlying the accumulation of prophage elements in bacterial genomes have yet to be understood. Here, we show that the local wastewater had 7% of lysogens (hosting mitomycin C-inducible prophages), and they showed resistance to superinfection by their corresponding lysates. Genomic analysis of four lysogens and four non-lysogens revealed the presence of multiple prophages (belonging to Myoviridae and Siphoviridae) in both lysogens and non-lysogens. For large-scale comparison, 2180 Escherichia coli genomes isolated from various sources across the globe and 523 genomes specifically isolated from diverse wastewaters were analyzed. A total of 15,279 prophages were predicted among 2180 E. coli genomes and 2802 prophages among 523 global wastewater isolates, with a mean of ~ 5 prophages per genome. These observations indicate that most putative prophages are relics of past bacteria-phage conflicts; they are "grounded" prophages that cannot excise from the bacterial genome. Prophage distribution analysis based on the sequence homology suggested the random distribution of E. coli prophages within and between E. coli clades. The independent occurrence pattern of these prophages indicates extensive horizontal transfers across the genomes. We modeled the eco-evolutionary dynamics to reconstruct the events that could have resulted in the prophage accumulation accounting for infection, superinfection immunity, and grounding. In bacteria-phage conflicts, the bacteria win by grounding the prophage, which could confer superinfection immunity.},
}

@article {pmid37842006,
year = {2023},
author = {López-Pérez, J and Otero, J and Sánchez-Osuna, M and Erill, I and Cortés, P and Llagostera, M},
title = {Impact of mutagenesis and lateral gene transfer processes in bacterial susceptibility to phage in food biocontrol and phage therapy.},
journal = {Frontiers in cellular and infection microbiology},
volume = {13},
number = {},
pages = {1266685},
pmid = {37842006},
issn = {2235-2988},
abstract = {INTRODUCTION: The emergence of resistance and interference mechanisms to phage infection can hinder the success of bacteriophage-based applications, but the significance of these mechanisms in phage therapy has not been determined. This work studies the emergence of Salmonella isolates with reduced susceptibility to a cocktail of three phages under three scenarios: i) Salmonella cultures (LAB), ii) biocontrol of cooked ham slices as a model of food safety (FOOD), and iii) oral phage therapy in broilers (PT).

METHODS: S. Typhimurium ATCC 14028 RifR variants with reduced phage susceptibility were isolated from the three scenarios and conventional and molecular microbiology techniques were applied to study them.

RESULTS AND DISCUSSION: In LAB, 92% of Salmonella isolates lost susceptibility to all three phages 24 h after phage infection. This percentage was lower in FOOD, with 4.3% of isolates not susceptible to at least two of the three phages after seven days at 4°C following phage treatment. In PT, 9.7% and 3.3 % of isolates from untreated and treated broilers, respectively, displayed some mechanism of interference with the life cycle of some of the phages. In LAB and FOOD scenarios, resistant variants carrying mutations in rfc and rfaJ genes involved in lipopolysaccharide synthesis (phage receptor) were identified. However, in PT, the significant decrease of EOP, ECOI, and burst size observed in isolates was prompted by lateral gene transfer of large IncI1 plasmids, which may encode phage defense mechanisms. These data indicate that the acquisition of specific conjugative plasmids has a stronger impact than mutagenesis on the emergence of reduced phage-susceptibility bacteria in certain environments. In spite of this, neither mechanism seems to significantly impair the success of Salmonella biocontrol and oral phage therapy.},
}

@article {pmid37841331,
year = {2023},
author = {Asif, M and Li-Qun, Z and Zeng, Q and Atiq, M and Ahmad, K and Tariq, A and Al-Ansari, N and Blom, J and Fenske, L and Alodaini, HA and Hatamleh, AA},
title = {Comprehensive genomic analysis of Bacillus paralicheniformis strain BP9, pan-genomic and genetic basis of biocontrol mechanism.},
journal = {Computational and structural biotechnology journal},
volume = {21},
number = {},
pages = {4647-4662},
pmid = {37841331},
issn = {2001-0370},
abstract = {Many Bacillus species are essential antibacterial agents, but their antibiosis potential still needs to be elucidated to its full extent. Here, we isolated a soil bacterium, BP9, which has significant antibiosis activity against fungal and bacterial pathogens. BP9 improved the growth of wheat seedlings via active colonization and demonstrated effective biofilm and swarming activity. BP9 sequenced genome contains 4282 genes with a mean G-C content of 45.94% of the whole genome. A single copy concatenated 802 core genes of 28 genomes, and their calculated average nucleotide identity (ANI) discriminated the strain BP9 from Bacillus licheniformis and classified it as Bacillus paralicheniformis. Furthermore, a comparative pan-genome analysis of 40 B. paralicheniformis strains suggested that the genetic repertoire of BP9 belongs to open-type genome species. A comparative analysis of a pan-genome dataset using the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Cluster of Orthologous Gene groups (COG) revealed the diversity of secondary metabolic pathways, where BP9 distinguishes itself by exhibiting a greater prevalence of loci associated with the metabolism and transportation of organic and inorganic substances, carbohydrate and amino acid for effective inhabitation in diverse environments. The primary secondary metabolites and their genes involved in synthesizing bacillibactin, fencing, bacitracin, and lantibiotics were identified as acquired through a recent Horizontal gene transfer (HGT) event, which contributes to a significant part of the strain`s antimicrobial potential. Finally, we report some genes essential for plant-host interaction identified in BP9, which reduce spore germination and virulence of multiple fungal and bacterial species. The effective colonization, diverse predicted metabolic pathways and secondary metabolites (antibiotics) suggest testing the suitability of strain BP9 as a potential bio-preparation in agricultural fields.},
}