@article {pmid39235644,
year = {2024},
author = {Jaswal, R and Dubey, H and Kiran, K and Rawal, H and Kumar, G and Rajarammohan, S and Deshmukh, R and Sonah, H and Prasad, P and Bhardwaj, SC and Gupta, N and Sharma, TR},
title = {Identification and functional characterization of the npc-2-like domain containing rust effector protein that suppresses cell death in plants.},
journal = {Molecular biology reports},
volume = {51},
number = {1},
pages = {962},
pmid = {39235644},
issn = {1573-4978},
mesh = {*Plant Diseases/microbiology ; *Phylogeny ; *Cell Death ; *Fungal Proteins/metabolism/genetics ; Nicotiana/microbiology/metabolism/genetics ; Basidiomycota/pathogenicity/metabolism/genetics ; Puccinia/pathogenicity/metabolism ; Protein Domains ; Molecular Docking Simulation ; Onions/microbiology/metabolism/genetics ; },
abstract = {The MD-2-related lipid-recognition (ML/Md-2) domain is a lipid/sterol-binding domain that are involved in sterol transfer and innate immunity in eukaryotes. Here we report a genome-wide survey of this family, identifying 84 genes in 30 fungi including plant pathogens. All the studied species were found to have varied ML numbers, and expansion of the family was observed in Rhizophagus irregularis (RI) with 33 genes. The molecular docking studies of these proteins with cholesterol derivatives indicate lipid-binding functional conservation across the animal and fungi kingdom. The phylogenetic studies among eukaryotic ML proteins showed that Puccinia ML members are more closely associated with animal (insect) npc2 proteins than other fungal ML members. One of the candidates from leaf rust fungus Puccinia triticina, Pt5643 was PCR amplified and further characterized using various studies such as qRT-PCR, subcellular localization studies, yeast functional complementation, signal peptide validation, and expression studies. The Pt5643 exhibits the highest expression on the 5th day post-infection (dpi). The confocal microscopy of Pt5643 in onion epidermal cells and N. benthamiana shows its location in the cytoplasm and nucleus. The functional complementation studies of Pt5643 in npc2 mutant yeast showed its functional similarity to the eukaryotic/yeast npc2 gene. Furthermore, the overexpression of Pt5643 also suppressed the BAX, NEP1, and H2O2-induced program cell death in Nicotiana species and yeast. Altogether the present study reports the novel function of ML domain proteins in plant fungal pathogens and their possible role as effector molecules in host defense manipulation.},
}

*Plant Diseases/microbiology
*Phylogeny
*Cell Death
*Fungal Proteins/metabolism/genetics
Nicotiana/microbiology/metabolism/genetics
Basidiomycota/pathogenicity/metabolism/genetics
Puccinia/pathogenicity/metabolism
Protein Domains
Molecular Docking Simulation
Onions/microbiology/metabolism/genetics

@article {pmid39235595,
year = {2024},
author = {Xu, R and Huang, C and Yang, B and Wang, S and Zhong, T and Ma, L and Shang, Q and Zhang, M and Chu, Z and Liu, X},
title = {Influence of Two-Dimensional Black Phosphorus on the Horizontal Transfer of Plasmid-Mediated Antibiotic Resistance Genes: Promotion or Inhibition?.},
journal = {Current microbiology},
volume = {81},
number = {10},
pages = {344},
pmid = {39235595},
issn = {1432-0991},
support = {52070063//National Natural Science Foundation of China/ ; 2308085Y38//Science Fund for Distinguished Young Scholars of Anhui Province/ ; 21-22RC30//Hefei University/ ; },
mesh = {*Plasmids/genetics ; *Gene Transfer, Horizontal ; *Phosphorus/metabolism ; *Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Conjugation, Genetic ; Escherichia coli/genetics/drug effects ; Nanostructures ; Bacterial Proteins/genetics/metabolism ; Gene Expression Regulation, Bacterial/drug effects ; Bacteria/genetics/drug effects ; },
abstract = {The problem of bacterial resistance caused by antibiotic abuse is seriously detrimental to global human health and ecosystem security. The two-dimensional nanomaterial (2D) such as black phosphorus (BP) is recently expected to become a new bacterial inhibitor and has been widely used in the antibacterial field due to its specific physicochemical properties. Nevertheless, the effects of 2D-BP on the propagation of antibiotic resistance genes (ARGs) in environments and the relevant mechanisms are not clear. Herein, we observed that the sub-inhibitory concentrations of 2D-BP dramatically increased the conjugative transfer of ARGs mediated by the RP4 plasmid up to 2.6-fold at the 125 mg/L exposure level compared with the untreated bacterial cells. Nevertheless, 2D-BP with the inhibitory concentration caused a dramatic decrease in the conjugative frequency. The phenotypic changes revealed that the increase of the conjugative transfer caused by 2D-BP exposure were attributed to the excessive reactive oxygen species and oxidative stress, and increased bacterial cell membrane permeability. The genotypic evidence demonstrated that 2D-BP affecting the horizontal gene transfer of ARGs was probably through the upregulation of mating pair formation genes (trbBp and traF) and DNA transfer and replication genes (trfAp and traJ), as well as the downregulation of global regulatory gene expression (korA, korB, and trbA). In summary, the changes in the functional and regulatory genes in the conjugative transfer contributed to the stimulation of conjugative transfer. This research aims to broaden our comprehension of how nanomaterials influence the dissemination of ARGs by elucidating their effects and mechanisms.},
}

*Plasmids/genetics
*Gene Transfer, Horizontal
*Phosphorus/metabolism
*Anti-Bacterial Agents/pharmacology
*Drug Resistance, Bacterial/genetics
Conjugation, Genetic
Escherichia coli/genetics/drug effects
Nanostructures
Bacterial Proteins/genetics/metabolism
Gene Expression Regulation, Bacterial/drug effects
Bacteria/genetics/drug effects

@article {pmid39233522,
year = {2024},
author = {Lee, JH and Tareen, AR and Kim, NH and Jeong, C and Kang, B and Lee, G and Kim, DW and Zahra, R and Lee, SH},
title = {Comparative Genomic Analyses of E. coli ST2178 Strains Originated from Wild Birds in Pakistan.},
journal = {Journal of microbiology and biotechnology},
volume = {34},
number = {10},
pages = {1-8},
doi = {10.4014/jmb.2407.07026},
pmid = {39233522},
issn = {1738-8872},
abstract = {The emergence and spread of multidrug-resistance (MDR) pathogenic Escherichia coli due to horizontal gene transfer of antibiotic resistance genes (ARGs) and virulence factors (VFs) is a global health concern, particularly in developing countries. While numerous studies have focused on major sequence types (STs), the implication of minor STs in ARG dissemination and their pathogenicity remains crucial. In this study, two E. coli strains (PEC1011 and PEC1012) were isolated from wild bird feces in Pakistan and identified as ST2178 based on their complete genome sequences. To understand this minor ST, 204 genome assemblies of ST2178 were comparatively analyzed with the isolates' genomes. The phylogenetic analyses revealed five subclades of ST2178. Subclade E strains were predominantly isolated from human specimens, whereas subclades A and B strains including strains PEC1011 and PEC1012, respectively, were frequently isolated from animal. Mobile genetic elements (MGEs) exhibited the positive correlation with ARGs but not with VFs in this ST. Plasmid-borne ARGs exhibited higher correlation with plasmid-borne MGEs, indicating the role of diverse mobile plasmid structures in ARG transmission. Subclade E exhibited diverse plasmid-borne ARG repertoires correlated with MGEs, marking it as a critical surveillance target. In the case of VFs, they exhibited phylogeny-dependent profiles. Strain PEC1012 harbored various plasmid-borne ARGs, which are similar with conserved ARG repertoires in subclade A. The presence of unique ARG insertion in pPEC1012 highlights the importance of subclade A in ARG dissemination. This study comprehensively elucidates the landscape of ST2178, identifying critical phylogenetic subclades and their characteristics in ARG and VF occurrence.},
}

@article {pmid39233087,
year = {2024},
author = {Kong, F and Qi, Z and Tong, H and Ren, N and You, S},
title = {Case study on the relationship between transmission of antibiotic resistance genes and microbial community under freeze-thaw cycle on cold-region dairy farm.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {175989},
doi = {10.1016/j.scitotenv.2024.175989},
pmid = {39233087},
issn = {1879-1026},
abstract = {Freeze-thaw cycle (FTC) is a naturally occurring phenomenon in high-latitude terrestrial ecosystems, which may exert influence on distribution and evolution of microbial community in the soil. The relationship between transmission of antibiotic resistance genes (ARGs) and microbial community was investigated upon the case study on the soil of cold-region dairy farm under seasonal FTC. The results demonstrated that 37 ARGs underwent decrease in the abundance of blaTEM from 80.4 % for frozen soil to 71.7 % for thawed soil, and that sul2 from 8.8 % for frozen soil to 6.5 % for thawed soil, respectively. Antibiotic deactivation was identified to be closely related to the highest relative abundance of blaTEM, and the spread of sulfonamide resistance genes (SRGs) occurred mainly via target modification. Firmicutes in frozen soil were responsible for dominating the abundance of ARGs by suppressing the native bacteria under starvation effect in cold regions, and then underwent horizontal gene transfer (HGT) among native bacteria through mobile genetic elements (MGEs). The TRB-C (32.6-49.1 %) and tnpA-06 (0.27-7.5 %) were significantly increased in frozen soil, while Int3 (0.67-10.6 %) and tnpA-04 (11.1-19.4 %) were up-regulated in thawed soil. Moreover, the ARGs in frozen soil primarily underwent HGT through MGEs, i.e. TRB-C and tnpA-06, with increased number of Firmicutes serving as carrier. The case study not only demonstrated relationship between transmission of ARGs and microbial community in the soil under practically relevant FTC condition, but also emphasized the importance for formulating better strategies for preventing FTC-induced ARGs in dairy farm in cold regions.},
}

@article {pmid39226958,
year = {2024},
author = {Muñoz, JSC and Aransiola, SA and Reddy, KV and Ranjit, P and Victor-Ekwebelem, MO and Oyedele, OJ and Pérez-Almeida, IB and Maddela, NR and Díaz, JMR},
title = {Antibiotic resistant bacteria and antibiotic resistance genes as contaminants of emerging concern: Occurrences, impacts, mitigations and future guidelines.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {175906},
doi = {10.1016/j.scitotenv.2024.175906},
pmid = {39226958},
issn = {1879-1026},
abstract = {Antibiotic resistance, driven by the proliferation of antibiotic resistance genes (ARGs) and antibiotic resistance bacteria (ARBs), has emerged as a pressing global health concern. Antimicrobial resistance is exacerbated by the widespread use of antibiotics in agriculture, aquaculture, and human medicine, leading to their accumulation in various environmental compartments such as soil, water, and sediments. The presence of ARGs in the environment, particularly in municipal water, animal husbandry, and hospital environments, poses significant risks to human health, as they can be transferred to potential human pathogens. Current remediation strategies, including the use of pyroligneous acid, coagulants, advanced oxidation, and bioelectrochemical systems, have shown promising results in reducing ARGs and ARBs from soil and water. However, these methods come with their own set of challenges, such as the need for elevated base levels in UV-activated persulfate and the long residence period required for photocatalysts. The future of combating antibiotic resistance lies in the development of standardized monitoring techniques, global collaboration, and the exploration of innovative remediation methods. Emphasis on combination therapies, advanced oxidation processes, and monitoring horizontal gene transfer can pave the way for a comprehensive approach to mitigate the spread of antibiotic resistance in the environment.},
}

@article {pmid39224035,
year = {2024},
author = {Chopra, A and Bhuvanagiri, G and Natu, K and Chopra, A},
title = {Role of CRISPR-Cas systems in periodontal disease pathogenesis and potential for periodontal therapy: A review.},
journal = {Molecular oral microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/omi.12483},
pmid = {39224035},
issn = {2041-1014},
abstract = {Clustered regularly interspaced short palindromic repeats (CRISPRs) are DNA sequences capable of editing a host genome sequence. CRISPR and its specific CRISPR-associated (Cas) protein complexes have been adapted for various applications. These include activating or inhibiting specific genetic sequences or acting as molecular scissors to cut and modify the host DNA precisely. CRISPR-Cas systems are also naturally present in many oral bacteria, where they aid in nutrition, biofilm formation, inter- and intraspecies communication (quorum sensing), horizontal gene transfer, virulence, inflammation modulation, coinfection, and immune response evasion. It even functions as an adaptive immune system, defending microbes against invading viruses and foreign genetic elements from other bacteria by targeting and degrading their DNA. Recently, CRISPR-Cas systems have been tested as molecular editing tools to manipulate specific genes linked with periodontal disease (such as periodontitis) and as novel methods of delivering antimicrobial agents to overcome antimicrobial resistance. With the rapidly increasing role of CRISPR in treating inflammatory diseases, its application in periodontal disease is also becoming popular. Therefore, this review aims to discuss the different types of CRISPR-Cas in oral microbes and their role in periodontal disease pathogenesis and precision periodontal therapy.},
}

@article {pmid39223450,
year = {2024},
author = {Valerio, F and Martel, C and Stefanescu, C and van Nouhuys, S and Kankare, M and Duplouy, A},
title = {Wolbachia strain diversity in a complex group of sympatric cryptic parasitoid wasp species.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {319},
pmid = {39223450},
issn = {1471-2180},
mesh = {Animals ; *Wolbachia/genetics/classification/isolation & purification ; *Wasps/microbiology ; *Symbiosis ; *Phylogeny ; Sympatry ; Gene Transfer, Horizontal ; Genetic Variation ; Lepidoptera/microbiology/parasitology ; },
abstract = {BACKGROUND: Maternally-inherited symbionts can induce pre-mating and/or post-mating reproductive isolation between sympatric host lineages, and speciation, by modifying host reproductive phenotypes. The large parasitoid wasp genus Cotesia (Braconidae) includes a diversity of cryptic species, each specialized in parasitizing one to few related Lepidoptera host species. Here, we characterized the infection status of an assemblage of 21 Cotesia species from 15 countries by several microbial symbionts, as a first step toward investigating whether symbionts may provide a barrier to gene flow between these parasitoid host lineages.

RESULTS: The symbiotic microbes Arsenophonus, Cardinium, Microsporidium and Spiroplasma were not detected in the Cotesia wasps. However, the endosymbiotic bacterium Wolbachia was present in at least eight Cotesia species, and hence we concentrated on it upon screening additional DNA extracts and SRAs from NCBI. Some of the closely related Cotesia species carry similar Wolbachia strains, but most Wolbachia strains showed patterns of horizontal transfer between phylogenetically distant host lineages.

CONCLUSIONS: The lack of co-phylogenetic signal between Wolbachia and Cotesia suggests that the symbiont and hosts have not coevolved to an extent that would drive species divergence between the Cotesia host lineages. However, as the most common facultative symbiont of Cotesia species, Wolbachia may still function as a key-player in the biology of the parasitoid wasps. Its precise role in the evolution of this complex clade of cryptic species remains to be experimentally investigated.},
}

Animals
*Wolbachia/genetics/classification/isolation & purification
*Wasps/microbiology
*Symbiosis
*Phylogeny
Sympatry
Gene Transfer, Horizontal
Genetic Variation
Lepidoptera/microbiology/parasitology

@article {pmid39222343,
year = {2024},
author = {Lyulina, AS and Liu, Z and Good, BH},
title = {Linkage equilibrium between rare mutations.},
journal = {Genetics},
volume = {},
number = {},
pages = {},
doi = {10.1093/genetics/iyae145},
pmid = {39222343},
issn = {1943-2631},
abstract = {Recombination breaks down genetic linkage by reshuffling existing variants onto new genetic backgrounds. These dynamics are traditionally quantified by examining the correlations between alleles, and how they decay as a function of the recombination rate. However, the magnitudes of these correlations are strongly influenced by other evolutionary forces like natural selection and genetic drift, making it difficult to tease out the effects of recombination. Here we introduce a theoretical framework for analyzing an alternative family of statistics that measure the homoplasy produced by recombination. We derive analytical expressions that predict how these statistics depend on the rates of recombination and recurrent mutation, the strength of negative selection and genetic drift, and the present-day frequencies of the mutant alleles. We find that the degree of homoplasy can strongly depend on this frequency scale, which reflects the underlying timescales over which these mutations occurred. We show how these scaling properties can be used to isolate the effects of recombination, and discuss their implications for the rates of horizontal gene transfer in bacteria.},
}

@article {pmid39221153,
year = {2024},
author = {Belay, WY and Getachew, M and Tegegne, BA and Teffera, ZH and Dagne, A and Zeleke, TK and Abebe, RB and Gedif, AA and Fenta, A and Yirdaw, G and Tilahun, A and Aschale, Y},
title = {Mechanism of antibacterial resistance, strategies and next-generation antimicrobials to contain antimicrobial resistance: a review.},
journal = {Frontiers in pharmacology},
volume = {15},
number = {},
pages = {1444781},
pmid = {39221153},
issn = {1663-9812},
abstract = {Antibacterial drug resistance poses a significant challenge to modern healthcare systems, threatening our ability to effectively treat bacterial infections. This review aims to provide a comprehensive overview of the types and mechanisms of antibacterial drug resistance. To achieve this aim, a thorough literature search was conducted to identify key studies and reviews on antibacterial resistance mechanisms, strategies and next-generation antimicrobials to contain antimicrobial resistance. In this review, types of resistance and major mechanisms of antibacterial resistance with examples including target site modifications, decreased influx, increased efflux pumps, and enzymatic inactivation of antibacterials has been discussed. Moreover, biofilm formation, and horizontal gene transfer methods has also been included. Furthermore, measures (interventions) taken to control antimicrobial resistance and next-generation antimicrobials have been discussed in detail. Overall, this review provides valuable insights into the diverse mechanisms employed by bacteria to resist the effects of antibacterial drugs, with the aim of informing future research and guiding antimicrobial stewardship efforts.},
}

@article {pmid39221073,
year = {2024},
author = {Xie, X and Deng, X and Chen, L and Yuan, J and Chen, H and Wei, C and Liu, X and Wuertz, S and Qiu, G},
title = {Integrated genomics provides insights into the evolution of the polyphosphate accumulation trait of Ca. Accumulibacter.},
journal = {Environmental science and ecotechnology},
volume = {20},
number = {},
pages = {100353},
pmid = {39221073},
issn = {2666-4984},
abstract = {Candidatus Accumulibacter, a prominent polyphosphate-accumulating organism (PAO) in wastewater treatment, plays a crucial role in enhanced biological phosphorus removal (EBPR). The genetic underpinnings of its polyphosphate accumulation capabilities, however, remain largely unknown. Here, we conducted a comprehensive genomic analysis of Ca. Accumulibacter-PAOs and their relatives within the Rhodocyclaceae family, identifying 124 core genes acquired via horizontal gene transfer (HGT) at its least common ancestor. Metatranscriptomic analysis of an enrichment culture of Ca. Accumulibacter revealed active transcription of 44 of these genes during an EBPR cycle, notably including the polyphosphate kinase 2 (PPK2) gene instead of the commonly recognized polyphosphate kinase 1 (PPK1) gene. Intriguingly, the phosphate regulon (Pho) genes showed minimal transcriptions, pointing to a distinctive fact of Pho dysregulation, where PhoU, the phosphate signaling complex protein, was not regulating the high-affinity phosphate transport (Pst) system, resulting in continuous phosphate uptake. To prevent phosphate toxicity, Ca. Accumulibacter utilized the laterally acquired PPK2 to condense phosphate into polyphosphate, resulting in the polyphosphate-accumulating feature. This study provides novel insights into the evolutionary emergence of the polyphosphate-accumulating trait in Ca. Accumulibacter, offering potential advancements in understanding the PAO phenotype in the EBPR process.},
}

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

@article {pmid39216666,
year = {2024},
author = {Qiu, T and Shen, L and Guo, Y and Gao, M and Gao, H and Li, Y and Zhao, G and Wang, X},
title = {Impact of aeration rate on the transfer range of antibiotic-resistant plasmids during manure composting.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {124851},
doi = {10.1016/j.envpol.2024.124851},
pmid = {39216666},
issn = {1873-6424},
abstract = {Conjugative plasmids are important vectors of mobile antibiotic resvistance genes (ARGs), facilitating their horizontal transfer within the environment. While composting is recognized as an effective method to reduce antibiotics and ARGs in animal manure, its impact on the bacterial host communities containing antibiotic-resistant plasmids remains unclear. In this study, we investigated the permissiveness of bacterial community during composting when challenged with multidrug-resistant conjugative RP4 plasmids, employing Pseudomonas putida as the donor strain. Ultimately, this represents the first exploration of the effects of aeration rates on the range of RP4 plasmid transfer hosts. Transconjugants were analyzed through fluorescent reporter gene-based fluorescence-activated cell sorting and Illumina sequencing. Overall, aeration rates were found to influence various physicochemical parameters of compost, including temperature, pH, total organic matter, total nitrogen, and potassium. Regarding RP4 plasmid host bacteria, the dominant phylum was determined to shift from Bacteroidetes in the raw material to Proteobacteria in the compost. Notably, a moderate-intensity aeration rate (0.05 L/min/L) was found to be more effective in reducing the diversity and richness of the RP4 plasmid host bacterial community. Following composting, the total percentage of dominant transconjugant-related genera decreased by 66.15-76.62%. Ultimately, this study determined that the aeration rate negatively impacts RP4 plasmid host abundance primarily through alterations to the environmental factors during composting. In summary, these findings enhance our understanding of plasmid host bacterial communities under varying composting aeration rates and offer novel insights into preventing the dissemination of ARGs from animal manure to farmland.},
}

@article {pmid39216410,
year = {2024},
author = {Vissapragada, M and Addala, S and Aggunna, M and Sodasani, M and Grandhi, AVKS and Yedidi, RS},
title = {Leveraging the potential of bacterial lateral gene transfer in boosting the efficacy of an edible probiotic prototype yogurt vaccine for COVID-19.},
journal = {Biochemical and biophysical research communications},
volume = {734},
number = {},
pages = {150622},
doi = {10.1016/j.bbrc.2024.150622},
pmid = {39216410},
issn = {1090-2104},
abstract = {Administration of coronavirus disease-2019 (COVID-19) vaccines with appropriate booster doses through painful injections under clinical supervision was challenging during the recent COVID-19 pandemic. As an alternative solution, we designed a safer, edible probiotic yogurt vaccine prototype (YoVac) that can be orally consumed by circumventing painful injections and clinical supervision. We hypothesized that YoVac prepared using Lactobacillus carrying an antigen coding gene (donor) can transfer the same to other bacteria (recipients) in the human gut microbiome (hgMb) through lateral gene transfer (LGT) for boosted antigen levels potentially triggering a robust immune response. In this study we confirmed the in vitro LGT efficiency of a plasmid (pRBD-Amp[r]) containing severe acute respiratory syndrome coronavirus-2 (SARS CoV-2) spike protein-receptor binding domain (RBD) coding gene along with an ampicillin-resistance gene (selection marker) from the probiotic Lactobacillus (donor) cultured from homemade yogurt to E. coli and Helicobacter pylori (recipients). Both the donor and recipient bacteria not only exhibited ampicillin-resistance from pRBD-Amp[r] but also expressed RBD protein. Furthermore, Lactobacillus isolated from YoVac consistently showed the expression of RBD protein over a period of one month confirming the shelf life of our prototype stored at 4 °C. Taken together, our in vitro results provide a preliminary basis for the potential in vivo transfer of RBD coding gene from YoVac to other bacterial species in the hgMb through LGT and may potentially boost the vaccine dosage by delegating them.},
}

@article {pmid39216330,
year = {2024},
author = {Fernández-Arévalo, U and Fuchs, J and Boll, M and Díaz, E},
title = {Transcriptional regulation of the anaerobic 3-hydroxybenzoate degradation pathway in Aromatoleum sp. CIB.},
journal = {Microbiological research},
volume = {288},
number = {},
pages = {127882},
doi = {10.1016/j.micres.2024.127882},
pmid = {39216330},
issn = {1618-0623},
abstract = {Phenolic compounds are commonly found in anoxic environments, where they serve as both carbon and energy sources for certain anaerobic bacteria. The anaerobic breakdown of m-cresol, catechol, and certain lignin-derived compounds yields the central intermediate 3-hydroxybenzoate/3-hydroxybenzoyl-CoA. In this study, we have characterized the transcription and regulation of the hbd genes responsible for the anaerobic degradation of 3-hydroxybenzoate in the β-proteobacterium Aromatoleum sp. CIB. The hbd cluster is organized in three catabolic operons and a regulatory hbdR gene that encodes a dimeric transcriptional regulator belonging to the TetR family. HbdR suppresses the activity of the three catabolic promoters (PhbdN, PhbdE and PhbdH) by binding to a conserved palindromic operator box (ATGAATGAN4TCATTCAT). 3-Hydroxybenzoyl-CoA, the initial intermediate of the 3-hydroxybenzoate degradation pathway, along with benzoyl-CoA, serve as effector molecules that bind to HbdR inducing the expression of the hbd genes. Moreover, the hbd genes are subject to additional regulation influenced by the presence of non-aromatic carbon sources (carbon catabolite repression), and their expression is induced in oxygen-deprived conditions by the AcpR transcriptional activator. The prevalence of the hbd cluster among members of the Aromatoleum/Thauera bacterial group, coupled with its association with mobile genetic elements, suggests acquisition through horizontal gene transfer. These findings significantly enhance our understanding of the regulatory mechanisms governing the hbd gene cluster in bacteria, paving the way for further exploration into the anaerobic utilization/valorization of phenolic compounds derived from lignin.},
}

@article {pmid39214976,
year = {2024},
author = {Yi, X and Liang, JL and Wen, P and Jia, P and Feng, SW and Liu, SY and Zhuang, YY and Guo, YQ and Lu, JL and Zhong, SJ and Liao, B and Wang, Z and Shu, WS and Li, JT},
title = {Giant viruses as reservoirs of antibiotic resistance genes.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {7536},
pmid = {39214976},
issn = {2041-1723},
mesh = {*Phylogeny ; *Giant Viruses/genetics ; *Genome, Viral/genetics ; Drug Resistance, Microbial/genetics ; Bacteriophages/genetics/isolation & purification ; Anti-Bacterial Agents/pharmacology ; Metagenome/genetics ; Gene Transfer, Horizontal ; Trimethoprim/pharmacology ; Drug Resistance, Bacterial/genetics ; },
abstract = {Nucleocytoplasmic large DNA viruses (NCLDVs; also called giant viruses), constituting the phylum Nucleocytoviricota, can infect a wide range of eukaryotes and exchange genetic material with not only their hosts but also prokaryotes and phages. A few NCLDVs were reported to encode genes conferring resistance to beta‑lactam, trimethoprim, or pyrimethamine, suggesting that they are potential vehicles for the transmission of antibiotic resistance genes (ARGs) in the biome. However, the incidence of ARGs across the phylum Nucleocytoviricota, their evolutionary characteristics, their dissemination potential, and their association with virulence factors remain unexplored. Here, we systematically investigated ARGs of 1416 NCLDV genomes including those of almost all currently available cultured isolates and high-quality metagenome-assembled genomes from diverse habitats across the globe. We reveal that 39.5% of them carry ARGs, which is approximately 37 times higher than that for phage genomes. A total of 12 ARG types are encoded by NCLDVs. Phylogenies of the three most abundant NCLDV-encoded ARGs hint that NCLDVs acquire ARGs from not only eukaryotes but also prokaryotes and phages. Two NCLDV-encoded trimethoprim resistance genes are demonstrated to confer trimethoprim resistance in Escherichia coli. The presence of ARGs in NCLDV genomes is significantly correlated with mobile genetic elements and virulence factors.},
}

*Phylogeny
*Giant Viruses/genetics
*Genome, Viral/genetics
Drug Resistance, Microbial/genetics
Bacteriophages/genetics/isolation & purification
Anti-Bacterial Agents/pharmacology
Metagenome/genetics
Gene Transfer, Horizontal
Trimethoprim/pharmacology
Drug Resistance, Bacterial/genetics

@article {pmid39047887,
year = {2024},
author = {Wu, X and Jia, W and Fang, Z and Sun, H and Wang, G and Liu, L and Zheng, M and Chen, G},
title = {Cyanobacteria mediate the dissemination of bacterial antibiotic resistance through conjugal transfer.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {359},
number = {},
pages = {124592},
doi = {10.1016/j.envpol.2024.124592},
pmid = {39047887},
issn = {1873-6424},
mesh = {*Drug Resistance, Bacterial/genetics ; *Microcystis/genetics ; *Gene Transfer, Horizontal ; *Cyanobacteria/genetics ; Anti-Bacterial Agents/pharmacology ; Conjugation, Genetic ; Genes, Bacterial ; Bacteria/genetics/drug effects ; },
abstract = {Cyanobacterial blooms are expanding world-wide in freshwater and marine environments, and can cause serious ecological and environmental issues, which also contribute to the spread of antibiotic resistance genes (ARGs). However, the mechanistic understanding of cyanobacteria-mediated resistance dynamics is not fully elucidated yet. We selected Microcystis aeruginosa as a model cyanobacteria to illustrate how cyanobacteria mediate the evolution and transfer processes of bacterial antibiotic resistance. The results show that the presence of cyanobacteria significantly decreased the abundance of antibiotic resistant bacteria (ARB) and antibiotic resistant genes (ARGs) by 3%-99% and 2%-18%, respectively. In addition, it clearly altered bacterial community structure, with the dominant genera evolving from Acinetobacter (27%) and Enterobacter (42%) to Porphyrobacter (59%). The abundance of ARGs positively correlated with Proteobacteria and Firmicutes, rather than Cyanobacteria, and Bacteroidetes. In the presence of cyanobacteria, the transfer events of bacterial resistance genes via conjugation were found to decrease by 10%-89% (p < 0.05). Surprisingly, we found an extradentary high transfer frequency (about 0.1) for the ARGs via plasmid conjugation from the bacteria into M. aeruginosa population. It confirmed the role of cyanobacterial population as the competent hosts to facilitate ARGs spreading. Our findings provide valuable information on the risk evaluation of ARGs caused by cyanobacterial blooms in aquatic environments, key for the protection and assessment of aquatic environmental quality.},
}

*Drug Resistance, Bacterial/genetics
*Microcystis/genetics
*Gene Transfer, Horizontal
*Cyanobacteria/genetics
Anti-Bacterial Agents/pharmacology
Conjugation, Genetic
Genes, Bacterial
Bacteria/genetics/drug effects

@article {pmid39214865,
year = {2024},
author = {Fonseca, DR and Day, LA and Crone, KK and Costa, KC},
title = {An Extracellular, Ca[2+]-Activated Nuclease (EcnA) Mediates Transformation in a Naturally Competent Archaeon.},
journal = {Molecular microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/mmi.15311},
pmid = {39214865},
issn = {1365-2958},
support = {MCB-2148165//National Science Foundation/ ; },
abstract = {Transformation, the uptake of DNA directly from the environment, is a major driver of gene flow in microbial populations. In bacteria, DNA uptake requires a nuclease that processes dsDNA to ssDNA, which is subsequently transferred into the cell and incorporated into the genome. However, the process of DNA uptake in archaea is still unknown. Previously, we cataloged genes essential to natural transformation in Methanococcus maripaludis, but few homologs of bacterial transformation-associated genes were identified. Here, we characterize one gene, MMJJ_16440 (named here as ecnA), to be an extracellular nuclease. We show that EcnA is Ca[2+]-activated, present on the cell surface, and essential for transformation. While EcnA can degrade several forms of DNA, the highest activity was observed with ssDNA as a substrate. Activity was also observed with circular dsDNA, suggesting that EcnA is an endonuclease. This is the first biochemical characterization of a transformation-associated protein in a member of the archaeal domain and suggests that both archaeal and bacterial transformation initiate in an analogous fashion.},
}

@article {pmid39214042,
year = {2024},
author = {Li, G and Long, TF and Zhou, SY and Xia, LJ and Gao, A and Wan, L and Diao, XY and He, YZ and Sun, RY and Yang, JT and Tang, SQ and Ren, H and Fang, LX and Liao, XP and Liu, YH and Chen, L and Sun, J},
title = {CRISPR-AMRtracker: A novel toolkit to monitor the antimicrobial resistance gene transfer in fecal microbiota.},
journal = {Drug resistance updates : reviews and commentaries in antimicrobial and anticancer chemotherapy},
volume = {77},
number = {},
pages = {101142},
doi = {10.1016/j.drup.2024.101142},
pmid = {39214042},
issn = {1532-2084},
abstract = {The spread of antibiotic resistance genes (ARGs), particularly those carried on plasmids, poses a major risk to global health. However, the extent and frequency of ARGs transfer in microbial communities among human, animal, and environmental sectors is not well understood due to a lack of effective tracking tools. We have developed a novel fluorescent tracing tool, CRISPR-AMRtracker, to study ARG transfer. It combines CRISPR/Cas9 fluorescence tagging, fluorescence-activated cell sorting, 16S rRNA gene sequencing, and microbial community analysis. CRISPR-AMRtracker integrates a fluorescent tag immediately downstream of ARGs, enabling the tracking of ARG transfer without compromising the host cell's antibiotic susceptibility, fitness, conjugation, and transposition. Notably, our experiments demonstrate that sfGFP-tagged plasmid-borne mcr-1 can transfer across diverse bacterial species within fecal samples. This innovative approach holds the potential to illuminate the dynamics of ARG dissemination and provide valuable insights to shape effective strategies in mitigating the escalating threat of antibiotic resistance.},
}

@article {pmid39213533,
year = {2024},
author = {Zeng, Q and Wu, X and Song, M and Jiang, L and Zeng, Q and Qiu, R and Luo, C},
title = {Opposite Effects of Planting on Antibiotic Resistomes in Rhizosphere Soil with Different Sulfamethoxazole Levels.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.4c04258},
pmid = {39213533},
issn = {1520-5118},
abstract = {Achieving consensus about the rhizosphere effect on soil antibiotic resistomes is challenging due to the variability in antibiotic concentrations, sources, and the elusory underlying mechanisms. Here, we characterized the antibiotic resistomes in both the rhizosphere and bulk soils of soybean plants grown in environments with varying levels of antibiotic contamination, using sulfamethoxazole (SMX) as a model compound. We also investigated the factors influencing resistome profiles. Soybean cultivation altered the structure of antibiotic-resistant genes (ARGs) and increased their absolute abundance. However, the rhizosphere effect on the relative abundance of ARGs was dependent on SMX concentrations. At low SMX levels, the rhizosphere effect was characterized by the inhibition of antibiotic-resistant bacteria (ARBs) and the promotion of sensitive bacteria. In contrast, at high SMX levels, the rhizosphere promoted the growth of ARBs and facilitated horizontal gene transfer of ARGs. This novel mechanism provides new insights into accurately assessing the rhizosphere effect on soil antibiotic resistomes.},
}

@article {pmid39213158,
year = {2024},
author = {Ma, Y and Kan, A and Johnson, DR},
title = {Metabolic interactions control the transfer and spread of plasmid-encoded antibiotic resistance during surface-associated microbial growth.},
journal = {Cell reports},
volume = {43},
number = {9},
pages = {114653},
doi = {10.1016/j.celrep.2024.114653},
pmid = {39213158},
issn = {2211-1247},
abstract = {Surface-associated microbial systems are hotspots for the spread of plasmid-encoded antibiotic resistance, but how surface association affects plasmid transfer and proliferation remains unclear. Surface association enables prolonged spatial proximities between different populations, which promotes plasmid transfer between them. However, surface association also fosters strong metabolic interactions between different populations, which can direct their spatial self-organization with consequences for plasmid transfer and proliferation. Here, we hypothesize that metabolic interactions direct the spatial self-organization of different populations and, in turn, regulate the spread of plasmid-encoded antibiotic resistance. We show that resource competition causes populations to spatially segregate, which represses plasmid transfer. In contrast, resource cross-feeding causes populations to spatially intermix, which promotes plasmid transfer. We further show that the spatial positionings that emerge from metabolic interactions determine the proliferation of plasmid recipients. Our results demonstrate that metabolic interactions are important regulators of both the transfer and proliferation of plasmid-encoded antibiotic resistance.},
}

@article {pmid39211246,
year = {2024},
author = {Hughes Lago, C and Blackburn, D and Kinder Pavlicek, M and Threadgill, DS},
title = {Comparative Genomic Analysis of Campylobacter rectus and Closely Related Species.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.07.26.605372},
pmid = {39211246},
issn = {2692-8205},
abstract = {Campylobacter rectus is a gram-negative, anaerobic bacterium strongly associated with periodontitis. It also causes various extraoral infections and is linked to adverse pregnancy outcomes in humans and murine models. C. rectus and related oral Campylobacters have been termed "emerging Campylobacter species" because infections by these organisms are likely underreported. Previously, no comparative methods have been used to analyze more than single C. rectus strains and until recently, very few C. rectus genomes have been publicly available. More sequenced genomes and comparative analyses are needed to study the genomic features and pathogenicity of this species. We sequenced eight new C. rectus strains and used comparative methods to identify regions of interest. An emphasis was put on the type III flagellar secretion system (T3SS), type IV secretion system (T4SS), and type VI secretion system (T6SS) because these protein complexes are important for pathogenesis in other Campylobacter species. RAST, BV-BRC, and other bioinformatics tools were used to assemble, annotate, and compare these regions in the genomes. The pan-genome of C. rectus consists of 2670 genes with core and accessory genomes of 1429 and 1241 genes, respectively. All isolates analyzed in this study have T3SS and T6SS hallmark proteins, while five of the isolates are missing a T4SS system. Twenty-one prophage clusters were identified across the panel of isolates, including four that appear intact. Overall, significant genomic islands were found, suggesting regions in the genomes that underwent horizontal gene transfer. Additionally, the high frequency of CRISPR arrays and other repetitive elements has led to genome rearrangements across the strains, including in areas adjacent to secretion system gene clusters. This study describes the substantial diversity present among C. rectus isolates and highlights tools/assays that have been developed to permit functional genomic studies. Additionally, we have expanded the studies on C. showae T4SS since we have two new C. showae genomes to report. We also demonstrate that unlike C. rectus , C showae does not demonstrate evidence of intact T6SS except for the strain CAM. The only strain of sequenced C. massilensis has neither T4SS or T6SS.},
}

@article {pmid39211212,
year = {2024},
author = {Marcarian, HQ and Sivakoses, A and Arias, AM and Ihedioha, OC and Lee, BR and Bishop, MC and Bothwell, ALM},
title = {Renal cancer cells acquire immune surface protein through trogocytosis and horizontal gene transfer.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.08.07.607036},
pmid = {39211212},
issn = {2692-8205},
abstract = {UNLABELLED: Trogocytosis is an underappreciated phenomenon that shapes the immune microenvironment surrounding many types of solid tumors. The consequences of membrane-bound proteins being deposited from a donor immune cell to a recipient cancer cell via trogocytosis are still unclear. Here, we report that human clear cell renal carcinoma tumors stably express the lymphoid markers CD45, CD56, CD14, and CD16. Flow cytometry performed on fresh kidney tumors revealed consistent CD45 expression on tumor cells, as well as varying levels of the other markers mentioned previously. These results were consistent with our immunofluorescent analysis, which also revealed colocalization of lymphoid markers with carbonic anhydrase 9 (CAIX), a standard kidney tumor marker. RNA analysis showed a significant upregulation of genes typically associated with immune cells in tumor cells following trogocytosis. Finally, we show evidence of chromosomal DNA being transferred from immune cells to tumor cells during trogocytosis. This horizontal gene transfer has transcriptional consequences in the recipient tumor cell, resulting in a fusion phenotype that expressed both immune and cancer specific proteins. This work demonstrates a novel mechanism by which tumor cell protein expression is altered through the acquisition of surface membrane fragments and genomic DNA from infiltrating lymphocytes. These results alter the way in which we understand tumor-immune cell interactions and may reveal new insights into the mechanisms by which tumors develop. Additionally, further studies into trogocytosis will help push the field towards the next generation of immunotherapies and biomarkers for treating renal cell carcinoma and other types of cancers.

SIGNIFICANCE STATEMENT: We have identified trogocytosis as a mechanism by which human clear cell renal carcinoma tumors acquire lymphocyte surface protein expression from tumor infiltrating immune cells. In addition to the transfer of membrane fragments, we have provided evidence to show that genomic DNA is transferred from a normal immune cell to a tumor cell during trogocytosis. This process alters the transcriptome of cancer cells such that they express significantly more mRNA for immune proteins such as the lymphocyte marker CD45 compared to tumor cells that have not undergone trogocytosis. This study provides an in-depth analysis of the interactions between cancer cells and tumor infiltrating lymphocytes, and how these interactions alter the development of human tumors.},
}

@article {pmid39210455,
year = {2024},
author = {Abdellati, S and Gestels, Z and Laumen, JGE and Van Dijck, C and De Baetselier, I and de Block, T and Van den Bossche, D and Vanbaelen, T and Kanesaka, I and Manoharan-Basil, SS and Kenyon, C},
title = {Antimicrobial susceptibility of commensal Neisseria spp. In parents and their children in Belgium: a cross-sectional survey.},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnae069},
pmid = {39210455},
issn = {1574-6968},
abstract = {BACKGROUND: Commensal Neisseria species are part of the oropharyngeal microbiome and play an important role in nitrate reduction and protecting against colonization by pathogenic bacteria. They do, however, also serve as a reservoir of antimicrobial resistance. Little is known about the prevalence of these species in the general population, how this varies by age and how antimicrobial susceptibility varies between species.

METHODS: We assessed the prevalence and antimicrobial susceptibility of commensal Neisseria species in the parents (n = 38) and children (n = 50) of 35 families in Belgium.

RESULTS: Various commensal Neisseria (n = 5) could be isolated from the participants. Most abundant were N. subflava and N. mucosa. N. subflava was detected in 77 of 88 (87.5%) individuals and N. mucosa in 64 of 88 (72.7%). N. mucosa was more prevalent in children (41/50 [82%]) than parents (23/38 [60.5%]; P < 0.05), while N. bacilliformis was more prevalent in parents (7/36 [19.4%]) than children (2/50 [4%]; P < 0.05). N. bacilliformis had high ceftriaxone minimum inhibitory concentrations (MICs; median MIC 0.5 mg/L; IQR 0.38-0.75). The ceftriaxone MICs of all Neisseria isolates were higher in the parents than in the children. This could be explained by a higher prevalence of N. bacilliformis in the parents.

INTERPRETATION: The N. bacilliformis isolates had uniformly high ceftriaxone MICs which warrant further investigation.},
}

@article {pmid39207571,
year = {2024},
author = {Smiatek, J},
title = {Principles of Molecular Evolution: Concepts from Non-equilibrium Thermodynamics for the Multilevel Theory of Learning.},
journal = {Journal of molecular evolution},
volume = {},
number = {},
pages = {},
pmid = {39207571},
issn = {1432-1432},
abstract = {We present a non-equilibrium thermodynamics approach to the multilevel theory of learning for the study of molecular evolution. This approach allows us to study the explicit time dependence of molecular evolutionary processes and their impact on entropy production. Interpreting the mathematical expressions, we can show that two main contributions affect entropy production of molecular evolution processes which can be identified as mutation and gene transfer effects. Accordingly, our results show that the optimal adaptation of organisms to external conditions in the context of evolutionary processes is driven by principles of minimum entropy production. Such results can also be interpreted as the basis of some previous postulates of the theory of learning. Although our macroscopic approach requires certain simplifications, it allows us to interpret molecular evolutionary processes using thermodynamic descriptions with reference to well-known biological processes.},
}

@article {pmid39207102,
year = {2024},
author = {Zhang, W and Fan, Y and Deng, W and Chen, Y and Wang, S and Kang, S and Steenwyk, JL and Xiang, M and Liu, X},
title = {Characterization of genome-wide phylogenetic conflict uncovers evolutionary modes of carnivorous fungi.},
journal = {mBio},
volume = {},
number = {},
pages = {e0213324},
doi = {10.1128/mbio.02133-24},
pmid = {39207102},
issn = {2150-7511},
abstract = {Mass extinction has often paved the way for rapid evolutionary radiation, resulting in the emergence of diverse taxa within specific lineages. The emergence and diversification of carnivorous nematode-trapping fungi (NTF) in Ascomycota have been linked to the Permian-Triassic (PT) extinction, but the processes underlying NTF radiation remain unclear. We conducted phylogenomic analyses using 23 genomes that represent three NTF lineages, each employing distinct nematode traps-mechanical traps (Drechslerella spp.), three-dimensional (3D) adhesive traps (Arthrobotrys spp.), and two-dimensional (2D) adhesive traps (Dactylellina spp.), and the genome of one non-NTF species as the outgroup. These analyses revealed multiple mechanisms that likely contributed to the tempo of the NTF evolution and rapid radiation. The species tree of NTFs based on 2,944 single-copy orthologous genes suggested that Drechslerella emerged earlier than Arthrobotrys and Dactylellina. Extensive genome-wide phylogenetic discordance was observed, mainly due to incomplete lineage sorting (ILS) between lineages. Two modes of non-vertical evolution (introgression and horizontal gene transfer) also contributed to phylogenetic discordance. The ILS genes that are associated with hyphal growth and trap morphogenesis (e.g., those associated with the cell membrane system and polarized cell division) exhibited signs of positive selection.IMPORTANCEBy conducting a comprehensive phylogenomic analysis of 23 genomes across three NTF lineages, the research reveals how diverse evolutionary mechanisms, including ILS and non-vertical evolution (introgression and horizontal gene transfer), contribute to the swift diversification of NTFs. These findings highlight the complex evolutionary dynamics that drive the rapid radiation of NTFs, providing valuable insights into the processes underlying their diversity and adaptation.},
}

@article {pmid39206372,
year = {2024},
author = {Kirk, A and Stavrinides, J},
title = {Distribution and comparative genomic analysis of antimicrobial gene clusters found in Pantoea.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1416674},
doi = {10.3389/fmicb.2024.1416674},
pmid = {39206372},
issn = {1664-302X},
abstract = {Members of the bacterial genus Pantoea produce a variety of antimicrobial products that are effective against plant, animal, and human pathogens. To date, little is known about the distribution and evolutionary history of these clusters. We surveyed the public databases for the 12 currently known antibiotic biosynthetic gene clusters found across Pantoea strains to determine their distribution. We show that some clusters, namely pantocin B, PNP-3, and PNP-4 are found strictly in Pantoea, while agglomerin, andrimid, AGA, dapdiamide, herbicolin, PNP-1, PNP-2, PNP-5, and pantocin A, are more broadly distributed in distantly related genera within Vibrionaceae, Pectobacteriaceae, Yersiniaceae, Morganellaceae, and Hafniaceae. We evaluated the evolutionary history of these gene clusters relative to a cpn60-based species tree, considering the flanking regions of each cluster, %GC, and presence of mobile genetic elements, and identified potential occurrences of horizontal gene transfer. Lastly, we also describe the biosynthetic gene cluster of pantocin B in the strain Pantoea agglomerans Eh318 more than 20 years after this antibiotic was first described.},
}

@article {pmid39203510,
year = {2024},
author = {Lv, N and Ni, J and Fang, S and Liu, Y and Wan, S and Sun, C and Li, J and Zhou, A},
title = {Potential Convergence to Accommodate Pathogenicity Determinants and Antibiotic Resistance Revealed in Salmonella Mbandaka.},
journal = {Microorganisms},
volume = {12},
number = {8},
pages = {},
doi = {10.3390/microorganisms12081667},
pmid = {39203510},
issn = {2076-2607},
support = {32260032//National Natural Science Foundation of China/ ; 32370143//National Natural Science Foundation of China/ ; 31800118//National Natural Science Foundation of China/ ; jxsq2019101054//Double Thousand Talents Plan of Jiangxi/ ; },
abstract = {Salmonella species are causal pathogens instrumental in human food-borne diseases. The pandemic survey related to multidrug resistant (MDR) Salmonella genomics enables the prevention and control of their dissemination. Currently, serotype Mbandaka is notorious as a multiple host-adapted non-typhoid Salmonella. However, its epidemic and MDR properties are still obscure, especially its genetic determinants accounting for virulence and MD resistance. Here, we aim to characterize the genetic features of a strain SMEH pertaining to Salmonella Mbandaka (S. Mbandaka), isolated from the patient's hydropericardium, using cell infections, a mouse model, antibiotic susceptibility test and comparative genomics. The antibiotic susceptibility testing showed that it could tolerate four antibiotics, including chloramphenicol, tetracycline, fisiopen and doxycycline by Kirby-Bauer (K-B) testing interpreted according to the Clinical and Laboratory Standards Institute (CLSI). Both the reproducibility in RAW 264.7 macrophages and invasion ability to infect HeLa cells with strain SMEH were higher than those of S. Typhimurium strain 14028S. In contrast, its attenuated virulence was determined in the survival assay using a mouse model. As a result, the candidate genetic determinants responsible for antimicrobial resistance, colonization/adaptability and their transferability were comparatively investigated, such as bacterial secretion systems and pathogenicity islands (SPI-1, SPI-2 and SPI-6). Moreover, collective efforts were made to reveal a potential role of the plasmid architectures in S. Mbandaka as the genetic reservoir to transfer or accommodate drug-resistance genes. Our findings highlight the essentiality of antibiotic resistance and risk assessment in S. Mbandaka. In addition, genomic surveillance is an efficient method to detect pathogens and monitor drug resistance. The genetic determinants accounting for virulence and antimicrobial resistance underscore the increasing clinical challenge of emerging MDR Mbandaka isolates, and provide insights into their prevention and treatment.},
}

@article {pmid39201699,
year = {2024},
author = {Li, H and Liang, T and Liu, Y and Wang, P and Wang, S and Zhao, M and Zhang, Y},
title = {Exploring Mitochondrial Heterogeneity and Evolutionary Dynamics in Thelephora ganbajun through Population Genomics.},
journal = {International journal of molecular sciences},
volume = {25},
number = {16},
pages = {},
doi = {10.3390/ijms25169013},
pmid = {39201699},
issn = {1422-0067},
support = {31870009//National Natural Science Foundation of China/ ; YNWR-QNBJ-2018-355//Top Young Talents Program of the Ten Thousand Talents Plan in Yunnan Province/ ; 2021KF009//YNCUB/ ; },
mesh = {*Genome, Mitochondrial ; *Evolution, Molecular ; Phylogeny ; Introns/genetics ; Mitochondria/genetics ; Basidiomycota/genetics ; DNA, Mitochondrial/genetics ; Genomics/methods ; Gene Transfer, Horizontal ; },
abstract = {Limited exploration in fungal mitochondrial genetics has uncovered diverse inheritance modes. The mitochondrial genomes are inherited uniparentally in the majority of sexual eukaryotes, our discovery of persistent mitochondrial heterogeneity within the natural population of the basidiomycete fungus Thelephora ganbajun represents a significant advance in understanding mitochondrial inheritance and evolution in eukaryotes. Here, we present a comprehensive analysis by sequencing and assembling the complete mitogenomes of 40 samples exhibiting diverse cox1 heterogeneity patterns from various geographical origins. Additionally, we identified heterogeneous variants in the nad5 gene, which, similar to cox1, displayed variability across multiple copies. Notably, our study reveals a distinct prevalence of introns and homing endonucleases in these heterogeneous genes. Furthermore, we detected potential instances of horizontal gene transfer involving homing endonucleases. Population genomic analyses underscore regional variations in mitochondrial genome composition among natural samples exhibiting heterogeneity. Thus, polymorphisms in heterogeneous genes, introns, and homing endonucleases significantly influence mitochondrial structure, structural variation, and evolutionary dynamics in this species. This study contributes valuable insights into mitochondrial genome architecture, population dynamics, and the evolutionary implications of mitochondrial heterogeneity in sexual eukaryotes.},
}

*Genome, Mitochondrial
*Evolution, Molecular
Phylogeny
Introns/genetics
Mitochondria/genetics
Basidiomycota/genetics
DNA, Mitochondrial/genetics
Genomics/methods
Gene Transfer, Horizontal

@article {pmid39200594,
year = {2024},
author = {Habibi, N and Uddin, S and Behbehani, M and Mustafa, AS and Al-Fouzan, W and Al-Sarawi, HA and Safar, H and Alatar, F and Al Sawan, RMZ},
title = {Aerosol-Mediated Spread of Antibiotic Resistance Genes: Biomonitoring Indoor and Outdoor Environments.},
journal = {International journal of environmental research and public health},
volume = {21},
number = {8},
pages = {},
doi = {10.3390/ijerph21080983},
pmid = {39200594},
issn = {1660-4601},
mesh = {*Aerosols/analysis ; *Gene Transfer, Horizontal ; Humans ; Biological Monitoring ; Drug Resistance, Microbial/genetics ; Air Microbiology ; Air Pollution, Indoor/analysis ; Environmental Monitoring ; Anti-Bacterial Agents/analysis ; Drug Resistance, Bacterial/genetics ; },
abstract = {Antimicrobial resistance (AMR) has emerged as a conspicuous global public health threat. The World Health Organization (WHO) has launched the "One-Health" approach, which encourages the assessment of antibiotic resistance genes (ARGs) within an environment to constrain and alleviate the development of AMR. The prolonged use and overuse of antibiotics in treating human and veterinary illnesses, and the inability of wastewater treatment plants to remove them have resulted in elevated concentrations of these metabolites in the surroundings. Microbes residing within these settings acquire resistance under selective pressure and circulate between the air-land interface. Initial evidence on the indoor environments of wastewater treatment plants, hospitals, and livestock-rearing facilities as channels of AMR has been documented. Long- and short-range transport in a downwind direction disseminate aerosols within urban communities. Inhalation of such aerosols poses a considerable occupational and public health risk. The horizontal gene transfer (HGT) is another plausible route of AMR spread. The characterization of ARGs in the atmosphere therefore calls for cutting-edge research. In the present review, we provide a succinct summary of the studies that demonstrated aerosols as a media of AMR transport in the atmosphere, strengthening the need to biomonitor these pernicious pollutants. This review will be a useful resource for environmental researchers, healthcare practitioners, and policymakers to issue related health advisories.},
}

*Aerosols/analysis
*Gene Transfer, Horizontal
Humans
Biological Monitoring
Drug Resistance, Microbial/genetics
Air Microbiology
Air Pollution, Indoor/analysis
Environmental Monitoring
Anti-Bacterial Agents/analysis
Drug Resistance, Bacterial/genetics

@article {pmid39200027,
year = {2024},
author = {Milani, G and Cortimiglia, C and Belloso Daza, MV and Greco, E and Bassi, D and Cocconcelli, PS},
title = {Microplastic-Mediated Transfer of Tetracycline Resistance: Unveiling the Role of Mussels in Marine Ecosystems.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {13},
number = {8},
pages = {},
doi = {10.3390/antibiotics13080727},
pmid = {39200027},
issn = {2079-6382},
support = {PE00000003//Italian Ministry of University and Research funded by the European Union - NextGenerationEU/ ; },
abstract = {The global threat of antimicrobial resistance (AMR) is exacerbated by the mobilization of antimicrobial resistance genes (ARGs) occurring in different environmental niches, including seawater. Marine environments serve as reservoirs for resistant bacteria and ARGs, further complicated by the ubiquity of microplastics (MPs). MPs can adsorb pollutants and promote bacterial biofilm formation, creating conditions favorable to the dissemination of ARGs. This study explores the dynamics of ARG transfer in the marine bivalve Mytilus galloprovincialis within a seawater model, focusing on the influence of polyethylene MPs on the mobilization of the Tn916-carrying tetM gene and plasmid-encoded ermB. Experiments revealed that biofilm formation on MPs by Enterococcus faecium and Listeria monocytogenes facilitated the transfer of the tetM resistance gene, but not the ermB gene. Furthermore, the presence of MPs significantly increased the conjugation frequency of tetM within mussels, indicating that MPs enhance the potential for ARG mobilization in marine environments. These findings highlight the role of MPs and marine organisms in ARG spread, underscoring the ecological and public health implications.},
}

@article {pmid39199982,
year = {2024},
author = {Yao, Y and Imirzalioglu, C and Falgenhauer, L and Falgenhauer, J and Heinmüller, P and , and Domann, E and Chakraborty, T},
title = {Plasmid-Mediated Spread of Carbapenem Resistance in Enterobacterales: A Three-Year Genome-Based Survey.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {13},
number = {8},
pages = {},
doi = {10.3390/antibiotics13080682},
pmid = {39199982},
issn = {2079-6382},
abstract = {The worldwide emergence and dissemination of carbapenem-resistant Gram-negative bacteria (CRGNB) is a challenging problem of antimicrobial resistance today. Outbreaks with CRGNB have severe consequences for both the affected healthcare settings as well as the patients with infection. Thus, bloodstream infections caused by metallo-ß-lactamase-producing Enterobacterales can often have clinical implications, resulting in high mortality rates due to delays in administering effective treatment and the limited availability of treatment options. The overall threat of CRGNB is substantial because carbapenems are used to treat infections caused by ESBL-producing Enterobacterales which also exist with high frequency within the same geographical regions. A genome-based surveillance of 589 CRGNB from 61 hospitals across the federal state Hesse in Germany was implemented using next-generation sequencing (NGS) technology to obtain a high-resolution landscape of carbapenem-resistant isolates over a three-year period (2017-2019). The study examined all reportable CRGNB isolates submitted by participating hospitals. This included isolates carrying known carbapenemases (435) together with carbapenem-resistant non-carbapenemase producers (154). Predominant carbapenemase producers included Klebsiella pneumoniae, Escherichia coli, Citrobacter freundii and Acinetobacter baumannii. Over 80% of 375 carbapenem-resistant determinants including KPC-, NDM-, VIM- and OXA-48-like ones detected in 520 Enterobacterales were plasmid-encoded, and half of these were dominated by a few incompatibility (Inc) types, viz., IncN, IncL/M, IncFII and IncF(K). Our results revealed that plasmids play an extraordinary role in the dissemination of carbapenem resistance in the heterogeneous CRGNB population. The plasmids were also associated with several multispecies dissemination events and local outbreaks throughout the study period, indicating the substantial role of horizontal gene transfer in carbapenemase spread. Furthermore, due to vertical and horizontal plasmid transfer, this can have an impact on implant-associated infections and is therefore important for antibiotic-loaded bone cement and drug-containing devices in orthopedic surgery. Future genomic surveillance projects should increase their focus on plasmid characterization.},
}

@article {pmid39198891,
year = {2024},
author = {Tian, F and Wainaina, JM and Howard-Varona, C and Domínguez-Huerta, G and Bolduc, B and Gazitúa, MC and Smith, G and Gittrich, MR and Zablocki, O and Cronin, DR and Eveillard, D and Hallam, SJ and Sullivan, MB},
title = {Prokaryotic-virus-encoded auxiliary metabolic genes throughout the global oceans.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {159},
pmid = {39198891},
issn = {2049-2618},
support = {ABI#1759874, ABI#2149505, OCE#1536989, OCE#1829831, and OCE#2019589//National Science Foundation/ ; #3790//Gordon and Betty Moore Foundation Investigator Award/ ; },
mesh = {*Oceans and Seas ; *Seawater/virology/microbiology ; Metagenomics ; Bacteria/genetics/classification/metabolism ; Viruses/genetics/classification/isolation & purification ; Prokaryotic Cells/metabolism/virology ; Metagenome ; Metabolic Networks and Pathways/genetics ; Gene Transfer, Horizontal ; Phosphatidylethanolamines/metabolism ; },
abstract = {BACKGROUND: Prokaryotic microbes have impacted marine biogeochemical cycles for billions of years. Viruses also impact these cycles, through lysis, horizontal gene transfer, and encoding and expressing genes that contribute to metabolic reprogramming of prokaryotic cells. While this impact is difficult to quantify in nature, we hypothesized that it can be examined by surveying virus-encoded auxiliary metabolic genes (AMGs) and assessing their ecological context.

RESULTS: We systematically developed a global ocean AMG catalog by integrating previously described and newly identified AMGs and then placed this catalog into ecological and metabolic contexts relevant to ocean biogeochemistry. From 7.6 terabases of Tara Oceans paired prokaryote- and virus-enriched metagenomic sequence data, we increased known ocean virus populations to 579,904 (up 16%). From these virus populations, we then conservatively identified 86,913 AMGs that grouped into 22,779 sequence-based gene clusters, 7248 (~ 32%) of which were not previously reported. Using our catalog and modeled data from mock communities, we estimate that ~ 19% of ocean virus populations carry at least one AMG. To understand AMGs in their metabolic context, we identified 340 metabolic pathways encoded by ocean microbes and showed that AMGs map to 128 of them. Furthermore, we identified metabolic "hot spots" targeted by virus AMGs, including nine pathways where most steps (≥ 0.75) were AMG-targeted (involved in carbohydrate, amino acid, fatty acid, and nucleotide metabolism), as well as other pathways where virus-encoded AMGs outnumbered cellular homologs (involved in lipid A phosphates, phosphatidylethanolamine, creatine biosynthesis, phosphoribosylamine-glycine ligase, and carbamoyl-phosphate synthase pathways).

CONCLUSIONS: Together, this systematically curated, global ocean AMG catalog and analyses provide a valuable resource and foundational observations to understand the role of viruses in modulating global ocean metabolisms and their biogeochemical implications. Video Abstract.},
}

*Oceans and Seas
*Seawater/virology/microbiology
Metagenomics
Bacteria/genetics/classification/metabolism
Viruses/genetics/classification/isolation & purification
Prokaryotic Cells/metabolism/virology
Metagenome
Metabolic Networks and Pathways/genetics
Gene Transfer, Horizontal
Phosphatidylethanolamines/metabolism

@article {pmid39198572,
year = {2024},
author = {Sastre-Dominguez, J and DelaFuente, J and Toribio-Celestino, L and Herencias, C and Herrador-Gómez, P and Costas, C and Hernández-García, M and Cantón, R and Rodríguez-Beltrán, J and Santos-Lopez, A and San Millan, A},
title = {Plasmid-encoded insertion sequences promote rapid adaptation in clinical enterobacteria.},
journal = {Nature ecology & evolution},
volume = {},
number = {},
pages = {},
pmid = {39198572},
issn = {2397-334X},
support = {757440-PLASREVOLUTION//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 895671-REPLAY//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 101077809-HorizonGT//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; PI19/00749//Ministry of Economy and Competitiveness | Instituto de Salud Carlos III (Institute of Health Carlos III)/ ; CD21/00115//Ministry of Economy and Competitiveness | Instituto de Salud Carlos III (Institute of Health Carlos III)/ ; PI23/01945//Ministry of Economy and Competitiveness | Instituto de Salud Carlos III (Institute of Health Carlos III)/ ; CP20/00154//Ministry of Economy and Competitiveness | Instituto de Salud Carlos III (Institute of Health Carlos III)/ ; PI21/01363//Ministry of Economy and Competitiveness | Instituto de Salud Carlos III (Institute of Health Carlos III)/ ; LCF/BQ/PR22/11920001//"la Caixa" Foundation (Caixa Foundation)/ ; Research Grant 2022//European Society of Clinical Microbiology and Infectious Diseases (ESCMID)/ ; },
abstract = {Plasmids are extrachromosomal genetic elements commonly found in bacteria. They are known to fuel bacterial evolution through horizontal gene transfer, and recent analyses indicate that they can also promote intragenomic adaptations. However, the role of plasmids as catalysts of bacterial evolution beyond horizontal gene transfer is poorly explored. In this study, we investigated the impact of a widespread conjugative plasmid, pOXA-48, on the evolution of several multidrug-resistant clinical enterobacteria. Combining experimental and within-patient evolution analyses, we unveiled that plasmid pOXA-48 promotes bacterial evolution through the transposition of plasmid-encoded insertion sequence 1 (IS1) elements. Specifically, IS1-mediated gene inactivation expedites the adaptation rate of clinical strains in vitro and fosters within-patient adaptation in the gut microbiota. We deciphered the mechanism underlying the plasmid-mediated surge in IS1 transposition, revealing a negative feedback loop regulated by the genomic copy number of IS1. Given the overrepresentation of IS elements in bacterial plasmids, our findings suggest that plasmid-mediated IS1 transposition represents a crucial mechanism for swift bacterial adaptation.},
}

@article {pmid39198281,
year = {2024},
author = {He, Z and Smets, BF and Dechesne, A},
title = {Mating Assay: Plating Below a Cell Density Threshold is Required for Unbiased Estimation of Plasmid Conjugation Frequency of RP4 Transfer Between E. coli Strains.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {109},
pmid = {39198281},
issn = {1432-184X},
support = {0236-00022B//Innovationsfonden/ ; 0236-00022B//Innovationsfonden/ ; 0236-00022B//Innovationsfonden/ ; PhD Scholarship//Sino-Danish Center/ ; PhD Scholarship//Sino-Danish Center/ ; },
mesh = {*Escherichia coli/genetics ; *Conjugation, Genetic ; *Plasmids/genetics ; Gene Transfer, Horizontal ; },
abstract = {Mating assays are common laboratory experiments for measuring the conjugation frequency, i.e. efficiency at which a plasmid transfers from a population of donor cells to a population of recipient cells. Selective plating remains a widely used quantification method to enumerate transconjugants at the end of such assays. However, conjugation frequencies may be inaccurately estimated because plasmid transfer can occur on transconjugant-selective plates rather than only during the intended mating duration. We investigated the influence of cell density on this phenomenon. We conducted mating experiments with IncPα plasmid RP4 harbored in Escherichia coli at a fixed cell density and mating conditions, inoculated a serial dilution of the mating mixture on transconjugant-selective plates or in transconjugant-selective broth, and compared the results to a model of cell-to-cell distance distribution. Our findings suggest that irrespective of the mating mode (liquid vs solid), the enumeration of transconjugants becomes significantly biased if the plated cell density exceeds 28 Colony Forming Unit (CFU)/mm[2] (or 1.68•10[5] CFU/standard 9 cm Petri dish). This threshold is determined with a 95% confidence interval of ± 4 CFU/mm[2] (± 2.46•10[4] CFU/standard 9 cm Petri dish). Liquid mating assays were more sensitive to this bias because the conjugation frequency of RP4 is several orders of magnitude lower in suspension compared to surface mating. Therefore, if selective plating is used, we recommend to plate at this density threshold and that negative controls are performed where donors and recipients are briefly mixed before plating at the same dilutions as for the actual mating assay. As an alternative, a liquid enumeration method can be utilized to increase the signal-to-noise ratio and allow for more accurate enumeration of transconjugants.},
}

*Escherichia coli/genetics
*Conjugation, Genetic
*Plasmids/genetics
Gene Transfer, Horizontal

@article {pmid39194517,
year = {2024},
author = {Yang, X and Liu, Z and Zhang, Y and Shi, X and Wu, Z},
title = {Dinoflagellate-Bacteria Interactions: Physiology, Ecology, and Evolution.},
journal = {Biology},
volume = {13},
number = {8},
pages = {},
pmid = {39194517},
issn = {2079-7737},
support = {42106093 and 41976130//National Natural Science Foundation of China/ ; 2022T150706//China Postdoctoral Science Foundation/ ; GPCGD223103FG015F//Comprehensive Protection and Utilization Program for the Coastal Zone of Guangdong 534 Province (Revision)/ ; DD20230460, DD20230107, and DD20242792//Marine Geological Survey 535 Program of China Geological Survey/ ; },
abstract = {Dinoflagellates and heterotrophic bacteria are two major micro-organism groups within marine ecosystems. Their coexistence has led to a co-evolutionary relationship characterized by intricate interactions that not only alter their individual behaviors but also exert a significant influence on the broader biogeochemical cycles. Our review commenced with an analysis of bacterial populations, both free-living and adherent to dinoflagellate surfaces. Members of Alphaproteobacteria, Gammaproteobacteria, and the Cytophaga-Flavobacterium-Bacteroides group are repeatedly found to be associated with dinoflagellates, with representation by relatively few genera, such as Methylophaga, Marinobacter, and Alteromonas. These bacterial taxa engage with dinoflagellates in a limited capacity, involving nutrient exchange, the secretion of pathogenic substances, or participation in chemical production. Furthermore, the genomic evolution of dinoflagellates has been profoundly impacted by the horizontal gene transfer from bacteria. The integration of bacterial genes into dinoflagellates has been instrumental in defining their biological characteristics and nutritional strategies. This review aims to elucidate the nuanced interactions between dinoflagellates and their associated bacteria, offering a detailed perspective on their complex relationship.},
}

@article {pmid39193949,
year = {2024},
author = {Kim, HJ and Koo, SH and Choi, Q},
title = {Horizontal Gene Transfer of blaNDM-5 Among Three Different Enterobacteriaceae Species Isolated from a Single Patient.},
journal = {Clinical laboratory},
volume = {70},
number = {8},
pages = {},
doi = {10.7754/Clin.Lab.2024.240309},
pmid = {39193949},
issn = {1433-6510},
mesh = {Humans ; *Gene Transfer, Horizontal ; *Microbial Sensitivity Tests ; *beta-Lactamases/genetics ; *Enterobacteriaceae/genetics/drug effects/isolation & purification ; *Anti-Bacterial Agents/pharmacology ; *Plasmids/genetics ; Enterobacteriaceae Infections/microbiology/diagnosis/drug therapy ; Whole Genome Sequencing ; Escherichia coli/genetics/drug effects/isolation & purification ; Klebsiella oxytoca/genetics/isolation & purification/drug effects ; Citrobacter/genetics/isolation & purification/drug effects ; },
abstract = {BACKGROUND: In this study, Escherichia coli, Klebsiella oxytoca, and Citrobacter amalonaticus carrying blaNDM-5 were isolated from a single patient.

METHODS: The antibiotic susceptibility of the isolates was evaluated by using E-test and agar dilution methods, and blaNDM-5 was identified in genomic and plasmid DNA by using polymerase chain reaction and sequencing. Whole genome sequencing and de novo assembly were used for species characterization, resistance gene identification, and plasmid analysis.

RESULTS: All three species had identical plasmids, which were similar to pEC463-NDM5, a plasmid harboring blaNDM-5. Transconjugation experiments confirmed the horizontal gene transfer of blaNDM-5, highlighting the need for a close monitoring of Enterobacteriaceae species harboring this gene.

CONCLUSIONS: This study conclusively demonstrates the propensity for horizontal gene transfer of blaNDM-5 among Enterobacteriaceae species, underlining the importance of vigilant monitoring to combat antibiotic resistance.},
}

Humans
*Gene Transfer, Horizontal
*Microbial Sensitivity Tests
*beta-Lactamases/genetics
*Enterobacteriaceae/genetics/drug effects/isolation & purification
*Anti-Bacterial Agents/pharmacology
*Plasmids/genetics
Enterobacteriaceae Infections/microbiology/diagnosis/drug therapy
Whole Genome Sequencing
Escherichia coli/genetics/drug effects/isolation & purification
Klebsiella oxytoca/genetics/isolation & purification/drug effects
Citrobacter/genetics/isolation & purification/drug effects

@article {pmid39191402,
year = {2024},
author = {Aoun, N and Georgoulis, SJ and Avalos, JK and Grulla, KJ and Miqueo, K and Tom, C and Lowe-Power, TM},
title = {A pangenomic atlas reveals eco-evolutionary dynamics that shape type VI secretion systems in plant-pathogenic Ralstonia.},
journal = {mBio},
volume = {},
number = {},
pages = {e0032324},
doi = {10.1128/mbio.00323-24},
pmid = {39191402},
issn = {2150-7511},
abstract = {Soilborne Ralstonia solanacearum species complex (RSSC) pathogens disrupt microbial communities as they invade roots and fatally wilt plants. RSSC pathogens secrete antimicrobial toxins using a type VI secretion system (T6SS). To investigate how evolution and ecology have shaped the T6SS of these bacterial pathogens, we analyzed the T6SS gene content and architecture across the RSSC and their evolutionary relatives. Our analysis reveals that two ecologically similar Burkholderiaceae taxa, xylem-pathogenic RSSC and Paracidovorax, have convergently evolved to wield large arsenals of T6SS toxins. To understand the mechanisms underlying genomic enrichment of T6SS toxins, we compiled an atlas of 1,066 auxiliary T6SS toxin clusters ("aux" clusters) across 99 high-quality RSSC genomes. We classified 25 types of aux clusters with toxins that predominantly target lipids, nucleic acids, or unknown cellular substrates. The aux clusters were located in diverse genetic neighborhoods and had complex phylogenetic distributions, suggesting frequent horizontal gene flow. Phages and other mobile genetic elements account for most of the aux cluster acquisition on the chromosome but very little on the megaplasmid. Nevertheless, RSSC genomes were more enriched in aux clusters on the megaplasmid. Although the single, ancestral T6SS was broadly conserved in the RSSC, the T6SS has been convergently lost in atypical, non-soilborne lineages. Overall, our data suggest dynamic interplay between the lifestyle of RSSC lineages and the evolution of T6SSes with robust arsenals of toxins. This pangenomic atlas poises the RSSC as an emerging, tractable model to understand the role of the T6SS in shaping pathogen populations.IMPORTANCEWe explored the eco-evolutionary dynamics that shape the inter-microbial warfare mechanisms of a globally significant plant pathogen, the Ralstonia solanacearum species complex. We discovered that most Ralstonia wilt pathogens have evolved extensive and diverse repertoires of type VI secretion system-associated antimicrobial toxins. These expansive toxin arsenals potentially enhance the ability of Ralstonia pathogens to invade plant microbiomes, enabling them to rapidly colonize and kill their host plants. We devised a classification system to categorize the Ralstonia toxins. Interestingly, many of the toxin gene clusters are encoded on mobile genetic elements, including prophages, which may be mutualistic symbionts that enhance the inter-microbial competitiveness of Ralstonia wilt pathogens. Moreover, our findings suggest that the convergent loss of this multi-gene trait contributes to genome reduction in two vector-transmitted lineages of Ralstonia pathogens. Our findings demonstrate that the interplay between microbial ecology and pathogen lifestyle shapes the evolution of a genetically complex antimicrobial weapon.},
}

@article {pmid39191296,
year = {2024},
author = {Xiao, Y and Qin, Y and Jiang, X and Gao, P},
title = {Effects of polypropylene microplastics on digestion performance, microbial community, and antibiotic resistance during microbial anaerobic digestion.},
journal = {Bioresource technology},
volume = {411},
number = {},
pages = {131358},
doi = {10.1016/j.biortech.2024.131358},
pmid = {39191296},
issn = {1873-2976},
abstract = {As an emerging pollutant, microplastics (MPs) have attracted increasing attention worldwide. The effects of polypropylene (PP) MPs on digestion performance, behaviors of dominant microbial communities, antibiotic resistance genes (ARGs) and mobile genetic elements in microbial anaerobic digesters were investigated. The results showed that the addition of PP-MPs to digesters led to an increase in methane production of 10.8% when 300 particles/g TSS of PP-MPs was introduced compared with that in digester not treated with PP-MPs. This increase was attributed to the enrichment of acetogens such as Syntrophobacter (42.0%), Syntrophorhabdus (27.0%), and Syntrophomonas (10.6%), and methanogens including Methanobacterium and Methanosaeta. tetX was highly enriched due to PP-MP exposure, whereas parC exhibited the greatest increase (35.5% - 222.7%). Horizontal gene transfer via ISCR1 and intI1 genes might play an important role in the spread of ARGs. Overall, these findings provide comprehensive insight into the ecological dynamics of PP-MPs during microbial anaerobic digestion.},
}

@article {pmid39191191,
year = {2024},
author = {Middendorf, PS and Zomer, AL and Bergval, IL and Jacobs-Reitsma, WF and den Besten, HMW and Abee, T},
title = {Host associations of Campylobacter jejuni and Campylobacter coli isolates carrying the L-fucose or d-glucose utilization cluster.},
journal = {International journal of food microbiology},
volume = {425},
number = {},
pages = {110855},
doi = {10.1016/j.ijfoodmicro.2024.110855},
pmid = {39191191},
issn = {1879-3460},
abstract = {Campylobacter was considered asaccharolytic, but is now known to carry saccharide metabolization pathways for L-fucose and d-glucose. We hypothesized that these clusters are beneficial for Campylobacter niche adaptation and may help establish human infection. We investigated the distribution of d-glucose and L-fucose clusters among ∼9600 C. jejuni and C. coli genomes of different isolation sources in the Netherlands, the United Kingdom, the United States of America and Finland. The L-fucose utilization cluster was integrated at the same location in all C. jejuni and C. coli genomes, and was flanked by the genes rpoB, rpoC, rspL, repsG and fusA, which are associated with functions in transcription as well as translation and in acquired drug resistance. In contrast, the flanking regions of the d-glucose utilization cluster were variable among the isolates, and integration sites were located within one of the three different 16S23S ribosomal RNA areas of the C. jejuni and C. coli genomes. In addition, we investigated whether acquisition of the L-fucose utilization cluster could be due to horizontal gene transfer between the two species and found three isolates for which this was the case: one C. jejuni isolate carrying a C. coli L-fucose cluster, and two C. coli isolates which carried a C. jejuni L-fucose cluster. Furthermore, L-fucose utilization cluster alignments revealed multiple frameshift mutations, most of which were commonly found in the non-essential genes for L-fucose metabolism, namely, Cj0484 and Cj0489. These findings support our hypothesis that the L-fucose cluster was integrated multiple times across the C. coli/C. jejuni phylogeny. Notably, association analysis using the C. jejuni isolates from the Netherlands showed a significant correlation between human C. jejuni isolates and C. jejuni isolates carrying the L-fucose utilization cluster. This correlation was even stronger when the Dutch isolates were combined with the isolates from the UK, the USA and Finland. No such correlations were observed for C. coli or for the d-glucose cluster for both species. This research provides insight into the spread and host associations of the L-fucose and d-glucose utilization clusters in C. jejuni and C. coli, and the potential benefits in human infection and/or proliferation in humans, conceivably after transmission from any reservoir.},
}

@article {pmid39190937,
year = {2024},
author = {Wen, AX and Herman, C},
title = {Horizontal gene transfer and beyond: the delivery of biological matter by bacterial membrane vesicles to host and bacterial cells.},
journal = {Current opinion in microbiology},
volume = {81},
number = {},
pages = {102525},
doi = {10.1016/j.mib.2024.102525},
pmid = {39190937},
issn = {1879-0364},
abstract = {Membrane vesicles (MVs) are produced in all domains of life. In eukaryotes, extracellular vesicles have been shown to mediate the horizontal transfer of biological material between cells [1]. Therefore, bacterial MVs are also thought to mediate horizontal material transfer to host cells and other bacteria, especially in the context of cell stress. In this review, we discuss the mechanisms of bacterial MV production, evidence that their contents can be trafficked to host cells and other bacteria, and the biological relevance of horizontal material transfer by bacterial MVs.},
}

@article {pmid39190025,
year = {2024},
author = {Alav, I and Pordelkhaki, P and Rodriguez-Navarro, J and Neo, O and Kessler, C and Awodipe, RJ and Cliffe, P and Pulavan, N and Marton, HL and Gibbons, S and Buckner, MMC},
title = {Natural products from food sources can alter the spread of antimicrobial resistance plasmids in Enterobacterales.},
journal = {Microbiology (Reading, England)},
volume = {170},
number = {8},
pages = {},
doi = {10.1099/mic.0.001496},
pmid = {39190025},
issn = {1465-2080},
mesh = {*Plasmids/genetics ; *Anti-Bacterial Agents/pharmacology ; *Klebsiella pneumoniae/drug effects/genetics ; *Escherichia coli/genetics/drug effects ; *beta-Lactamases/genetics/metabolism ; *Biological Products/pharmacology ; Drug Resistance, Bacterial/genetics ; Conjugation, Genetic ; Bacterial Proteins/genetics/metabolism ; Enterobacteriaceae/drug effects/genetics ; Microbial Sensitivity Tests ; Food Microbiology ; Gene Transfer, Horizontal ; },
abstract = {Antimicrobial resistance (AMR) poses a significant threat to global public health. Notably, resistance to carbapenem and extended-spectrum β-lactam antibiotics in Gram-negative bacteria is a major impediment to treating infections. Genes responsible for antibiotic resistance are frequently carried on plasmids, which can transfer between bacteria. Therefore, exploring strategies to prevent this transfer and the prevalence of AMR plasmids is timely and pertinent. Here, we show that certain natural product extracts and associated pure compounds can reduce the conjugation of AMR plasmids into new bacterial hosts. Using our established high-throughput fluorescence-based flow cytometry assay, we found that the natural products were more active in reducing transmission of the IncK extended-spectrum β-lactamase-encoding plasmid pCT in Escherichia coli EC958c, compared to Klebsiella pneumoniae Ecl8 carrying the IncFII carbapenemase-encoding plasmid pKpQIL. The exception was the natural product rottlerin, also active in K. pneumoniae. In classical conjugation assays, rottlerin also reduced the conjugation frequency of the IncFII bla NDM-1 carrying plasmid pCPE16_3 from a clinical K. pneumoniae isolate. Our data indicate that the natural products tested here, in their current molecular structure, reduced conjugation by a small amount, which is unlikely to achieve a large-scale reduction in AMR in bacterial populations. However, certain natural products like rottlerin could provide a foundation for further research into compounds with effective anti-plasmid activity.},
}

*Plasmids/genetics
*Anti-Bacterial Agents/pharmacology
*Klebsiella pneumoniae/drug effects/genetics
*Escherichia coli/genetics/drug effects
*beta-Lactamases/genetics/metabolism
*Biological Products/pharmacology
Drug Resistance, Bacterial/genetics
Conjugation, Genetic
Bacterial Proteins/genetics/metabolism
Enterobacteriaceae/drug effects/genetics
Microbial Sensitivity Tests
Food Microbiology
Gene Transfer, Horizontal

@article {pmid39189989,
year = {2024},
author = {Brewer, TE and Wagner, A},
title = {Horizontal gene transfer of a key translation factor and its role in polyproline proteome evolution.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msae180},
pmid = {39189989},
issn = {1537-1719},
abstract = {Prolines cause ribosomes to stall during translation due to their rigid structure. This phenomenon occurs in all domains of life and is exacerbated at polyproline motifs. Such stalling can be eased by the elongation factor P (EF-P) in bacteria. We discovered a potential connection between the loss of ancestral EF-P, the appearance of horizontally transferred EF-P variants, and genomic signs of EF-P dysfunction. Horizontal transfer of the efp gene has occurred several times among bacteria and is associated with the loss of highly conserved polyproline motifs. In this study, we pinpoint cases of horizontal EF-P transfer among a diverse set of bacteria and examine genomic features associated with these events in the phyla Thermotogota and Planctomycetes. In these phyla, horizontal EF-P transfer is also associated with the loss of entire polyproline motif containing proteins, whose expression is likely dependent on EF-P. In particular, three proteases (Lon, ClpC, and FtsH) and three tRNA synthetases (ValS, IleS1, IleS2) appear highly sensitive to EF-P transfer. The conserved polyproline motifs within these proteins all reside within close proximity to ATP-binding-regions, some of which are crucial for their function. Our work shows that an ancient EF-P dysfunction has left genomic traces that persist to this day, although it remains unclear whether this dysfunction was strictly due to loss of ancestral EF-P or was related to the appearance of an exogenous variant. The latter possibility would imply that the process of 'domesticating' a horizontally transferred efp gene can perturb the overall function of EF-P.},
}

@article {pmid39189956,
year = {2024},
author = {Zheng, X and Huang, L},
title = {Diverse non-canonical electron bifurcating [FeFe]-hydrogenases of separate evolutionary origins in Hydrogenedentota.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0099924},
doi = {10.1128/msystems.00999-24},
pmid = {39189956},
issn = {2379-5077},
abstract = {UNLABELLED: Hydrogenedentota, a globally distributed bacterial phylum-level lineage, is poorly understood. Here, we established a comprehensive genomic catalog of Hydrogenedentota, including a total of seven clades (or families) with 179 genomes, and explored the metabolic potential and evolutionary history of these organisms. We show that a single genome, especially those belonging to Clade 6, often encodes multiple hydrogenases with genomes in Clade 2, which rarely encode hydrogenases being the exception. Notably, most members of Hydrogenedentota contain a group A3 [FeFe]-hydrogenase (BfuABC) with a non-canonical electron bifurcation mechanism, in addition to substrate-level phosphorylation and electron transport-linked phosphorylation pathways, in energy conservation. Furthermore, we show that BfuABC from Hydrogenedentota fall into five sub-types. Phylogenetic analysis reveals five independent routes for the evolution of BfuABC homologs in Hydrogenedentota. We speculate that the five sub-types of BfuABC might be acquired from Bacillota (synonym Firmicutes) through separate horizontal gene transfer events. These data shed light on the diversity and evolution of bifurcating [FeFe]-hydrogenases and provide insight into the strategy of Hydrogenedentota to adapt to survival in various habitats.

IMPORTANCE: The phylum Hydrogenedentota is widely distributed in various environments. However, their physiology, ecology, and evolutionary history remain unknown, primarily due to the limited availability of the genomes and the lack of cultured representatives of the phylum. Our results have increased the knowledge of the genetic and metabolic diversity of these organisms and shed light on their diverse energy conservation strategies, especially those involving electron bifurcation with a non-canonical mechanism, which are likely responsible for their wide distribution. Besides, the organization and phylogenetic relationships of gene clusters coding for BfuABC in Hydrogenedentota provide valuable clues to the evolutionary history of group A3 electron bifurcating [FeFe]-hydrogenases.},
}

@article {pmid39189770,
year = {2024},
author = {Kopejtka, K and Tomasch, J and Shivaramu, S and Saini, MK and Kaftan, D and Koblížek, M},
title = {Minimal transcriptional regulation of horizontally transferred photosynthesis genes in phototrophic bacterium Gemmatimonas phototrophica.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0070624},
doi = {10.1128/msystems.00706-24},
pmid = {39189770},
issn = {2379-5077},
abstract = {UNLABELLED: The first phototrophic member of the bacterial phylum Gemmatimonadota, Gemmatimonas phototrophica AP64[T], received all its photosynthesis genes via distant horizontal gene transfer from a purple bacterium. Here, we investigated how these acquired genes, which are tightly controlled by oxygen and light in the ancestor, are integrated into the regulatory system of its new host. G. phototrophica grew well under aerobic and semiaerobic conditions, with almost no difference in gene expression. Under aerobic conditions, the growth of G. phototrophica was optimal at 80 µmol photon m[-2] s[-1], while higher light intensities had an inhibitory effect. The transcriptome showed only a minimal response to the dark-light shift at optimal light intensity, while the exposure to a higher light intensity (200 µmol photon m[-2] s[-1]) induced already stronger but still transient changes in gene expression. Interestingly, a singlet oxygen defense was not activated under any conditions tested. Our results indicate that G. phototrophica possesses neither the oxygen-dependent repression of photosynthesis genes known from purple bacteria nor the light-dependent repression described in aerobic anoxygenic phototrophs. Instead, G. phototrophica has evolved as a low-light species preferring reduced oxygen concentrations. Under these conditions, the bacterium can safely employ its photoheterotrophic metabolism without the need for complex regulatory mechanisms.

IMPORTANCE: Horizontal gene transfer is one of the main mechanisms by which bacteria acquire new genes. However, it represents only the first step as the transferred genes have also to be functionally and regulatory integrated into the recipient's cellular machinery. Gemmatimonas phototrophica, a member of bacterial phylum Gemmatimonadota, acquired its photosynthesis genes via distant horizontal gene transfer from a purple bacterium. Thus, it represents a unique natural experiment, in which the entire package of photosynthesis genes was transplanted into a distant host. We show that G. phototrophica lacks the regulation of photosynthesis gene expressions in response to oxygen concentration and light intensity that are common in purple bacteria. This restricts its growth to low-light habitats with reduced oxygen. Understanding the regulation of horizontally transferred genes is important not only for microbial evolution but also for synthetic biology and the engineering of novel organisms, as these rely on the successful integration of foreign genes.},
}

@article {pmid39189747,
year = {2024},
author = {Duchin Rapp, Y and Lipsman, V and Yuda, L and Kublanov, IV and Matsliyah, D and Segev, E},
title = {Algal exudates promote conjugation in marine Roseobacters.},
journal = {mBio},
volume = {},
number = {},
pages = {e0106224},
doi = {10.1128/mbio.01062-24},
pmid = {39189747},
issn = {2150-7511},
abstract = {UNLABELLED: Horizontal gene transfer (HGT) is a pivotal mechanism driving bacterial evolution, conferring adaptability within dynamic marine ecosystems. Among HGT mechanisms, conjugation mediated by type IV secretion systems (T4SSs) plays a central role in the ecological success of marine bacteria. However, the conditions promoting conjugation events in the marine environment are not well-understood. Roseobacters, abundant marine bacteria commonly associated with algae, possess a multitude of T4SSs. Many Roseobacters are heterotrophic bacteria that rely on algal secreted compounds to support their growth. These compounds attract bacteria, facilitating colonization and attachment to algal cells. Algae and their metabolites bring bacteria into close proximity, potentially promoting bacterial HGT. Investigation across various Roseobacters revealed that algal exudates indeed enhance plasmid transfer through conjugation. While algal exudates do not influence the transcription of bacterial conjugative machinery genes, they promote bacterial attachment, potentially stabilizing proximity and facilitating HGT. Notably, under conditions where attachment is less advantageous, the impact of algal exudates on conjugation is reduced. These findings suggest that algae enhance bacterial conjugation primarily by fostering attachment and highlight the importance of studying bacterial HGT within the context of algal-bacterial interactions.

IMPORTANCE: This study explores how algal-bacterial interactions influence horizontal gene transfer (HGT) among marine bacteria. HGT, a key driver of bacterial evolution, is facilitated by conjugation mediated by type IV secretion systems (T4SSs). Through investigating Roseobacters, abundant marine bacteria often found to be associated with algae, the study reveals that algal exudates enhance plasmid transfer via conjugation. This enhancement is attributed to the promotion of bacterial attachment by algal compounds, emphasizing the role of algal-bacterial interactions in shaping genetic exchange within dynamic marine ecosystems. Understanding these mechanisms is crucial for elucidating bacterial adaptability and evolution in the marine environment.},
}

@article {pmid39187833,
year = {2024},
author = {Yutin, N and Tolstoy, I and Mutz, P and Wolf, YI and Krupovic, M and Koonin, EV},
title = {DNA polymerase swapping in Caudoviricetes bacteriophages.},
journal = {Virology journal},
volume = {21},
number = {1},
pages = {200},
pmid = {39187833},
issn = {1743-422X},
mesh = {*DNA-Directed DNA Polymerase/genetics ; *Phylogeny ; *Viral Proteins/genetics/metabolism ; Evolution, Molecular ; Genome, Viral ; Caudovirales/genetics/classification ; DNA, Viral/genetics ; Bacteriophages/genetics/enzymology/classification ; DNA Replication ; },
abstract = {BACKGROUND: Viruses with double-stranded (ds) DNA genomes in the realm Duplodnaviria share a conserved structural gene module but show a broad range of variation in their repertoires of DNA replication proteins. Some of the duplodnaviruses encode (nearly) complete replication systems whereas others lack (almost) all genes required for replication, relying on the host replication machinery. DNA polymerases (DNAPs) comprise the centerpiece of the DNA replication apparatus. The replicative DNAPs are classified into 4 unrelated or distantly related families (A-D), with the protein structures and sequences within each family being, generally, highly conserved. More than half of the duplodnaviruses encode a DNAP of family A, B or C. We showed previously that multiple pairs of closely related viruses in the order Crassvirales encode DNAPs of different families.

METHODS: Groups of phages in which DNAP swapping likely occurred were identified as subtrees of a defined depth in a comprehensive evolutionary tree of tailed bacteriophages that included phages with DNAPs of different families. The DNAP swaps were validated by constrained tree analysis that was performed on phylogenetic tree of large terminase subunits, and the phage genomes encoding swapped DNAPs were aligned using Mauve. The structures of the discovered unusual DNAPs were predicted using AlphaFold2.

RESULTS: We identified four additional groups of tailed phages in the class Caudoviricetes in which the DNAPs apparently were swapped on multiple occasions, with replacements occurring both between families A and B, or A and C, or between distinct subfamilies within the same family. The DNAP swapping always occurs "in situ", without changes in the organization of the surrounding genes. In several cases, the DNAP gene is the only region of substantial divergence between closely related phage genomes, whereas in others, the swap apparently involved neighboring genes encoding other proteins involved in phage genome replication. In addition, we identified two previously undetected, highly divergent groups of family A DNAPs that are encoded in some phage genomes along with the main DNAP implicated in genome replication.

CONCLUSIONS: Replacement of the DNAP gene by one encoding a DNAP of a different family occurred on many independent occasions during the evolution of different families of tailed phages, in some cases, resulting in very closely related phages encoding unrelated DNAPs. DNAP swapping was likely driven by selection for avoidance of host antiphage mechanisms targeting the phage DNAP that remain to be identified, and/or by selection against replicon incompatibility.},
}

*DNA-Directed DNA Polymerase/genetics
*Phylogeny
*Viral Proteins/genetics/metabolism
Evolution, Molecular
Genome, Viral
Caudovirales/genetics/classification
DNA, Viral/genetics
Bacteriophages/genetics/enzymology/classification
DNA Replication

@article {pmid39186748,
year = {2024},
author = {Pradel, N and Bartoli, M and Koenen, M and Bale, N and Neumann-Schaal, M and Spröer, C and Bunk, B and Rohde, M and Pester, M and Spring, S},
title = {Description and genome analysis of a novel archaeon isolated from a syntrophic pyrite-forming enrichment culture and reclassification of Methanospirillum hungatei strains GP1 and SK as Methanospirillum purgamenti sp. nov.},
journal = {PloS one},
volume = {19},
number = {8},
pages = {e0308405},
pmid = {39186748},
issn = {1932-6203},
mesh = {*Methanospirillum/genetics/metabolism ; *Phylogeny ; *Genome, Archaeal ; Sulfides/metabolism ; Iron/metabolism ; RNA, Ribosomal, 16S/genetics ; Methane/metabolism ; },
abstract = {The archaeal isolate J.3.6.1-F.2.7.3T was obtained from an anaerobic enrichment culture, where it may play an important role in methane production during pyrite formation. The new isolate formed a species-level clade with Methanospirillum hungatei strains GP1 and SK, which is separate from the type strain JF-1T. Cultivation-independent surveys indicate the occurrence of this phylogenetic group in sediments and anaerobic digesters. The abundance of this clade appears to be negatively affected by high nitrogen loads, indicating a sensitivity to certain nitrogen compounds that is not known in M. hungatei JF-1T. The relatively large core genome of this Methanospirillum clade is indicative of niche specialization and efficient control of horizontal gene transfer. Genes for nitrogenase and F420-dependent secondary alcohol dehydrogenase contribute to the metabolic versatility of this lineage. Characteristics of the new isolate such as the ability to utilize 2-propanol as an electron donor or the requirement for acetate as a carbon source are found also in the strains GP1 and SK, but not in the type strain M. hungatei JF-1T. Based on the genomic differences to related species, a new species within the genus Methanospirillum is proposed with the name M. purgamenti sp. nov. The determined phenotypic characteristics support this proposal and indicate a metabolic adaptation to a separate ecological niche.},
}

*Methanospirillum/genetics/metabolism
*Phylogeny
*Genome, Archaeal
Sulfides/metabolism
Iron/metabolism
RNA, Ribosomal, 16S/genetics
Methane/metabolism

@article {pmid39184916,
year = {2024},
author = {Han, H and He, T and Wu, Y and He, T and Zhou, W},
title = {Multidimensional analysis of tumor stem cells: from biological properties, metabolic adaptations to immune escape mechanisms.},
journal = {Frontiers in cell and developmental biology},
volume = {12},
number = {},
pages = {1441081},
pmid = {39184916},
issn = {2296-634X},
abstract = {As a key factor in tumorigenesis, progression, recurrence and metastasis, the biological properties, metabolic adaptations and immune escape mechanisms of CSCs are the focus of current oncological research. CSCs possess self-renewal, multidirectional differentiation and tumorigenicity, and their mechanisms of action can be elucidated by the clonal evolution, hierarchical model and the dynamic CSCs model, of which the dynamic model is widely recognized due to its better explanation of the function and origin of CSCs. The origin hypothesis of CSCs involves cell-cell fusion, horizontal gene transfer, genomic instability and microenvironmental regulation, which together shape the diversity of CSCs. In terms of classification, CSCs include primary CSCs (pri-CSCs), precancerous stem cells (pre-CSCs), migratory CSCs (mig-CSCs), and chemo-radiotherapy-resistant CSCs (cr-CSCs and rr-CSCs), with each type playing a specific role in tumor progression. Surface markers of CSCs, such as CD24, CD34, CD44, CD90, CD133, CD166, EpCAM, and LGR5, offer the possibility of identifying, isolating, and targeting CSCs, but the instability and heterogeneity of their expression increase the difficulty of treatment. CSCs have adapted to their survival needs through metabolic reprogramming, showing the ability to flexibly switch between glycolysis and oxidative phosphorylation (OXPHOS), as well as adjustments to amino acid and lipid metabolism. The Warburg effect typifies their metabolic profiles, and altered glutamine and fatty acid metabolism further contributes to the rapid proliferation and survival of CSCs. CSCs are able to maintain their stemness by regulating the metabolic networks to maintain their stemness characteristics, enhance antioxidant defences, and adapt to therapeutic stress. Immune escape is another strategy for CSCs to maintain their survival, and CSCs can effectively evade immune surveillance through mechanisms such as up-regulating PD-L1 expression and promoting the formation of an immunosuppressive microenvironment. Together, these properties reveal the multidimensional complexity of CSCs, underscoring the importance of a deeper understanding of the biology of CSCs for the development of more effective tumor therapeutic strategies. In the future, therapies targeting CSCs will focus on precise identification of surface markers, intervention of metabolic pathways, and overcoming immune escape, with the aim of improving the relevance and efficacy of cancer treatments, and ultimately improving patient prognosis.},
}

@article {pmid39184814,
year = {2024},
author = {Chen, N and Li, Y and Liang, X and Qin, K and Zhang, Y and Wang, J and Wu, Q and Gupta, TB and Ding, Y},
title = {Bacterial extracellular vesicle: A non-negligible component in biofilm life cycle and challenges in biofilm treatments.},
journal = {Biofilm},
volume = {8},
number = {},
pages = {100216},
pmid = {39184814},
issn = {2590-2075},
abstract = {Bacterial biofilms, especially those formed by pathogens, have been increasingly impacting human health. Bacterial extracellular vesicle (bEV), a kind of spherical membranous structure released by bacteria, has not only been reported to be a component of the biofilm matrix but also plays a non-negligible role in the biofilm life cycle. Nevertheless, a comprehensive overview of the bEVs functions in biofilms remains elusive. In this review, we summarize the biogenesis and distinctive features characterizing bEVs, and consolidate the current literature on their functions and proposed mechanisms in the biofilm life cycle. Furthermore, we emphasize the formidable challenges associated with vesicle interference in biofilm treatments. The primary objective of this review is to raise awareness regarding the functions of bEVs in the biofilm life cycle and lay the groundwork for the development of novel therapeutic strategies to control or even eliminate bacterial biofilms.},
}

@article {pmid39182428,
year = {2024},
author = {Ando, S and Tanaka, R and Ito, H},
title = {Activity examination of plant Mg-dechelatase and its bacterial homolog in plants and in vitro.},
journal = {Plant physiology and biochemistry : PPB},
volume = {215},
number = {},
pages = {109073},
doi = {10.1016/j.plaphy.2024.109073},
pmid = {39182428},
issn = {1873-2690},
abstract = {Chlorophyll a serves as a photosynthetic pigment in plants. Its degradation is initiated by the extraction of the central Mg by the Mg-dechelatase enzyme, which is encoded by Stay-Green (SGR). Plant SGR is believed to be derived from bacterial SGR homolog obtained through horizontal gene transfer into photosynthetic eukaryotes. However, it is not known how the bacterial SGR homolog was modified to function in plants. To assess its adaptation mechanism in plants, a bacterial SGR homolog derived from the Anaerolineae bacterium SM23_63 was introduced into plants. It was found that the bacterial SGR homolog metabolized chlorophyll in plants. However, its chlorophyll catabolic activity was lower than that of plant SGR. Recombinant proteins of the bacterial SGR homolog exhibited higher activity than those of the plant SGR. The reduced chlorophyll catabolic activity of bacterial SGR homologs in plants may be associated with low hydrophobicity of the entrance to the catalytic site compared to that of plant SGR. This hinders the enzyme access to chlorophyll, which is localized in hydrophobic environments. This study offers insights into the molecular changes underlying the optimization of enzyme function.},
}

@article {pmid39107250,
year = {2024},
author = {Barragan, AC and Latorre, SM and Malmgren, A and Harant, A and Win, J and Sugihara, Y and Burbano, HA and Kamoun, S and Langner, T},
title = {Multiple Horizontal Mini-chromosome Transfers Drive Genome Evolution of Clonal Blast Fungus Lineages.},
journal = {Molecular biology and evolution},
volume = {41},
number = {8},
pages = {},
pmid = {39107250},
issn = {1537-1719},
support = {//Gatsby Charitable Foundation/ ; UKRI-BBSRC//UK Research and Innovation Biotechnology and Biological Sciences Research Council/ ; /ERC_/European Research Council/International ; 743165//BLASTOFF/ ; 101077853//PANDEMIC/ ; RSWF\R1\191011//Royal Society/ ; },
mesh = {*Gene Transfer, Horizontal ; *Evolution, Molecular ; Chromosomes, Fungal/genetics ; Ascomycota/genetics ; Plant Diseases/microbiology ; Genome, Fungal ; },
abstract = {Crop disease pandemics are often driven by asexually reproducing clonal lineages of plant pathogens that reproduce asexually. How these clonal pathogens continuously adapt to their hosts despite harboring limited genetic variation, and in absence of sexual recombination remains elusive. Here, we reveal multiple instances of horizontal chromosome transfer within pandemic clonal lineages of the blast fungus Magnaporthe (Syn. Pyricularia) oryzae. We identified a horizontally transferred 1.2Mb accessory mini-chromosome which is remarkably conserved between M. oryzae isolates from both the rice blast fungus lineage and the lineage infecting Indian goosegrass (Eleusine indica), a wild grass that often grows in the proximity of cultivated cereal crops. Furthermore, we show that this mini-chromosome was horizontally acquired by clonal rice blast isolates through at least nine distinct transfer events over the past three centuries. These findings establish horizontal mini-chromosome transfer as a mechanism facilitating genetic exchange among different host-associated blast fungus lineages. We propose that blast fungus populations infecting wild grasses act as genetic reservoirs that drive genome evolution of pandemic clonal lineages that afflict cereal crops.},
}

*Gene Transfer, Horizontal
*Evolution, Molecular
Chromosomes, Fungal/genetics
Ascomycota/genetics
Plant Diseases/microbiology
Genome, Fungal

@article {pmid39089095,
year = {2024},
author = {Zhuang, M and Yan, W and Xiong, Y and Wu, Z and Cao, Y and Sanganyado, E and Siame, BA and Chen, L and Kashi, Y and Leung, KY},
title = {Horizontal plasmid transfer promotes antibiotic resistance in selected bacteria in Chinese frog farms.},
journal = {Environment international},
volume = {190},
number = {},
pages = {108905},
doi = {10.1016/j.envint.2024.108905},
pmid = {39089095},
issn = {1873-6750},
mesh = {Animals ; *Plasmids/genetics ; China ; *Gene Transfer, Horizontal ; *Bacteria/genetics/drug effects ; Anti-Bacterial Agents/pharmacology ; Farms ; Drug Resistance, Bacterial/genetics ; Rana catesbeiana/microbiology/genetics ; Drug Resistance, Microbial/genetics ; Microbiota/genetics ; },
abstract = {The emergence and dissemination of antibiotic resistance genes (ARGs) in the ecosystem are global public health concerns. One Health emphasizes the interconnectivity between different habitats and seeks to optimize animal, human, and environmental health. However, information on the dissemination of antibiotic resistance genes (ARGs) within complex microbiomes in natural habitats is scarce. We investigated the prevalence of antibiotic resistant bacteria (ARB) and the spread of ARGs in intensive bullfrog (Rana catesbeiana) farms in the Shantou area of China. Antibiotic susceptibilities of 361 strains, combined with microbiome analyses, revealed Escherichia coli, Edwardsiella tarda, Citrobacter and Klebsiella sp. as prevalent multidrug resistant bacteria on these farms. Whole genome sequencing of 95 ARB identified 250 large plasmids that harbored a wide range of ARGs. Plasmid sequences and sediment metagenomes revealed an abundance of tetA, sul1, and aph(3″)-Ib ARGs. Notably, antibiotic resistance (against 15 antibiotics) highly correlated with plasmid-borne rather than chromosome-borne ARGs. Based on sequence similarities, most plasmids (62%) fell into 32 distinct groups, indicating a potential for horizontal plasmid transfer (HPT) within the frog farm microbiome. HPT was confirmed in inter- and intra-species conjugation experiments. Furthermore, identical mobile ARGs, flanked by mobile genetic elements (MGEs), were found in different locations on the same plasmid, or on different plasmids residing in the same or different hosts. Our results suggest a synergy between MGEs and HPT to facilitate ARGs dissemination in frog farms. Mining public databases retrieved similar plasmids from different bacterial species found in other environmental niches globally. Our findings underscore the importance of HPT in mediating the spread of ARGs in frog farms and other microbiomes of the ecosystem.},
}

Animals
*Plasmids/genetics
China
*Gene Transfer, Horizontal
*Bacteria/genetics/drug effects
Anti-Bacterial Agents/pharmacology
Farms
Drug Resistance, Bacterial/genetics
Rana catesbeiana/microbiology/genetics
Drug Resistance, Microbial/genetics
Microbiota/genetics

@article {pmid39180708,
year = {2024},
author = {Witt, ASA and Carvalho, JVRP and Serafim, MSM and Arias, NEC and Rodrigues, RAL and Abrahão, JS},
title = {The GC% landscape of the Nucleocytoviricota.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {},
number = {},
pages = {},
pmid = {39180708},
issn = {1678-4405},
support = {88882.348380/2010-1//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; 405249/2022-5//Ministry of Science and Technology/ ; 406441/2022-7//Ministry of Science and Technology/ ; },
abstract = {Genomic studies on sequence composition employ various approaches, such as calculating the proportion of guanine and cytosine within a given sequence (GC% content), which can shed light on various aspects of the organism's biology. In this context, GC% can provide insights into virus-host relationships and evolution. Here, we present a comprehensive gene-by-gene analysis of 61 representatives belonging to the phylum Nucleocytoviricota, which comprises viruses with the largest genomes known in the virosphere. Parameters were evaluated not only based on the average GC% of a given viral species compared to the entire phylum but also considering gene position and phylogenetic history. Our results reveal that while some families exhibit similar GC% among their representatives (e.g., Marseilleviridae), others such as Poxviridae, Phycodnaviridae, and Mimiviridae have members with discrepant GC% values, likely reflecting adaptation to specific biological cycles and hosts. Interestingly, certain genes located at terminal regions or within specific genomic clusters show GC% values distinct from the average, suggesting recent acquisition or unique evolutionary pressures. Horizontal gene transfer and the presence of potential paralogs were also assessed in genes with the most discrepant GC% values, indicating multiple evolutionary histories. Taken together, to the best of our knowledge, this study represents the first global and gene-by-gene analysis of GC% distribution and profiles within genomes of Nucleocytoviricota members, highlighting their diversity and identifying potential new targets for future studies.},
}

@article {pmid39179660,
year = {2024},
author = {Wang, S and Sun, S and Wang, Q and Chen, H and Guo, Y and Cai, M and Yin, Y and Ma, S and Wang, H},
title = {PathoTracker: an online analytical metagenomic platform for Klebsiella pneumoniae feature identification and outbreak alerting.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {1038},
pmid = {39179660},
issn = {2399-3642},
support = {32141001//National Natural Science Foundation of China (National Science Foundation of China)/ ; 81991533//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Klebsiella pneumoniae/genetics/isolation & purification ; *Metagenomics/methods ; Humans ; *Disease Outbreaks ; *Klebsiella Infections/microbiology/epidemiology/diagnosis ; *Phylogeny ; China/epidemiology ; Nanopore Sequencing/methods ; Databases, Genetic ; Genome, Bacterial ; },
abstract = {Clinical metagenomics (CMg) Nanopore sequencing can facilitate infectious disease diagnosis. In China, sub-lineages ST11-KL64 and ST11-KL47 Carbapenem-resistant Klebsiella pneumoniae (CRKP) are widely prevalent. We propose PathoTracker, a specially compiled database and arranged method for strain feature identification in CMg samples and CRKP traceability. A database targeting high-prevalence horizontal gene transfer in CRKP strains and a ST11-only database for distinguishing two sub-lineages in China were created. To make the database user-friendly, facilitate immediate downstream strain feature identification from raw Nanopore metagenomic data, and avoid the need for phylogenetic analysis from scratch, we developed data analysis methods. The methods included pre-performed phylogenetic analysis, gene-isolate-cluster index and multilevel pan-genome database and reduced storage space by 10-fold and random-access memory by 52-fold compared with normal methods. PathoTracker can provide accurate and fast strain-level analysis for CMg data after 1 h Nanopore sequencing, allowing early warning of outbreaks. A user-friendly page (http://PathoTracker.pku.edu.cn/) was developed to facilitate online analysis, including strain-level feature, species identifications and phylogenetic analyses. PathoTracker proposed in this study will aid in the downstream analysis of CMg.},
}

*Klebsiella pneumoniae/genetics/isolation & purification
*Metagenomics/methods
Humans
*Disease Outbreaks
*Klebsiella Infections/microbiology/epidemiology/diagnosis
*Phylogeny
China/epidemiology
Nanopore Sequencing/methods
Databases, Genetic
Genome, Bacterial

@article {pmid39176446,
year = {2024},
author = {Ahmed, M and Kayal, E and Lavrov, DV},
title = {Mitochondrial DNA of the demosponge Acanthella acuta: Linear Architecture and Other Unique Features.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evae168},
pmid = {39176446},
issn = {1759-6653},
abstract = {While Acanthella acuta (Schmidt 1862), a common demosponge found in the Mediterranean Sea and Atlantic Ocean, is-morphologically-little distinguishable from other sponges, its mitochondrial DNA (mtDNA) is unique within the class. In contrast to all other studied demosponges, mtDNA of A. acuta is inferred to be linear and displays several unusual features: inverted terminal repeats, group II introns in three mt-genes, and two unique ORFs. One of the ORFs (ORF1535) combines a DNA-polymerase domain with a DNA-directed RNA-polymerase domain, while the second bears no discernible similarity to any reported sequences. The group II intron within the cox2 gene is the first such intron reported in an animal. Our phylogenetic analyses indicate that the cox1 intron is related to similar introns found in other demosponges, while the cox2 intron is likely not of animal origin. The two domains found within ORF1535 do not share a common origin and, along with the cox2 intron, were likely acquired by horizontal transfer. The findings of this paper open new avenues of exploration in the understanding of mtDNA linearization within Metazoa.},
}

@article {pmid39174812,
year = {2024},
author = {Döcker, J and Linz, S and Wicke, K},
title = {Bounding the Softwired Parsimony Score of a Phylogenetic Network.},
journal = {Bulletin of mathematical biology},
volume = {86},
number = {10},
pages = {121},
pmid = {39174812},
issn = {1522-9602},
support = {XXXX//Marsden Fund/ ; },
mesh = {*Phylogeny ; *Models, Genetic ; *Mathematical Concepts ; Algorithms ; Evolution, Molecular ; Sequence Alignment/statistics & numerical data ; },
abstract = {In comparison to phylogenetic trees, phylogenetic networks are more suitable to represent complex evolutionary histories of species whose past includes reticulation such as hybridisation or lateral gene transfer. However, the reconstruction of phylogenetic networks remains challenging and computationally expensive due to their intricate structural properties. For example, the small parsimony problem that is solvable in polynomial time for phylogenetic trees, becomes NP-hard on phylogenetic networks under softwired and parental parsimony, even for a single binary character and structurally constrained networks. To calculate the parsimony score of a phylogenetic network N, these two parsimony notions consider different exponential-size sets of phylogenetic trees that can be extracted from N and infer the minimum parsimony score over all trees in the set. In this paper, we ask: What is the maximum difference between the parsimony score of any phylogenetic tree that is contained in the set of considered trees and a phylogenetic tree whose parsimony score equates to the parsimony score of N? Given a gap-free sequence alignment of multi-state characters and a rooted binary level-k phylogenetic network, we use the novel concept of an informative blob to show that this difference is bounded by k + 1 times the softwired parsimony score of N. In particular, the difference is independent of the alignment length and the number of character states. We show that an analogous bound can be obtained for the softwired parsimony score of semi-directed networks, while under parental parsimony on the other hand, such a bound does not hold.},
}

*Phylogeny
*Models, Genetic
*Mathematical Concepts
Algorithms
Evolution, Molecular
Sequence Alignment/statistics & numerical data

@article {pmid39173632,
year = {2024},
author = {Yang, XY and Shen, Z and Wang, C and Nakanishi, K and Fu, TM},
title = {DdmDE eliminates plasmid invasion by DNA-guided DNA targeting.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2024.07.028},
pmid = {39173632},
issn = {1097-4172},
abstract = {Horizontal gene transfer is a key driver of bacterial evolution, but it also presents severe risks to bacteria by introducing invasive mobile genetic elements. To counter these threats, bacteria have developed various defense systems, including prokaryotic Argonautes (pAgos) and the DNA defense module DdmDE system. Through biochemical analysis, structural determination, and in vivo plasmid clearance assays, we elucidate the assembly and activation mechanisms of DdmDE, which eliminates small, multicopy plasmids. We demonstrate that DdmE, a pAgo-like protein, acts as a catalytically inactive, DNA-guided, DNA-targeting defense module. In the presence of guide DNA, DdmE targets plasmids and recruits a dimeric DdmD, which contains nuclease and helicase domains. Upon binding to DNA substrates, DdmD transitions from an autoinhibited dimer to an active monomer, which then translocates along and cleaves the plasmids. Together, our findings reveal the intricate mechanisms underlying DdmDE-mediated plasmid clearance, offering fundamental insights into bacterial defense systems against plasmid invasions.},
}

@article {pmid39173362,
year = {2024},
author = {Zhang, Y and Zuo, S and Zheng, Q and Yu, G and Wang, Y},
title = {Removal of antibiotic resistant bacteria and antibiotic resistance genes by an electrochemically driven UV/chlorine process for decentralized water treatment.},
journal = {Water research},
volume = {265},
number = {},
pages = {122298},
doi = {10.1016/j.watres.2024.122298},
pmid = {39173362},
issn = {1879-2448},
abstract = {The UV/chlorine (UV/Cl2) process is a developing advanced oxidation process and can efficiently remove antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs). However, the transportation and storage of chlorine solutions limit the application of the UV/Cl2 process, especially for decentralized water treatment. To overcome the limitation, an electrochemically driven UV/Cl2 process (E-UV/Cl2) where Cl2 can be electrochemically produced in situ from anodic oxidation of chloride (Cl[-]) ubiquitously present in various water matrices was evaluated in this study. >5-log inactivation of the ARB (E. coli) was achieved within 5 s of the E-UV/Cl2 process, and no photoreactivation of the ARB was observed after the treatment. In addition to the ARB, intracellular and extracellular ARGs (tetA, sul1, sul2, and ermB) could be effectively degraded (e.g., log(C0/C) > 4 for i-ARGs) within 5 min of the E-UV/Cl2 process. Atomic force microscopy showed that the most of the i-ARGs were interrupted into short fragments (< 30 nm) during the E-UV/Cl2 process, which can thus effectively prevent the self-repair of i-ARGs and the horizontal gene transfer. Modelling results showed that the abatement efficiencies of i-ARG correlated positively with the exposures of •OH, Cl2[-]•, and ClO• during the E-UV/Cl2 process. Due to the short treatment time (5 min) required for ARB and ARG removal, insignificant concentrations of trihalomethanes (THMs) were generated during of the E-UV/Cl2 process, and the energy consumption (EEO) of ARG removal was ∼0.20‒0.27 kWh/m[3]-log, which is generally comparable to that of the UV/Cl2 process (0.18-0.23 kWh/m[3]-log). These results demonstrate that the E-UV/Cl2 process can provide a feasible and attractive alternative to the UV/Cl2 process for ARB and ARG removal in decentralized water treatment system.},
}

@article {pmid39172952,
year = {2024},
author = {Zhou, W and Karan, KR and Gu, W and Klein, HU and Sturm, G and De Jager, PL and Bennett, DA and Hirano, M and Picard, M and Mills, RE},
title = {Somatic nuclear mitochondrial DNA insertions are prevalent in the human brain and accumulate over time in fibroblasts.},
journal = {PLoS biology},
volume = {22},
number = {8},
pages = {e3002723},
doi = {10.1371/journal.pbio.3002723},
pmid = {39172952},
issn = {1545-7885},
mesh = {Humans ; *DNA, Mitochondrial/genetics ; *Fibroblasts/metabolism ; *Brain/metabolism ; Male ; Female ; Cell Nucleus/metabolism ; Middle Aged ; Adult ; Aged ; Longevity/genetics ; Aging/physiology/genetics ; },
abstract = {The transfer of mitochondrial DNA into the nuclear genomes of eukaryotes (Numts) has been linked to lifespan in nonhuman species and recently demonstrated to occur in rare instances from one human generation to the next. Here, we investigated numtogenesis dynamics in humans in 2 ways. First, we quantified Numts in 1,187 postmortem brain and blood samples from different individuals. Compared to circulating immune cells (n = 389), postmitotic brain tissue (n = 798) contained more Numts, consistent with their potential somatic accumulation. Within brain samples, we observed a 5.5-fold enrichment of somatic Numt insertions in the dorsolateral prefrontal cortex (DLPFC) compared to cerebellum samples, suggesting that brain Numts arose spontaneously during development or across the lifespan. Moreover, an increase in the number of brain Numts was linked to earlier mortality. The brains of individuals with no cognitive impairment (NCI) who died at younger ages carried approximately 2 more Numts per decade of life lost than those who lived longer. Second, we tested the dynamic transfer of Numts using a repeated-measures whole-genome sequencing design in a human fibroblast model that recapitulates several molecular hallmarks of aging. These longitudinal experiments revealed a gradual accumulation of 1 Numt every ~13 days. Numtogenesis was independent of large-scale genomic instability and unlikely driven by cell clonality. Targeted pharmacological perturbations including chronic glucocorticoid signaling or impairing mitochondrial oxidative phosphorylation (OxPhos) only modestly increased the rate of numtogenesis, whereas patient-derived SURF1-mutant cells exhibiting mtDNA instability accumulated Numts 4.7-fold faster than healthy donors. Combined, our data document spontaneous numtogenesis in human cells and demonstrate an association between brain cortical somatic Numts and human lifespan. These findings open the possibility that mito-nuclear horizontal gene transfer among human postmitotic tissues produces functionally relevant human Numts over timescales shorter than previously assumed.},
}

Humans
*DNA, Mitochondrial/genetics
*Fibroblasts/metabolism
*Brain/metabolism
Male
Female
Cell Nucleus/metabolism
Middle Aged
Adult
Aged
Longevity/genetics
Aging/physiology/genetics

@article {pmid39172793,
year = {2024},
author = {Chen, X and Wang, M and Luo, L and Liu, X and An, L and Nie, Y and Wu, XL},
title = {The evolution of autonomy from two cooperative specialists in fluctuating environments.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {35},
pages = {e2317182121},
doi = {10.1073/pnas.2317182121},
pmid = {39172793},
issn = {1091-6490},
support = {2018YFA0902100//MOST | National Key Research and Development Program of China (NKPs)/ ; 91951204//Data Center of Management Science, National Natural Science Foundation of China - Peking University (DCMS, NSFC-PKU)/ ; },
mesh = {*Naphthalenes/metabolism ; Gene Transfer, Horizontal ; Biological Evolution ; Symbiosis ; Microbial Consortia/genetics/physiology ; Genotype ; },
abstract = {From microbes to humans, organisms perform numerous tasks for their survival, including food acquisition, migration, and reproduction. A complex biological task can be performed by either an autonomous organism or by cooperation among several specialized organisms. However, it remains unclear how autonomy and cooperation evolutionarily switch. Specifically, it remains unclear whether and how cooperative specialists can repair deleted genes through direct genetic exchange, thereby regaining metabolic autonomy. Here, we address this question by experimentally evolving a mutualistic microbial consortium composed of two specialists that cooperatively degrade naphthalene. We observed that autonomous genotypes capable of performing the entire naphthalene degradation pathway evolved from two cooperative specialists and dominated the community. This evolutionary transition was driven by the horizontal gene transfer (HGT) between the two specialists. However, this evolution was exclusively observed in the fluctuating environment alternately supplied with naphthalene and pyruvate, where mutualism and competition between the two specialists alternated. The naphthalene-supplied environment exerted selective pressure that favors the expansion of autonomous genotypes. The pyruvate-supplied environment promoted the coexistence and cell density of the cooperative specialists, thereby increasing the likelihood of HGT. Using a mathematical model, we quantitatively demonstrate that environmental fluctuations facilitate the evolution of autonomy through HGT when the relative growth rate and carrying capacity of the cooperative specialists allow enhanced coexistence and higher cell density in the competitive environment. Together, our results demonstrate that cooperative specialists can repair deleted genes through a direct genetic exchange under specific conditions, thereby regaining metabolic autonomy.},
}

*Naphthalenes/metabolism
Gene Transfer, Horizontal
Biological Evolution
Symbiosis
Microbial Consortia/genetics/physiology
Genotype

@article {pmid39106433,
year = {2024},
author = {Tan, Y and Aravind, L and Zhang, D},
title = {Genomic Underpinnings of Cytoplasmic Incompatibility: CIF Gene-Neighborhood Diversification Through Extensive Lateral Transfers and Recombination in Wolbachia.},
journal = {Genome biology and evolution},
volume = {16},
number = {8},
pages = {},
doi = {10.1093/gbe/evae171},
pmid = {39106433},
issn = {1759-6653},
support = {//Saint Louis University/ ; //Intramural Research Program of the NIH/ ; /LM/NLM NIH HHS/United States ; },
mesh = {*Wolbachia/genetics ; *Gene Transfer, Horizontal ; *Recombination, Genetic ; Evolution, Molecular ; Phylogeny ; Genome, Bacterial ; Cytoplasm/genetics ; Animals ; Bacterial Proteins/genetics ; },
abstract = {Cytoplasmic incompatibility (CI), a non-Mendelian genetic phenomenon, involves the manipulation of host reproduction by Wolbachia, a maternally transmitted alphaproteobacterium. The underlying mechanism is centered around the CI Factor (CIF) system governed by two genes, cifA and cifB, where cifB induces embryonic lethality, and cifA counteracts it. Recent investigations have unveiled intriguing facets of this system, including diverse cifB variants, prophage association in specific strains, copy number variation, and rapid component divergence, hinting at a complex evolutionary history. We utilized comparative genomics to systematically classify CIF systems, analyze their locus structure and domain architectures, and reconstruct their diversification and evolutionary trajectories. Our new classification identifies ten distinct CIF types, featuring not just versions present in Wolbachia, but also other intracellular bacteria, and eukaryotic hosts. Significantly, our analysis of CIF loci reveals remarkable variability in gene composition and organization, encompassing an array of diverse endonucleases, variable toxin domains, deubiquitinating peptidases (DUBs), prophages, and transposons. We present compelling evidence that the components within the loci have been diversifying their sequences and domain architectures through extensive, independent lateral transfers and interlocus recombination involving gene conversion. The association with diverse transposons and prophages, coupled with selective pressures from host immunity, likely underpins the emergence of CIF loci as recombination hotspots. Our investigation also posits the origin of CifB-REase domains from mobile elements akin to CR (Crinkler-RHS-type) effectors and Tribolium Medea1 factor, which is linked to another non-Mendelian genetic phenomenon. This comprehensive genomic analysis offers novel insights into the molecular evolution and genomic foundations of Wolbachia-mediated host reproductive control.},
}

*Wolbachia/genetics
*Gene Transfer, Horizontal
*Recombination, Genetic
Evolution, Molecular
Phylogeny
Genome, Bacterial
Cytoplasm/genetics
Animals
Bacterial Proteins/genetics

@article {pmid39168346,
year = {2024},
author = {Li, J and Li, C and Han, Y and Yang, J and Hu, Y and Xu, H and Zhou, Y and Zuo, J and Tang, Y and Lei, C and Li, C and Wang, H},
title = {Bacterial membrane vesicles from swine farm microbial communities harboring and safeguarding diverse functional genes promoting horizontal gene transfer.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {175639},
doi = {10.1016/j.scitotenv.2024.175639},
pmid = {39168346},
issn = {1879-1026},
abstract = {Antibiotic resistance (AMR) poses a significant global health challenge, with swine farms recognized as major reservoirs of antibiotic resistance genes (ARGs). Recently, bacterial membrane vesicles (BMVs) have emerged as novel carriers mediating horizontal gene transfer. However, little is known about the ARGs carried by BMVs in swine farm environments and their transfer potential. This study investigated the distribution, sources, and microbiological origins of BMVs in three key microbial habitats of swine farms (feces, soil, and fecal wastewater), along with the ARGs and mobile genetic elements (MGEs) they harbor. Characterization of BMVs revealed particle sizes ranging from 20 to 500 nm and concentrations from 10[8] to 10[12] particles/g, containing DNA and proteins. Metagenomic sequencing identified BMVs predominantly composed of members of the Proteobacteria phyla, including Pseudomonadaceae, Moraxellaceae, and Enterobacteriaceae, carrying diverse functional genes encompassing resistance to 14 common antibiotics and 74,340 virulence genes. Notably, multidrug resistance, tetracycline, and chloramphenicol resistance genes were particularly abundant. Furthermore, BMVs harbored various MGEs, primarily plasmids, and demonstrated the ability to protect their DNA cargo from degradation and facilitate horizontal gene transfer, including the transmission of resistance genes. In conclusion, this study reveals widespread presence of BMVs carrying ARGs and potential virulence genes in swine farm feces, soil, and fecal wastewater. These findings not only provide new insights into the role of extracellular DNA in the environment but also highlight concerns regarding the gene transfer potential mediated by BMVs and associated health risks.},
}

@article {pmid39167960,
year = {2024},
author = {Nasu, T and Maeda, S},
title = {Escherichia coli persisters in biofilm can perform horizontal gene transfer by transformation.},
journal = {Biochemical and biophysical research communications},
volume = {738},
number = {},
pages = {150549},
doi = {10.1016/j.bbrc.2024.150549},
pmid = {39167960},
issn = {1090-2104},
abstract = {Persisters represent a subset of cells that exhibit transient tolerance to antimicrobials. These persisters can withstand sudden exposure to antimicrobials, even as the majority of normal cells perish. In this study, we have demonstrated the capacity of ampicillin-tolerant and alkali-tolerant persisters to execute horizontal gene transfer via in situ transformation within biofilms. Air-solid biofilms, comprising two Escherichia coli populations each with a distinct plasmid, were formed on agar media. They were treated with lethal doses of ampicillin or NaOH for 24 h, followed by a 1-min glass-ball roll. This process led to a high frequency of horizontal plasmid transfer (10[-7]-10[-6] per cell) from dead cells to surviving persisters within the biofilms. Plasmid transfer was DNase-sensitive and also occurred by adding purified plasmid DNA to plasmid-free biofilms, demonstrating a transformation mechanism. This marks the first evidence of persisters' novel ability for horizontal gene transfer, via transformation.},
}

@article {pmid39166873,
year = {2024},
author = {Kwan, S-Y and Sabotta, CM and Cruz, LR and Wong, MC and Ajami, NJ and McCormick, JB and Fisher-Hoch, SP and Beretta, L},
title = {Gut phageome in Mexican Americans: a population at high risk for metabolic dysfunction-associated steatotic liver disease and diabetes.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0043424},
doi = {10.1128/msystems.00434-24},
pmid = {39166873},
issn = {2379-5077},
abstract = {Mexican Americans are disproportionally affected by metabolic dysfunction-associated steatotic liver disease (MASLD), which often co-occurs with diabetes. Despite extensive evidence on the causative role of the gut microbiome in MASLD, studies determining the involvement of the gut phageome are scarce. In this cross-sectional study, we characterized the gut phageome in Mexican Americans of South Texas by stool shotgun metagenomic sequencing of 340 subjects, concurrently screened for liver steatosis by transient elastography. Inter-individual variations in the phageome were associated with gender, country of birth, diabetes, and liver steatosis. The phage signatures for diabetes and liver steatosis were subsequently determined. Enrichment of Inoviridae was associated with both diabetes and liver steatosis. Diabetes was further associated with the enrichment of predominantly temperate Escherichia phages, some of which possessed virulence factors. Liver steatosis was associated with the depletion of Lactococcus phages r1t and BK5-T, and enrichment of the globally prevalent Crassvirales phages, including members of genus cluster IX (Burzaovirus coli, Burzaovirus faecalis) and VI (Kahnovirus oralis). The Lactococcus phages showed strong correlations and co-occurrence with Lactococcus lactis, while the Crassvirales phages, B. coli, B. faecalis, and UAG-readthrough crAss clade correlated and co-occurred with Prevotella copri. In conclusion, we identified the gut phageome signatures for two closely linked metabolic diseases with significant global burden. These phage signatures may have utility in risk modeling and disease prevention in this high-risk population, and identification of potential bacterial targets for phage therapy.IMPORTANCEPhages influence human health and disease by shaping the gut bacterial community. Using stool samples from a high-risk Mexican American population, we provide insights into the gut phageome changes associated with diabetes and liver steatosis, two closely linked metabolic diseases with significant global burden. Common to both diseases was an enrichment of Inoviridae, a group of phages that infect bacterial hosts chronically without lysis, allowing them to significantly influence bacterial growth, virulence, motility, biofilm formation, and horizontal gene transfer. Diabetes was additionally associated with the enrichment of Escherichia coli-infecting phages, some of which contained virulence factors. Liver steatosis was additionally associated with the depletion of Lactococcus lactis-infecting phages, and enrichment of Crassvirales phages, a group of virulent phages with high global prevalence and persistence across generations. These phageome signatures may have utility in risk modeling, as well as identify potential bacterial targets for phage therapy.},
}

@article {pmid39166856,
year = {2024},
author = {Karpenko, A and Shelenkov, A and Manzeniuk, I and Kulikova, N and Gevorgyan, A and Mikhaylova, Y and Akimkin, V},
title = {Whole genome analysis of multidrug-resistant Escherichia coli isolate collected from drinking water in Armenia revealed the plasmid-borne mcr-1.1-mediated colistin resistance.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0075124},
doi = {10.1128/spectrum.00751-24},
pmid = {39166856},
issn = {2165-0497},
abstract = {UNLABELLED: The rate of polymyxin-resistant Enterobacteriaceae, as well as human and animal infections caused by them, is increasing worldwide, posing a high epidemiological threat since colistin represents a last-resort antibiotic to treat complicated infections. The study of environmental niches, in particular, aquatic ecosystems in terms of genome analysis of inhabiting antimicrobial-resistant (AMR) microorganisms as reservoirs of acquired resistance determinants (AMR genes), represents a specific concern from a One Health approach. Here, we present a phenotypic AMR analysis and molecular characterization of Escherichia coli isolate found in municipal drinking water after an accident in the water supply system of a residential building in Armenia in 2021. CrieF1144 E. coli isolate was resistant to ampicillin, ampicillin/sulbactam, cefuroxime, ciprofloxacin, levofloxacin, trimethoprim/sulfamethoxazole, colistin, and tigecycline, whereas whole genome sequencing (WGS) revealed blaTEM-1B, tet(A), and a combination of dfrA14 with sul1 resistance determinants, which corresponds well with phenotypic resistance above. Moreover, the multidrug-resistant isolate studied harbored mcr-1.1 gene on a conjugative 251 Kb IncHI2 plasmid, whose structure was determined using hybrid short- and long-reads assembly. CrieF1141_p1 plasmid carried all antimicrobial resistance genes revealed in the isolate and did not harbor any virulence determinants, so it could contribute to the spread of AMR genes in the bacterial population. Two copies of ISApl1 transposase-encoding element, which is likely to mediate mcr-1.1 gene mobilization, were revealed surrounding this gene in a plasmid.

IMPORTANCE: Evolutionary patterns of Escherichia coli show that they usually develop into highly pathogenic forms by acquiring fitness advantages such as antimicrobial resistance (AMR) and various virulence factors through horizontal gene transfer mediated by mobile elements. This has led to high prevalence of multidrug-resistant (MDR) strains, which highlights the relevancy of enhanced surveillance to monitor and prevent transmission of the MDR bacteria to human and animal populations. However, the limited number of reports regarding the whole genome sequencing (WGS) investigation of MDR E. coli strains isolated from drinking water and harboring mcr genes hampers the adoption of a comprehensive approach to address the relationship between environmental E. coli populations and human and veterinary infections. Our results highlight the relevance of analyzing the environment, especially water, as a part of the surveillance programs to understand the origins and dissemination of antimicrobial resistance within the One Health concept.},
}

@article {pmid39166427,
year = {2024},
author = {Wu, JJ and Deng, QW and Qiu, YY and Liu, C and Lin, CF and Ru, YL and Sun, Y and Lai, J and Liu, LX and Shen, XX and Pan, R and Zhao, YP},
title = {Post-transfer adaptation of HGT-acquired genes and contribution to guanine metabolic diversification in land plants.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.20040},
pmid = {39166427},
issn = {1469-8137},
support = {32071484//National Natural Science Foundation of China/ ; 32200231//National Natural Science Foundation of China/ ; 32371691//National Natural Science Foundation of China/ ; LZ21C030003//Natural Science Foundation of Zhejiang Province/ ; LZ23C020002//Natural Science Foundation of Zhejiang Province/ ; LR23C140001//Natural Science Foundation of Zhejiang Province/ ; 2023000CC0010//Beijing Life Science Academy/ ; 226-2023-00021//Fundamental Research Funds for the Central Universities/ ; 2022YFD1401600//National Key Research and Development Program of China/ ; },
abstract = {Horizontal gene transfer (HGT) is a major driving force in the evolution of prokaryotic and eukaryotic genomes. Despite recent advances in distribution and ecological importance, the extensive pattern, especially in seed plants, and post-transfer adaptation of HGT-acquired genes in land plants remain elusive. We systematically identified 1150 foreign genes in 522 land plant genomes that were likely acquired via at least 322 distinct transfers from nonplant donors and confirmed that recent HGT events were unevenly distributed between seedless and seed plants. HGT-acquired genes evolved to be more similar to native genes in terms of average intron length due to intron gains, and HGT-acquired genes containing introns exhibited higher expression levels than those lacking introns, suggesting that intron gains may be involved in the post-transfer adaptation of HGT in land plants. Functional validation of bacteria-derived gene GuaD in mosses and gymnosperms revealed that the invasion of foreign genes introduced a novel bypass of guanine degradation and resulted in the loss of native pathway genes in some gymnosperms, eventually shaping three major types of guanine metabolism in land plants. We conclude that HGT has played a critical role in land plant evolution.},
}

@article {pmid39165128,
year = {2024},
author = {Trost, K and Knopp, MR and Wimmer, JLE and Tria, FDK and Martin, WF},
title = {A universal and constant rate of gene content change traces pangenome flux to LUCA.},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnae068},
pmid = {39165128},
issn = {1574-6968},
abstract = {Prokaryotic genomes constantly undergo gene flux via lateral gene transfer, generating a pangenome structure consisting of a conserved core genome surrounded by a more variable accessory genome shell. Over time, flux generates change in genome content. Here we measure and compare the rate of genome flux for 5 655 prokaryotic genomes as a function of amino acid sequence divergence in 36 universally distributed proteins of the informational core (IC). We find a clock of gene content change. The long-term average rate of gene content flux is remarkably constant across all higher prokaryotic taxa sampled, whereby the size of the accessory genome-the proportion of the genome harboring gene content difference for genome pairs-varies across taxa. The proportion of species-level accessory genes per genome, varies from 0% (Chlamydia) to 30-33% (Alphaproteobacteria, Gammaproteobacteria, Clostridia). A clock-like rate of gene content change across all prokaryotic taxa sampled suggest that pangenome structure is a general feature of prokaryotic genomes and that it has been in existence since the divergence of bacteria and archaea.},
}

@article {pmid39163267,
year = {2024},
author = {Kloub, L and Gosselin, S and Graf, J and Gogarten, JP and Bansal, MS},
title = {Investigating Additive and Replacing Horizontal Gene Transfers Using Phylogenies and Whole Genomes.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evae180},
pmid = {39163267},
issn = {1759-6653},
abstract = {Horizontal gene transfer (HGT) is fundamental to microbial evolution and adaptation. When a gene is horizontally transferred, it may either add itself as a new gene to the recipient genome (possibly displacing non-homologous genes) or replace an existing homologous gene. Currently, studies do not usually distinguish between "additive" and "replacing" HGTs, and their relative frequencies, integration mechanisms, and specific roles in microbial evolution are poorly understood. In this work, we develop a novel computational framework for large-scale classification of HGTs as either additive or replacing. Our framework leverages recently developed phylogenetic approaches for HGT detection and classifies HGTs inferred between terminal edges based on gene orderings along genomes and phylogenetic relationships between the microbial species under consideration. The resulting 9 method, called DART, is highly customizable and scalable and can classify a large fraction of inferred HGTs with high confidence and statistical support. Our application of DART to a large dataset of thousands of gene families from 103 Aeromonas genomes provides insights into the relative frequencies, functional biases, and integration mechanisms of additive and replacing HGTs. Among other results, we find that (i) the relative frequency of additive HGT increases with increasing phylogenetic distance, (ii) replacing HGT dominates at shorter phylogenetic distances, (iii) additive and replacing HGTs have strikingly different functional profiles, (iv) homologous recombination in flanking regions of a novel gene may be a frequent integration mechanism for additive HGT, and (v) phages and mobile genetic elements likely play an important role in facilitating additive HGT.},
}

@article {pmid39162532,
year = {2024},
author = {Ito, Y and Hashimoto, Y and Suzuki, M and Kaneko, N and Yoshida, M and Nakayama, H and Tomita, H},
title = {The emergence of metronidazole-resistant Prevotella bivia harboring nimK gene in Japan.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0056224},
doi = {10.1128/spectrum.00562-24},
pmid = {39162532},
issn = {2165-0497},
abstract = {UNLABELLED: We present the identification and characterization of the complete genome of metronidazole (MTZ)-resistant Prevotella bivia strain TOH-2715 [minimum inhibitory concentration (MIC): 8 mg/L], isolated from the urine of an elderly Japanese woman, as well as details of its mobile genetic elements (MGEs) containing antimicrobial resistance (AMR) genes and its relationship with other bacterial species determined using whole-genome sequencing (WGS) data. TOH-2715 possessed two chromosomes with putative MGEs containing AMR genes. Two AMR-related MGE regions were present in chromosome 2. MGE-region 1 (7,821 bp) included Tn6456, where nimK was located, and MGE-region 2 (58.8 Kbp) included the integrative and conjugative element (ICE), where tet(Q) and ermF were located. The genetic structure of the ICE of TOH-2715 was similar to that of CTnDOT-family transposons, where ermF and tet(Q) are located. A search of public databases revealed that nimK was present in Prevotella spp., including P. bivia, and was partially composed of a Tn6456-like element lacking the efflux transporter gene qacE and the Crp/Fnr family transcriptional regulator gene in some cases. Core ICE gene analysis showed that ICEs similar to that of TOH-2715 were present in Prevotella spp. and Bacteroides spp., suggesting horizontal gene transfer among anaerobes. This is the report of WGS analysis of an MTZ-resistant clinical strain of P. bivia (TOH-2715) with Tn6456 encoding nimK. Other submitted genomes have described the presence of nimK, but none of them have described MTZ resistance. Additionally, we described putative MGE regions containing the AMR gene within the genus Prevotella and among anaerobes, raising concerns about the future spread of nimK among anaerobes.

IMPORTANCE: Metronidazole (MTZ) is an important antimicrobial agent in anaerobic infections and is widely used in clinical settings. The rate of MTZ resistance in anaerobic bacteria has been increasing in recent years, and the nim gene (nitro-imidazole reductase) is one of the resistance mechanisms. Prevotella bivia is found in humans in the urinary tract and vagina and is known to cause infections in some cases. One of the nim genes, nimK, has recently been discovered in this species of bacteria, but there are no reports of antimicrobial resistance (AMR)-related regions in its whole genome level. In this study, we analyzed the AMR region of nimK-positive P. bivia derived from clinical specimens based on comparisons with other anaerobic genomes. P. bivia was found to be engaged in horizontal gene transfer with other anaerobic bacteria, and the future spread of the nimK gene is a concern.},
}

@article {pmid39162515,
year = {2024},
author = {Wang, Z and Hülpüsch, C and Foesel, B and Traidl-Hoffmann, C and Reiger, M and Schloter, M},
title = {Genomic and functional divergence of Staphylococcus aureus strains from atopic dermatitis patients and healthy individuals: insights from global and local scales.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0057124},
doi = {10.1128/spectrum.00571-24},
pmid = {39162515},
issn = {2165-0497},
abstract = {Atopic dermatitis (AD) is the most common chronic inflammatory skin disease worldwide and is characterized by a complex interplay with skin microbiota, with Staphylococcus aureus often abnormally more abundant in AD patients than in healthy individuals (HE). S. aureus harbors diverse strains with varied genetic compositions and functionalities, which exhibit differential connections with the severity of AD. However, the differences in S. aureus strains between AD and HE remain unclear, with most variations seen at a specific geographic level, implying spontaneous adaptations rather than systematic distinctions. This study presents genomic and functional differences between these S. aureus strains from AD and HE on both global and local levels. We observed reduced gene content diversity but increased functional variation in the global AD-associated strains. Two additional AD-dominant clusters emerged, with Cluster 1 enriched in transposases and Cluster 2 showcasing genes linked to adaptability and antibiotic resistance. Particularly, robust evidence illustrates that the lantibiotic operon of S. aureus, involved in the biosynthesis of lantibiotics, was acquired via horizontal gene transfer from environmental bacteria. Comparisons of the gene abundance profiles in functional categories also indicate limited zoonotic potential between human and animal isolates. Local analysis mirrored global gene diversity but showed distinct functional variations between AD and HE strains. Overall, this research provides foundational insights into the genomic evolution, adaptability, and antibiotic resistance of S. aureus, with significant implications for clinical microbiology.IMPORTANCEOur study uncovers significant genomic variations in Staphylococcus aureus strains associated with atopic dermatitis. We observed adaptive evolution tailored to the disease microenvironment, characterized by a smaller pan-genome than strains from healthy skin both on the global and local levels. Key functional categories driving strain diversification include "replication and repair" and "transporters," with transposases being pivotal. Interestingly, the local strains predominantly featured metal-related genes, whereas global ones emphasized antimicrobial resistances, signifying scale-dependent diversification nuances. We also pinpointed horizontal gene transfer events, indicating interactions between human-associated and environmental bacteria. These insights expand our comprehension of S. aureus's genetic adaptation in atopic dermatitis, yielding valuable implications for clinical approaches.},
}

@article {pmid39159726,
year = {2024},
author = {Zhang, Y and Wang, N and Wan, J and Jousset, A and Jiang, G and Wang, X and Wei, Z and Xu, Y and Shen, Q},
title = {Exploring the antibiotic resistance genes removal dynamics in chicken manure by composting.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {131309},
doi = {10.1016/j.biortech.2024.131309},
pmid = {39159726},
issn = {1873-2976},
abstract = {Prolonged antibiotic usage in livestock farming leads to the accumulation of antibiotic resistance genes in animal manure. Composting has been shown as an effective way of removing antibiotic resistance from manures, but the specific mechanisms remain unclear. This study used time-series sampling and metagenomics to analyse the resistome types and their bacterial host in chicken manures. Composting significantly altered the physicochemical properties and microbiome composition, reduced antibiotic resistance genes by 65.71 %, mobile genetic elements by 68.15 % and horizontal gene transfer frequency. Source tracking revealed that Firmicutes, Actinobacteria, and Proteobacteria are the major bacterial hosts involved in resistome and gene transfer events. Composting reduces the resistome risk by targeting pathogens such as Staphylococcus aureus. Structural equation modelling confirmed that composting reduces resistome risk by changing pH and pathogen abundance. This study demonstrates that composting is an effective strategy for mitigating resistome risk in chicken manure, thereby supporting the "One Health" initiative.},
}

@article {pmid39158272,
year = {2024},
author = {Upreti, C and Kumar, P and Durso, LM and Palmer, KL},
title = {CRISPR-Cas inhibits plasmid transfer and immunizes bacteria against antibiotic resistance acquisition in manure.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0087624},
doi = {10.1128/aem.00876-24},
pmid = {39158272},
issn = {1098-5336},
abstract = {The horizontal transfer of antibiotic resistance genes among bacteria is a pressing global issue. The bacterial defense system clustered regularly interspaced short palindromic repeats (CRISPR)-Cas acts as a barrier to the spread of antibiotic resistance plasmids, and CRISPR-Cas-based antimicrobials can be effective to selectively deplete antibiotic-resistant bacteria. While significant surveillance efforts monitor the spread of antibiotic-resistant bacteria in the clinical context, a major, often overlooked aspect of the issue is resistance emergence in agriculture. Farm animals are commonly treated with antibiotics, and antibiotic resistance in agriculture is on the rise. Yet, CRISPR-Cas efficacy has not been investigated in this setting. Here, we evaluate the prevalence of CRISPR-Cas in agricultural Enterococcus faecalis strains and its antiplasmid efficacy in an agricultural niche: manure. Analyzing 1,986 E. faecalis genomes from human and animal hosts, we show that the prevalence of CRISPR-Cas subtypes is similar between clinical and agricultural E. faecalis strains. Using plasmid conjugation assays, we found that CRISPR-Cas is a significant barrier against resistance plasmid transfer in manure. Finally, we used a CRISPR-based antimicrobial approach to cure resistant E. faecalis of erythromycin resistance, but this was limited by delivery efficiency of the CRISPR antimicrobial in manure. However, immunization of bacteria against resistance gene acquisition in manure was highly effective. Together, our results show that E. faecalis CRISPR-Cas is prevalent and effective in an agricultural setting and has the potential to be utilized for depleting antibiotic-resistant populations. Our work has broad implications for tackling antibiotic resistance in the increasingly relevant agricultural setting, in line with a One Health approach.IMPORTANCEAntibiotic resistance is a growing global health crisis in human and veterinary medicine. Previous work has shown technologies based on CRISPR-Cas-a bacterial defense system-to be effective in tackling antibiotic resistance. Here we test if CRISPR-Cas is present and effective in agricultural niches, specifically in the ubiquitously present bacterium, Enterococcus faecalis. We show that CRISPR-Cas is both prevalent and functional in manure and has the potential to be used to specifically kill bacteria carrying antibiotic resistance genes. This study demonstrates the utility of CRISPR-Cas-based strategies for control of antibiotic resistance in agricultural settings.},
}

@article {pmid39158107,
year = {2024},
author = {Ming, Y and Abdullah Al, M and Zhang, D and Zhu, W and Liu, H and Cai, L and Yu, X and Wu, K and Niu, M and Zeng, Q and He, Z and Yan, Q},
title = {Insights into the evolutionary and ecological adaption strategies of nirS- and nirK-type denitrifying communities.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e17507},
doi = {10.1111/mec.17507},
pmid = {39158107},
issn = {1365-294X},
support = {SML2020SP004//Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; SML2023SP237//Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; SML2021SP203//Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; SML2023SP205//Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; 42377111//National Natural Science Foundation of China/ ; //Ocean Negative Carbon Emissions (ONCE) Program/ ; },
abstract = {Denitrification is a crucial process in the global nitrogen cycle, in which two functionally equivalent genes, nirS and nirK, catalyse the critical reaction and are usually used as marker genes. The nirK gene can function independently, whereas nirS requires additional genes to encode nitrite reductase and is more sensitive to environmental factors than nirK. However, the ecological differentiation mechanisms of those denitrifying microbial communities and their adaptation strategies to environmental stresses remain unclear. Here, we conducted metagenomic analysis for sediments and bioreactor samples from Lake Donghu, China. We found that nirS-type denitrifying communities had a significantly lower horizontal gene transfer frequency than that of nirK-type denitrifying communities, and nirS gene phylogeny was more congruent with taxonomy than that of nirK gene. Metabolic reconstruction of metagenome-assembled genomes further revealed that nirS-type denitrifying communities have robust metabolic systems for energy conservation, enabling them to survive under environmental stresses. Nevertheless, nirK-type denitrifying communities seemed to adapt to oxygen-limited environments with the ability to utilize various carbon and nitrogen compounds. Thus, this study provides novel insights into the ecological differentiation mechanism of nirS and nirK-type denitrifying communities, as well as the regulation of the global nitrogen cycle and greenhouse gas emissions.},
}

@article {pmid39153565,
year = {2024},
author = {Yang, C and Yan, S and Zhang, B and Yao, X and Mo, J and Rehman, F and Guo, J},
title = {Spatiotemporal distribution of the planktonic microbiome and antibiotic resistance genes in a typical urban river contaminated by macrolide antibiotics.},
journal = {Environmental research},
volume = {},
number = {},
pages = {119808},
doi = {10.1016/j.envres.2024.119808},
pmid = {39153565},
issn = {1096-0953},
abstract = {The widespread application of macrolide antibiotics has caused antibiotic resistance pollution, threatening the river ecological health. In this study, five macrolide antibiotics (azithromycin, clarithromycin, roxithromycin, erythromycin, and anhydro erythromycin A) were monitored in the Zao River across three hydrological periods (April, July, and December). Simultaneously, the changes in antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and planktonic bacterial communities were determined using metagenomic sequencing. A clear pollution gradient was observed for azithromycin and roxithromycin, with the concentrations in the dry season surpassing those in other seasons. The highest concentration was observed for azithromycin (1.36 μg/L). The abundance of MLS resistance genes increased along the Zao River during the dry season, whereas the opposite trend was obtained during the wet season. A significant correlation between the levels of MLS resistance genes and macrolide antibiotics was identified during the dry season. Notably, compared with the reference site, the abundance of transposase in the effluent from wastewater treatment plants (WWTPs) was significantly elevated in both dry and wet seasons, whereas the abundance of insertion sequences (IS) and plasmids declined during the dry season. The exposure to wastewater containing macrolide antibiotics altered the diversity of planktonic bacterial communities. The bacterial host for ARGs appeared to be Pseudomonas, primarily associated with multidrug subtypes. Moreover, the ARG subtypes were highly correlated with MGEs (transposase and istA). The partial least-squares path model (PLS-PM) demonstrated a positive correlation between the abundance of MGEs and ARGs, indicating the significance of horizontal gene transfer (HGT) in the dissemination of ARGs within the Zao River. Environmental variables, such as TN and NO3[-]-N, were significantly correlated with the abundance of MGEs, ARGs, and bacteria. Collectively, our findings could provide insights into the shift patterns of the microbiome and ARGs across the contamination gradient of AZI and ROX in the river.},
}

@article {pmid39153075,
year = {2024},
author = {Panickar, A and Manoharan, A and Anbarasu, A and Ramaiah, S},
title = {Respiratory tract infections: an update on the complexity of bacterial diversity, therapeutic interventions and breakthroughs.},
journal = {Archives of microbiology},
volume = {206},
number = {9},
pages = {382},
pmid = {39153075},
issn = {1432-072X},
support = {IRIS ID: 2021-11889//Indian Council of Medical Research/ ; },
mesh = {*Respiratory Tract Infections/microbiology/drug therapy ; Humans ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Bacteria/genetics/drug effects/classification ; Drug Resistance, Bacterial ; Bacterial Infections/microbiology/drug therapy ; Virulence ; },
abstract = {Respiratory tract infections (RTIs) have a significant impact on global health, especially among children and the elderly. The key bacterial pathogens Streptococcus pneumoniae, Haemophilus influenzae, Klebsiella pneumoniae, Staphylococcus aureus and non-fermenting Gram Negative bacteria such as Acinetobacter baumannii and Pseudomonas aeruginosa are most commonly associated with RTIs. These bacterial pathogens have evolved a diverse array of resistance mechanisms through horizontal gene transfer, often mediated by mobile genetic elements and environmental acquisition. Treatment failures are primarily due to antimicrobial resistance and inadequate bacterial engagement, which necessitates the development of alternative treatment strategies. To overcome this, our review mainly focuses on different virulence mechanisms and their resulting pathogenicity, highlighting different therapeutic interventions to combat resistance. To prevent the antimicrobial resistance crisis, we also focused on leveraging the application of artificial intelligence and machine learning to manage RTIs. Integrative approaches combining mechanistic insights are crucial for addressing the global challenge of antimicrobial resistance in respiratory infections.},
}

*Respiratory Tract Infections/microbiology/drug therapy
Humans
*Anti-Bacterial Agents/pharmacology/therapeutic use
Bacteria/genetics/drug effects/classification
Drug Resistance, Bacterial
Bacterial Infections/microbiology/drug therapy
Virulence

@article {pmid39149034,
year = {2024},
author = {Kadkhoda, H and Gholizadeh, P and Samadi Kafil, H and Ghotaslou, R and Pirzadeh, T and Ahangarzadeh Rezaee, M and Nabizadeh, E and Feizi, H and Aghazadeh, M},
title = {Role of CRISPR-Cas systems and anti-CRISPR proteins in bacterial antibiotic resistance.},
journal = {Heliyon},
volume = {10},
number = {14},
pages = {e34692},
pmid = {39149034},
issn = {2405-8440},
abstract = {The emergence and development of antibiotic resistance in bacteria is a serious threat to global public health. Antibiotic resistance genes (ARGs) are often located on mobile genetic elements (MGEs). They can be transferred among bacteria by horizontal gene transfer (HGT), leading to the spread of drug-resistant strains and antibiotic treatment failure. CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated genes) is one of the many strategies bacteria have developed under long-term selection pressure to restrict the HGT. CRISPR-Cas systems exist in about half of bacterial genomes and play a significant role in limiting the spread of antibiotic resistance. On the other hand, bacteriophages and other MGEs encode a wide range of anti-CRISPR proteins (Acrs) to counteract the immunity of the CRISPR-Cas system. The Acrs could decrease the CRISPR-Cas system's activity against phages and facilitate the acquisition of ARGs and virulence traits for bacteria. This review aimed to assess the relationship between the CRISPR-Cas systems and Acrs with bacterial antibiotic resistance. We also highlighted the CRISPR technology and Acrs to control and prevent antibacterial resistance. The CRISPR-Cas system can target nucleic acid sequences with high accuracy and reliability; therefore, it has become a novel gene editing and gene therapy tool to prevent the spread of antibiotic resistance. CRISPR-based approaches may pave the way for developing smart antibiotics, which could eliminate multidrug-resistant (MDR) bacteria and distinguish between pathogenic and beneficial microorganisms. Additionally, the engineered anti-CRISPR gene-containing phages in combination with antibiotics could be used as a cutting-edge treatment approach to reduce antibiotic resistance.},
}

@article {pmid39148687,
year = {2024},
author = {Santos, AJDC and Dias, RS and da Silva, CHM and Vidigal, PMP and de Sousa, MP and da Silva, CC and de Paula, SO},
title = {Genomic analysis of Oceanotoga teriensis strain UFV_LIMV02, a multidrug-resistant thermophilic bacterium isolated from an offshore oil reservoir.},
journal = {Access microbiology},
volume = {6},
number = {8},
pages = {},
pmid = {39148687},
issn = {2516-8290},
abstract = {Bacteria of the species Oceanotoga teriensis belong to the family Petrotogaceae, are Gram-negative bacilli, are moderately thermophilic and are included in the group of thiosulfate-reducing bacteria, being capable of significantly accelerating corrosion in metallic structures. However, no in-depth study on the genome, antibiotic resistance and mobile elements has been carried out so far. In this work, the isolation, phenotypic and genotypic characterization of the multi-resistant O. teriensis UFV_LIMV02 strain was carried out, from water samples from an offshore oil extraction platform in Rio de Janeiro (Brazil). We determined that the isolate has a genome of 2 812 778 bp in size, with 26 % GC content, organized into 34 contigs. Genomic annotation using Rapid Annotation using Subsystem Technology revealed the presence of genes related to resistance to antibiotics and heavy metals. By evaluating the antimicrobial resistance of the isolate using the disc diffusion technique, resistance was verified for the classes of antibiotics, beta-lactams, fluoroquinolones, aminoglycosides, sulfonamides, lincosamides and rifamycins, a total of 14 antibiotics. The search for genomic islands, prophages and defence systems against phage infection revealed the presence of five genomic islands in its genome, containing genes related to resistance to heavy metals and antibiotics, most of which are efflux pumps and several transposases. No prophage was found in its genome; however, nine different defence systems against phage infection were detected. When analysing the clustered regularly interspaced short palindromic repeat (CRISPR) systems, four CRISPR arrays, classified as types I-B and III-B, with 272 spacers, can provide the strain with immunity to different mobile genetic elements and bacteriophage infection. The results found in this study show that the isolate UFV_LIVM02 is an environmental bacterium, resistant to different classes of antibiotics, and that the proteins encoded by the predicted genomic islands may be associated with the development of greater resistance to antibiotics and heavy metals. They provide evidence that environmental bacteria found in offshore oil exploration residues may pose a risk for the spread of antibiotic resistance genes. More comprehensive studies on the microbial community present in oil waste are needed to assess the risks of horizontal gene transfer.},
}

@article {pmid39147525,
year = {2024},
author = {Wu, Q and Li, W and Kwok, LY and Lv, H and Sun, J and Sun, Z},
title = {Regional variation and adaptive evolution in Bifidobacterium pseudocatenulatum: Insights into genomic and functional diversity in human gut.},
journal = {Food research international (Ottawa, Ont.)},
volume = {192},
number = {},
pages = {114840},
doi = {10.1016/j.foodres.2024.114840},
pmid = {39147525},
issn = {1873-7145},
mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; *Phylogeny ; *Genome, Bacterial ; *Bifidobacterium pseudocatenulatum/genetics/metabolism ; Genetic Variation ; Genomics ; Diet ; },
abstract = {Bifidobacterium pseudocatenulatum is a prevalent gut microbe in humans of all ages and plays a crucial role in host health. However, its adaptive evolutionary characteristics remain poorly understood. This study analyzed the genome of 247 B. pseudocatenulatum isolates from Chinese, Vietnamese, Japanese and other region populations using population genomics and functional genomics. Our findings revealed high genetic heterogeneity and regional clustering within B. pseudocatenulatum isolates. Significant differences were observed in genome characteristics, phylogeny, and functional genes. Specifically, Chinese and Vietnamese isolates exhibited a higher abundance of genes involved in the metabolism of plant-derived carbohydrates (GH13, GH43, and GH5 enzyme families), aligning with the predominantly vegetable-, wheat- and fruit-based diets of these populations. Additionally, we found widespread transmission of antibiotic resistance genes (tetO and tetW) through mobile genetic elements, such as genomic islands (GIs), resulting in substantial intra-regional differences. Our findings highlight distinct adaptive evolution in B. pseudocatenulatum driven by gene specialization, possibly in response to regional variations in diet and lifestyle. This study sheds light on bifidobacteria colonization mechanisms in the host gut. IMPORTANCE: Gut microbiota, as a key link in the gut-brain axis, helps to maintain the health of the organism, among which, Bifidobacterium pseudocatenulatum (B. pseudocatenulatum) is an important constituent member of the gut microbiota, which plays an important role in maintaining the balance of gut microbiota. The probiotic properties of B. pseudocatenulatum have been widely elaborated, and in order to excavate its evolutionary features at the genomic level, here we focused on the genetic background and evolutionary mechanism of the B. pseudocatenulatum genomes isolated from the intestinal tracts of different populations. Ultimately, based on the phylogenetic tree, we found that B. pseudocatenulatum has high genetic diversity and regional clustering phenomenon, in which plant-derived carbohydrate metabolism genes (GH13, GH43, GH5) showed significant regional differences, and this genetic differentiation drove the adaptive evolution, which likely shaped by diet and lifestyle.},
}

*Gastrointestinal Microbiome/genetics
Humans
*Phylogeny
*Genome, Bacterial
*Bifidobacterium pseudocatenulatum/genetics/metabolism
Genetic Variation
Genomics
Diet

@article {pmid39144201,
year = {2024},
author = {Pramanik, S and Sil, AK},
title = {Anti-foam cell activity of metabolites of a bacterium isolated from yogurt.},
journal = {Food science and biotechnology},
volume = {33},
number = {11},
pages = {2597-2610},
pmid = {39144201},
issn = {2092-6456},
abstract = {UNLABELLED: Existing literature documents the beneficial effects of probiotics against atherosclerosis, a major cause of human death. However, it suffers from a serious limitation due to horizontal gene transfer. Therefore, currently, efforts are targeted to examine the beneficial effects of metabolites obtained from probiotics. In this context, the current study isolated a bacterium from yogurt and investigated the effect of its metabolites on foam cell formation, a key event for developing atherosclerosis. Results showed that the cell-free conditioned medium (CM) of this isolate and di-chloro methane extract of CM (CME) not only prevented the formation but also reduced the level of preformed foam cells. To understand the mechanism, the GC-MS study revealed the presence of compounds known to exert anti-atherogenic activities like anti-oxidant, anti-NF-κB, and lipolytic activities. Consistently, CME exhibited substantial anti-oxidant and anti-NF-κB activity. In conclusion, metabolites of this bacterium have anti-atherogenic activities and thus have therapeutic potential.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10068-023-01515-7.},
}

@article {pmid39141729,
year = {2024},
author = {Lai, S and Wang, H and Bork, P and Chen, WH and Zhao, XM},
title = {Long-read sequencing reveals extensive gut phageome structural variations driven by genetic exchange with bacterial hosts.},
journal = {Science advances},
volume = {10},
number = {33},
pages = {eadn3316},
doi = {10.1126/sciadv.adn3316},
pmid = {39141729},
issn = {2375-2548},
mesh = {*Bacteriophages/genetics ; Humans ; *Gastrointestinal Microbiome/genetics ; *Bacteria/virology/genetics ; *Gene Transfer, Horizontal ; Metagenomics/methods ; Genetic Variation ; Virome/genetics ; Genome, Viral ; High-Throughput Nucleotide Sequencing ; },
abstract = {Genetic variations are instrumental for unraveling phage evolution and deciphering their functional implications. Here, we explore the underlying fine-scale genetic variations in the gut phageome, especially structural variations (SVs). By using virome-enriched long-read metagenomic sequencing across 91 individuals, we identified a total of 14,438 nonredundant phage SVs and revealed their prevalence within the human gut phageome. These SVs are mainly enriched in genes involved in recombination, DNA methylation, and antibiotic resistance. Notably, a substantial fraction of phage SV sequences share close homology with bacterial fragments, with most SVs enriched for horizontal gene transfer (HGT) mechanism. Further investigations showed that these SV sequences were genetic exchanged between specific phage-bacteria pairs, particularly between phages and their respective bacterial hosts. Temperate phages exhibit a higher frequency of genetic exchange with bacterial chromosomes and then virulent phages. Collectively, our findings provide insights into the genetic landscape of the human gut phageome.},
}

*Bacteriophages/genetics
Humans
*Gastrointestinal Microbiome/genetics
*Bacteria/virology/genetics
*Gene Transfer, Horizontal
Metagenomics/methods
Genetic Variation
Virome/genetics
Genome, Viral
High-Throughput Nucleotide Sequencing

@article {pmid39141562,
year = {2024},
author = {Karan, J and Mandal, S and Khan, G and Arya, H and Samhita, L},
title = {Enhanced Extraction of Low-Molecular Weight DNA from Wastewater for Comprehensive Assessment of Antimicrobial Resistance.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {209},
pages = {},
doi = {10.3791/66899},
pmid = {39141562},
issn = {1940-087X},
mesh = {*Wastewater/microbiology/chemistry ; Polyethylene Glycols/chemistry ; Molecular Weight ; DNA, Bacterial/genetics/isolation & purification ; Drug Resistance, Microbial/genetics ; Drug Resistance, Bacterial/genetics ; },
abstract = {Environmental surveillance is recognized as an important tool for assessing public health in the post-pandemic era. Water, in particular wastewater, has emerged as the source of choice to sample pathogen burdens in the environment. Wastewater from open drains and community water treatment plants is a reservoir of both pathogens and antimicrobial resistance (AMR) genes, and frequently comes in contact with humans. While there are many methods of tracking AMR from water, isolating good-quality DNA at high yields from heterogeneous samples remains a challenge. To compensate, sample volumes often need to be high, creating practical constraints. Additionally, environmental DNA is frequently fragmented, and the sources of AMR (plasmids, phages, linear DNA) consist of low-molecular-weight DNA. Yet, few extraction processes have focused on methods for high-yield extraction of linear and low-molecular-weight DNA. Here, a simple method for high-yield linear DNA extraction from small volumes of wastewater using the precipitation properties of polyethylene glycol (PEG) is reported. This study makes a case for increasing overall DNA yields from water samples collected for metagenomic analyses by enriching the proportion of linear DNA. In addition, enhancing low-molecular-weight DNA overcomes the current problem of under-sampling environmental AMR due to a focus on high-molecular-weight and intracellular DNA. This method is expected to be particularly useful when extracellular DNA exists but at low concentrations, such as with effluents from treatment plants. It should also enhance the environmental sampling of AMR gene fragments that spread through horizontal gene transfer.},
}

*Wastewater/microbiology/chemistry
Polyethylene Glycols/chemistry
Molecular Weight
DNA, Bacterial/genetics/isolation & purification
Drug Resistance, Microbial/genetics
Drug Resistance, Bacterial/genetics

@article {pmid39096644,
year = {2024},
author = {Wu, Q and Wu, GG and Pan, KN and Wang, XP and Li, HY and Tian, Z and Jin, RC and Fan, NS},
title = {Beta-blocker drives the conjugative transfer of multidrug resistance genes in pure and complex biological systems.},
journal = {Journal of hazardous materials},
volume = {477},
number = {},
pages = {135403},
doi = {10.1016/j.jhazmat.2024.135403},
pmid = {39096644},
issn = {1873-3336},
mesh = {*Metoprolol ; *Plasmids/genetics ; *Conjugation, Genetic/drug effects ; Drug Resistance, Multiple, Bacterial/genetics/drug effects ; Adrenergic beta-Antagonists/pharmacology ; Gene Transfer, Horizontal ; Bacteria/genetics/drug effects/metabolism ; Anti-Bacterial Agents/pharmacology ; Genes, MDR/genetics ; Microbiota/drug effects ; },
abstract = {Drug resistance poses a high risk to human health. Extensive use of non-antibiotic drugs contributes to antibiotic resistance genes (ARGs) transfer. However, how they affect the spread of broad-host plasmids in complex biological systems remains unknown. This study investigated the effect of metoprolol on the transfer frequency and host range of ARGs in both intrageneric and intergeneric pure culture systems, as well as in anammox microbiome. The results showed that environmental concentrations of metoprolol significantly promoted the intrageneric and intergeneric conjugative transfer. Initially, metoprolol induced excessive oxidative stress, resulting in high cell membrane permeability and bacterial SOS response. Meanwhile, more pili formation increased the adhesion and contact between bacteria, and the abundance of conjugation-related genes also increased significantly. Activation of the electron transport chain provided more ATP for this energy-consuming process. The underlying mechanism was further verified in the complex anammox conjugative system. Metoprolol induced the enrichment of ARGs and mobile genetic elements. The enhanced bacterial interaction and energy generation facilitated the high conjugative transfer frequency of ARGs. In addition, plasmid-borne ARGs tended to transfer to opportunistic pathogens. This work raises public concerns about the health and ecological risks of non-antibiotic drugs.},
}

*Metoprolol
*Plasmids/genetics
*Conjugation, Genetic/drug effects
Drug Resistance, Multiple, Bacterial/genetics/drug effects
Adrenergic beta-Antagonists/pharmacology
Gene Transfer, Horizontal
Bacteria/genetics/drug effects/metabolism
Anti-Bacterial Agents/pharmacology
Genes, MDR/genetics
Microbiota/drug effects

@article {pmid39139006,
year = {2024},
author = {Rao, Y and Wang, Y and Zhang, H and Wang, Y and He, Q and Yuan, X and Guo, J and Chen, H},
title = {A Strategy of Killing Two Birds With One Stone for Blocking Drug Resistance Spread With Engineered Bdellovibrio bacteriovorus.},
journal = {Advanced materials (Deerfield Beach, Fla.)},
volume = {},
number = {},
pages = {e2406910},
doi = {10.1002/adma.202406910},
pmid = {39139006},
issn = {1521-4095},
support = {21935008//National Natural Science Foundation of China/ ; SKJY2021042//Livelihood Technology Project of Suzhou/ ; 23KJA150008//Jiangsu Province Higher Education Natural Science Research Major Project/ ; //Priority Academic Program Development of Jiangsu Higher Education Institutions/ ; },
abstract = {Drug-resistant pathogens significantly threaten human health and life. Simply killing drug-resistant pathogens cannot effectively eliminate their threat since the drug-resistant genes (DRGs) released from dead drug-resistant pathogens are difficult to eliminate and can further spread via horizontal gene transfer, leading to the spread of drug resistance. The development of antibacterial materials with sterilization and DRGs cleavage activities is highly crucial. Herein, a living system, Ce-PEA@Bdello, is fabricated with bacterial killing and DRGs cleavage activities for blocking bacterial drug resistance dissemination by engineered Bdellovibrio bacteriovorus (Bdello). Ce-PEA@Bdello is obtained by engineering Bdello with dopamine and a multinuclear cerium (IV) complex. Ce-PEA@Bdello can penetrate and eliminate kanamycin-resistant P. aeruginosa (Kan[R]) biofilms via the synergistic effect of predatory Bdello and photothermal polydopamine under near-infrared light. Additionally, the DNase-mimicking ability of Ce-PEA@Bdello endows it with genome and plasmid DNA cleavage ability. An in vivo study reveals that Ce-PEA@Bdello can eliminate P. aeruginosa (Kan[R]) and cleave DRGs in scald/burn infected wounds to block the spread of drug resistance and accelerate wound healing. This bioactive system constructed from natural living materials offers a promising means for blocking the spread of drug resistance.},
}

@article {pmid39135654,
year = {2024},
author = {Winter, M and Vos, M and Buckling, A and Johnsen, PJ and Harms, K},
title = {Effect of chemotherapeutic agents on natural transformation frequency in Acinetobacter baylyi.},
journal = {Access microbiology},
volume = {6},
number = {7},
pages = {},
pmid = {39135654},
issn = {2516-8290},
abstract = {Natural transformation is the ability of a bacterial cell to take up extracellular DNA which is subsequently available for recombination into the chromosome (or maintenance as an extrachromosomal element). Like other mechanisms of horizontal gene transfer, natural transformation is a significant driver for the dissemination of antimicrobial resistance. Recent studies have shown that many pharmaceutical compounds such as antidepressants and anti-inflammatory drugs can upregulate transformation frequency in the model species Acinetobacter baylyi. Chemotherapeutic compounds have been shown to increase the abundance of antimicrobial resistance genes and increase colonization rates of potentially pathogenic bacteria in patient gastrointestinal tracts, indicating an increased risk of infection and providing a pool of pathogenicity or resistance genes for transformable commensal bacteria. We here test for the effect of six cancer chemotherapeutic compounds on A. baylyi natural transformation frequency, finding two compounds, docetaxel and daunorubicin, to significantly decrease transformation frequency, and daunorubicin to also decrease growth rate significantly. Enhancing our understanding of the effect of chemotherapeutic compounds on the frequency of natural transformation could aid in preventing the horizontal spread of antimicrobial resistance genes.},
}

@article {pmid39132438,
year = {2024},
author = {Liu, H and Fan, S and Zhang, X and Yuan, Y and Zhong, W and Wang, L and Wang, C and Zhou, Z and Zhang, S and Geng, Y and Peng, G and Wang, Y and Zhang, K and Yan, Q and Luo, Y and Shi, K and Zhong, Z},
title = {Antibiotic-resistant characteristics and horizontal gene transfer ability analysis of extended-spectrum β-lactamase-producing Escherichia coli isolated from giant pandas.},
journal = {Frontiers in veterinary science},
volume = {11},
number = {},
pages = {1394814},
pmid = {39132438},
issn = {2297-1769},
abstract = {Extended-spectrum β-lactamase (ESBL)-producing Escherichia coli (ESBL-EC) is regarded as one of the most important priority pathogens within the One Health interface. However, few studies have investigated the occurrence of ESBL-EC in giant pandas, along with their antibiotic-resistant characteristics and horizontal gene transfer abilities. In this study, we successfully identified 12 ESBL-EC strains (8.33%, 12/144) out of 144 E. coli strains which isolated from giant pandas. We further detected antibiotic resistance genes (ARGs), virulence-associated genes (VAGs) and mobile genetic elements (MGEs) among the 12 ESBL-EC strains, and the results showed that 13 ARGs and 11 VAGs were detected, of which bla CTX-M (100.00%, 12/12, with 5 variants observed) and papA (83.33%, 10/12) were the most prevalent, respectively. And ISEcp1 (66.67%, 8/12) and IS26 (66.67%, 8/12) were the predominant MGEs. Furthermore, horizontal gene transfer ability analysis of the 12 ESBL-EC showed that all bla CTX-M genes could be transferred by conjugative plasmids, indicating high horizontal gene transfer ability. In addition, ARGs of rmtB and sul2, VAGs of papA, fimC and ompT, MGEs of ISEcp1 and IS26 were all found to be co-transferred with bla CTX-M. Phylogenetic analysis clustered these ESBL-EC strains into group B2 (75.00%, 9/12), D (16.67%, 2/12), and B1 (8.33%, 1/12), and 10 sequence types (STs) were identified among 12 ESBL-EC (including ST48, ST127, ST206, ST354, ST648, ST1706, and four new STs). Our present study showed that ESBL-EC strains from captive giant pandas are reservoirs of ARGs, VAGs and MGEs that can co-transfer with bla CTX-M via plasmids. Transmissible ESBL-EC strains with high diversity of resistance and virulence elements are a potential threat to humans, animals and surrounding environment.},
}

@article {pmid39128935,
year = {2024},
author = {Wang, W and Ge, Q and Wen, J and Zhang, H and Guo, Y and Li, Z and Xu, Y and Ji, D and Chen, C and Guo, L and Xu, M and Shi, C and Fan, G and Xie, C},
title = {Horizontal gene transfer and symbiotic microorganisms regulate the adaptive evolution of intertidal algae, Porphyra sense lato.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {976},
pmid = {39128935},
issn = {2399-3642},
support = {42176117//National Natural Science Foundation of China (National Science Foundation of China)/ ; U21A20265//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32100514//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Gene Transfer, Horizontal ; *Symbiosis/genetics ; *Porphyra/microbiology/genetics ; Adaptation, Physiological/genetics ; Phylogeny ; Biological Evolution ; },
abstract = {Intertidal algae may adapt to environmental challenges by acquiring genes from other organisms and relying on symbiotic microorganisms. Here, we obtained a symbiont-free and chromosome-level genome of Pyropia haitanensis (47.2 Mb), a type of intertidal algae, by using multiple symbiont screening methods. We identified 286 horizontal gene transfer (HGT) genes, 251 of which harbored transposable elements (TEs), reflecting the importance of TEs for facilitating the transfer of genes into P. haitanensis. Notably, the bulked segregant analysis revealed that two HGT genes, sirohydrochlorin ferrochelatase and peptide-methionine (R)-S-oxide reductase, play a significant role in the adaptation of P. haitanensis to heat stress. Besides, we found Pseudomonas, Actinobacteria, and Bacteroidetes are the major taxa among the symbiotic bacteria of P. haitanensis (nearly 50% of the HGT gene donors). Among of them, a heat-tolerant actinobacterial strain (Saccharothrix sp.) was isolated and revealed to be associated with the heat tolerance of P. haitanensis through its regulatory effects on the genes involved in proline synthesis (proC), redox homeostasis (ggt), and protein folding (HSP20). These findings contribute to our understanding of the adaptive evolution of intertidal algae, expanding our knowledge of the HGT genes and symbiotic microorganisms to enhance their resilience and survival in challenging intertidal environments.},
}

*Gene Transfer, Horizontal
*Symbiosis/genetics
*Porphyra/microbiology/genetics
Adaptation, Physiological/genetics
Phylogeny
Biological Evolution

@article {pmid39127705,
year = {2024},
author = {Park, H and Bulzu, PA and Shabarova, T and Kavagutti, VS and Ghai, R and Kasalický, V and Jezberová, J},
title = {Uncovering the genomic basis of symbiotic interactions and niche adaptations in freshwater picocyanobacteria.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {150},
pmid = {39127705},
issn = {2049-2618},
support = {20‑12496X//Grantová Agentura Ceské Republiky (GAČR)/ ; 20‑12496X//Grantová Agentura Ceské Republiky (GAČR)/ ; 23-05081S//Grantová Agentura Ceské Republiky (GAČR)/ ; 19-23261S//Grantová Agentura Ceské Republiky (GAČR)/ ; 20‑12496X//Grantová Agentura Ceské Republiky (GAČR)/ ; 19-23261S//Grantová Agentura Ceské Republiky (GAČR)/ ; 19-23261S//Grantová Agentura Ceské Republiky (GAČR)/ ; },
mesh = {*Symbiosis ; *Fresh Water/microbiology ; *Genome, Bacterial ; *Phylogeny ; *Cyanobacteria/genetics/classification ; Adaptation, Physiological/genetics ; Europe ; Ecosystem ; Gene Transfer, Horizontal ; Genomics ; },
abstract = {BACKGROUND: Picocyanobacteria from the genera Prochlorococcus, Synechococcus, and Cyanobium are the most widespread photosynthetic organisms in aquatic ecosystems. However, their freshwater populations remain poorly explored, due to uneven and insufficient sampling across diverse inland waterbodies.

RESULTS: In this study, we present 170 high-quality genomes of freshwater picocyanobacteria from non-axenic cultures collected across Central Europe. In addition, we recovered 33 genomes of their potential symbiotic partners affiliated with four genera, Pseudomonas, Mesorhizobium, Acidovorax, and Hydrogenophaga. The genomic basis of symbiotic interactions involved heterotrophs benefiting from picocyanobacteria-derived nutrients while providing detoxification of ROS. The global abundance patterns of picocyanobacteria revealed ecologically significant ecotypes, associated with trophic status, temperature, and pH as key environmental factors. The adaptation of picocyanobacteria in (hyper-)eutrophic waterbodies could be attributed to their colonial lifestyles and CRISPR-Cas systems. The prevailing CRISPR-Cas subtypes in picocyanobacteria were I-G and I-E, which appear to have been acquired through horizontal gene transfer from other bacterial phyla.

CONCLUSIONS: Our findings provide novel insights into the population diversity, ecology, and evolutionary strategies of the most widespread photoautotrophs within freshwater ecosystems. Video Abstract.},
}

*Symbiosis
*Fresh Water/microbiology
*Genome, Bacterial
*Phylogeny
*Cyanobacteria/genetics/classification
Adaptation, Physiological/genetics
Europe
Ecosystem
Gene Transfer, Horizontal
Genomics

@article {pmid39125965,
year = {2024},
author = {Sadowska-Bartosz, I and Bartosz, G},
title = {Antioxidant Defense in the Toughest Animals on the Earth: Its Contribution to the Extreme Resistance of Tardigrades.},
journal = {International journal of molecular sciences},
volume = {25},
number = {15},
pages = {},
pmid = {39125965},
issn = {1422-0067},
mesh = {Animals ; *Tardigrada/metabolism/genetics ; *Antioxidants/metabolism ; Oxidative Stress ; Earth, Planet ; Trehalose/metabolism ; },
abstract = {Tardigrades are unique among animals in their resistance to dehydration, mainly due to anhydrobiosis and tun formation. They are also very resistant to high-energy radiation, low and high temperatures, low and high pressure, and various chemical agents, Interestingly, they are resistant to ionizing radiation both in the hydrated and dehydrated states to a similar extent. They are able to survive in the cosmic space. Apparently, many mechanisms contribute to the resistance of tardigrades to harmful factors, including the presence of trehalose (though not common to all tardigrades), heat shock proteins, late embryogenesis-abundant proteins, tardigrade-unique proteins, DNA repair proteins, proteins directly protecting DNA (Dsup and TDR1), and efficient antioxidant system. Antioxidant enzymes and small-molecular-weight antioxidants are an important element in the tardigrade resistance. The levels and activities of many antioxidant proteins is elevated by anhydrobiosis and UV radiation; one explanation for their induction during dehydration is provided by the theory of "preparation for oxidative stress", which occurs during rehydration. Genes coding for some antioxidant proteins are expanded in tardigrades; some genes (especially those coding for catalases) were hypothesized to be of bacterial origin, acquired by horizontal gene transfer. An interesting antioxidant protein found in tardigrades is the new Mn-dependent peroxidase.},
}

Animals
*Tardigrada/metabolism/genetics
*Antioxidants/metabolism
Oxidative Stress
Earth, Planet
Trehalose/metabolism

@article {pmid39125866,
year = {2024},
author = {Cheng, X and Liu, X and Jordan, KW and Yu, J and Whitworth, RJ and Park, Y and Chen, MS},
title = {Frequent Acquisition of Glycoside Hydrolase Family 32 (GH32) Genes from Bacteria via Horizontal Gene Transfer Drives Adaptation of Invertebrates to Diverse Sources of Food and Living Habitats.},
journal = {International journal of molecular sciences},
volume = {25},
number = {15},
pages = {},
pmid = {39125866},
issn = {1422-0067},
mesh = {*Gene Transfer, Horizontal ; *Glycoside Hydrolases/genetics/metabolism ; Animals ; *Bacteria/genetics/enzymology ; *Phylogeny ; Invertebrates/genetics ; Adaptation, Physiological/genetics ; Ecosystem ; Evolution, Molecular ; },
abstract = {Glycoside hydrolases (GHs, also called glycosidases) catalyze the hydrolysis of glycosidic bonds in polysaccharides. Numerous GH genes have been identified from various organisms and are classified into 188 families, abbreviated GH1 to GH188. Enzymes in the GH32 family hydrolyze fructans, which are present in approximately 15% of flowering plants and are widespread across microorganisms. GH32 genes are rarely found in animals, as fructans are not a typical carbohydrate source utilized in animals. Here, we report the discovery of 242 GH32 genes identified in 84 animal species, ranging from nematodes to crabs. Genetic analyses of these genes indicated that the GH32 genes in various animals were derived from different bacteria via multiple, independent horizontal gene transfer events. The GH32 genes in animals appear functional based on the highly conserved catalytic blades and triads in the active center despite the overall low (35-60%) sequence similarities among the predicted proteins. The acquisition of GH32 genes by animals may have a profound impact on sugar metabolism for the recipient organisms. Our results together with previous reports suggest that the acquired GH32 enzymes may not only serve as digestive enzymes, but also may serve as effectors for manipulating host plants, and as metabolic enzymes in the non-digestive tissues of certain animals. Our results provide a foundation for future studies on the significance of horizontally transferred GH32 genes in animals. The information reported here enriches our knowledge of horizontal gene transfer, GH32 functions, and animal-plant interactions, which may result in practical applications. For example, developing crops via targeted engineering that inhibits GH32 enzymes could aid in the plant's resistance to animal pests.},
}

*Gene Transfer, Horizontal
*Glycoside Hydrolases/genetics/metabolism
Animals
*Bacteria/genetics/enzymology
*Phylogeny
Invertebrates/genetics
Adaptation, Physiological/genetics
Ecosystem
Evolution, Molecular

@article {pmid39125715,
year = {2024},
author = {Bucka-Kolendo, J and Kiousi, DE and Dekowska, A and Mikołajczuk-Szczyrba, A and Karadedos, DM and Michael, P and Galanis, A and Sokołowska, B},
title = {Exploration of Alicyclobacillus spp. Genome in Search of Antibiotic Resistance.},
journal = {International journal of molecular sciences},
volume = {25},
number = {15},
pages = {},
pmid = {39125715},
issn = {1422-0067},
mesh = {*Alicyclobacillus/genetics/drug effects ; *Genome, Bacterial ; *Microbial Sensitivity Tests ; *Anti-Bacterial Agents/pharmacology ; Whole Genome Sequencing ; Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; Guaiacol/pharmacology/analogs & derivatives ; },
abstract = {The study investigates the antibiotic resistance (AR) profiles and genetic determinants in three strains of guaiacol-producing Alicyclobacillus spp. isolated from orchard soil and pears. Their phenotypic characteristics, such as spore formation; resistance to different factors, including drugs or disinfectants; or production of off-flavor compounds, can affect the taste and aroma of spoiled products. Food and beverages are potential vectors for the transfer of antibiotic resistance genes, which is a growing health concern; thus, microorganisms in food and beverages should not be a potential source of drug resistance to consumers. Whole-genome sequencing (WGS) was utilized to identify antibiotic resistance genes, metabolic pathways, and elements associated with guaiacol and halophenol production. Minimum inhibitory concentration (MIC) testing revealed that all strains were susceptible to eight out of nine tested antibiotics (ampicillin, gentamycin, kanamycin, streptomycin, clindamycin, tetracycline, chloramphenicol, and vancomycin) but exhibited high resistance to erythromycin. Analysis indicated that the erythromycin resistance gene, ribosomal RNA small subunit methyltransferase A (RsmA), was intrinsic and likely acquired through horizontal gene transfer (HGT). The comprehensive genomic analysis provides insights into the molecular mechanisms of antibiotic resistance in Alicyclobacillus spp., highlighting the potential risk of these bacteria as vectors for antibiotic resistance genes in the food chain. This study expands the understanding of the genetic makeup of these spoilage bacteria and their role in antimicrobial resistance dissemination.},
}

*Alicyclobacillus/genetics/drug effects
*Genome, Bacterial
*Microbial Sensitivity Tests
*Anti-Bacterial Agents/pharmacology
Whole Genome Sequencing
Drug Resistance, Bacterial/genetics
Gene Transfer, Horizontal
Guaiacol/pharmacology/analogs & derivatives

@article {pmid39122691,
year = {2024},
author = {Williams, SK and Jerlström Hultqvist, J and Eglit, Y and Salas-Leiva, DE and Curtis, B and Orr, RJS and Stairs, CW and Atalay, TN and MacMillan, N and Simpson, AGB and Roger, AJ},
title = {Extreme mitochondrial reduction in a novel group of free-living metamonads.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {6805},
pmid = {39122691},
issn = {2041-1723},
support = {FRN-142349//Gouvernement du Canada | Canadian Institutes of Health Research (Instituts de Recherche en Santé du Canada)/ ; },
mesh = {*Mitochondria/metabolism/genetics ; *Phylogeny ; *Proteome/metabolism/genetics ; Transcriptome ; Eukaryota/genetics/metabolism/classification ; Gene Transfer, Horizontal ; Iron-Sulfur Proteins/metabolism/genetics ; },
abstract = {Metamonads are a diverse group of heterotrophic microbial eukaryotes adapted to living in hypoxic environments. All metamonads but one harbour metabolically altered 'mitochondrion-related organelles' (MROs) with reduced functions, however the degree of reduction varies. Here, we generate high-quality draft genomes, transcriptomes, and predicted proteomes for five recently discovered free-living metamonads. Phylogenomic analyses placed these organisms in a group we name the 'BaSk' (Barthelonids+Skoliomonads) clade, a deeply branching sister group to the Fornicata, a phylum that includes parasitic and free-living flagellates. Bioinformatic analyses of gene models shows that these organisms are predicted to have extremely reduced MRO proteomes in comparison to other free-living metamonads. Loss of the mitochondrial iron-sulfur cluster assembly system in some organisms in this group appears to be linked to the acquisition in their common ancestral lineage of a SUF-like minimal system Fe/S cluster pathway by lateral gene transfer. One of the isolates, Skoliomonas litria, appears to have lost all other known MRO pathways. No proteins were confidently assigned to the predicted MRO proteome of this organism suggesting that the organelle has been lost. The extreme mitochondrial reduction observed within this free-living anaerobic protistan clade demonstrates that mitochondrial functions may be completely lost even in free-living organisms.},
}

*Mitochondria/metabolism/genetics
*Phylogeny
*Proteome/metabolism/genetics
Transcriptome
Eukaryota/genetics/metabolism/classification
Gene Transfer, Horizontal
Iron-Sulfur Proteins/metabolism/genetics

@article {pmid37754684,
year = {2023},
author = {Zhang, Y and Kitazumi, A and Liao, Y-T and de Los Reyes, BG and Wu, VCH},
title = {Metagenomic investigation reveals bacteriophage-mediated horizontal transfer of antibiotic resistance genes in microbial communities of an organic agricultural ecosystem.},
journal = {Microbiology spectrum},
volume = {11},
number = {5},
pages = {e0022623},
pmid = {37754684},
issn = {2165-0497},
support = {2030-42000-0055-000-D//USDA | Agricultural Research Service (ARS)/ ; },
mesh = {*Bacteriophages/genetics ; *Gene Transfer, Horizontal ; *Metagenomics ; *Agriculture ; *Bacteria/genetics/virology/drug effects ; *Microbiota/genetics ; Metagenome ; Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Ecosystem ; Drug Resistance, Bacterial/genetics ; Soil Microbiology ; },
abstract = {Antibiotic resistance has become a serious health concern worldwide. The potential impact of viruses, bacteriophages in particular, on spreading antibiotic resistance genes is still controversial due to the complexity of bacteriophage-bacterial interactions within diverse environments. In this study, we determined the microbiome profiles and the potential antibiotic resistance gene (ARG) transfer between bacterial and viral populations in different agricultural samples using a high-resolution analysis of the metagenomes. The results of this study provide compelling genetic evidence for ARG transfer through bacteriophage-bacteria interactions, revealing the inherent risks associated with bacteriophage-mediated ARG transfer across the agricultural microbiome.},
}

*Bacteriophages/genetics
*Gene Transfer, Horizontal
*Metagenomics
*Agriculture
*Bacteria/genetics/virology/drug effects
*Microbiota/genetics
Metagenome
Drug Resistance, Microbial/genetics
Anti-Bacterial Agents/pharmacology
Ecosystem
Drug Resistance, Bacterial/genetics
Soil Microbiology

@article {pmid39121985,
year = {2024},
author = {Yan, Y and Lu, H and Liang, X and Xu, T and Yan, S and Yu, Y and Wang, Y},
title = {The virulence plasmid associated with AHPND in shrimp appears to have originated from Vibrio owensii through a process of homologous recombination of parental plasmids and the transposable insertion of two large fragments.},
journal = {Journal of invertebrate pathology},
volume = {206},
number = {},
pages = {108173},
doi = {10.1016/j.jip.2024.108173},
pmid = {39121985},
issn = {1096-0805},
abstract = {Acute hepatopancreatic necrosis disease (AHPND) is a highly contagious and lethal disease of shrimp caused by Vibrio strains carrying the virulence plasmid (pAHPND) containing the pirAB virulence genes. Through analysis of plasmid sequence similarity, clustering, and phylogeny, a horizontal transfer element similar to IS91 was discovered within the pAHPND plasmid. Additionally, two distinct clades of plasmids related to pAHPND (designated as pAHPND-r1 and pAHPND-r2) were identified, which may serve as potential parental plasmids for pAHPND. The available evidence, including the difference in G+C content between the plasmid and its host, codon usage preference, and plasmid recombination event prediction, suggests that the formation of the pAHPND plasmid in the Vibrio owensii strain was likely due to the synergistic effect of the recombinase RecA and the associated proteins RecBCD on the pAHPND-r1 and pAHPND-r2, resulting in the recombination and formation of the precursor plasmid for pAHPND (pre-pAHPND). The emergence of pAHPND was found to be a result of successive insertions of the horizontal transfer elements of pirAB-Tn903 and IS91-like segment, which led to the deletion of one third of the pre-pAHPND. This plasmid was then able to spread horizontally to other Vibrio strains, contributing to the epidemics of AHPND. These findings shed light on previously unknown mechanisms involved in the emergence of pAHPND and improve our understanding of the disease's spread.},
}

@article {pmid39119206,
year = {2024},
author = {Zaer-Anaqz, Z and Khakvar, R and Mohammadi, SA and Bannazadeh Baghi, H and Koolivand, D},
title = {Physicochemical Characterization of Novel Bacteriophages of Pseudomonas syringe from Northwest Iran.},
journal = {PHAGE (New Rochelle, N.Y.)},
volume = {5},
number = {2},
pages = {99-106},
pmid = {39119206},
issn = {2641-6549},
abstract = {Bacterial canker, caused by Pseudomonas syringae, is a devastating disease of stone fruit trees worldwide. The bacterium has a broad host range and a high capacity for adaptation and dissemination, owing to its high mutation rate and horizontal gene transfer. Traditional control methods based on copper compounds and antibiotics have resulted in the development of resistance in the bacterial population. Thus, alternative approaches are needed, such as phage therapy. This study aimed to characterize the physicochemical and biological properties of novel Pseudomonas syringae pv. syringae (Pss)-specific phages isolated from the soils of northwestern Iran. Seventy-five phage isolates were obtained, and their host range was determined against various bacterial pathogens. Five phages exhibiting the highest lytic activity against Pss and a narrow host range were selected for subsequent analysis. The stability of the selected phages was assessed under different conditions such as ultraviolet irradiation, temperature, pH, NaCl concentration, and chloroform exposure. The selected phages demonstrated significant effectiveness in vivo, exerting substantial suppression on the population of Pss. This reduction was observed for both individual phages and when the phages were utilized as a mixture. The findings indicate that phages have the potential to be used as biocontrol agents in agriculture.},
}

@article {pmid39119203,
year = {2024},
author = {Delesalle, VA and Ankeriasniemi, RE and Lewis, CM and Mody, JM and Roy, AM and Sarvis, WA and Vo, DD and Walsh, AE and Zappia, RJ},
title = {Introducing Casbah, Kronus, and MmasiCarm, Members of the Mycobacteriophage Subcluster B3.},
journal = {PHAGE (New Rochelle, N.Y.)},
volume = {5},
number = {2},
pages = {84-90},
pmid = {39119203},
issn = {2641-6549},
abstract = {BACKGROUND: As part of a large science education effort, bacteriophages that lyse Mycobacterium smegmatis mc[2]155 continue to be discovered.

MATERIALS AND METHODS: Phages were isolated from soil samples from urban sites in the Northeastern United States. Their genomes were sequenced, assembled, and bioinformatically compared.

RESULTS: Three lytic siphoviruses belonging to subcluster B3 with high similarity to each other and other B3 mycobacteriophages were isolated. These phages contain double-stranded DNA genomes (68,754 to 69,495 bp) with high GC content (67.4-67.5%) and 102-104 putative protein coding genes. Notable features include a HicA-like toxin and 33 genes exclusive to subcluster B3. One phage had an intein in its terminase sequence.

CONCLUSIONS: Genomic analyses of these phages provide insights into genome evolution and horizontal gene transfer (HGT). The networks for HGT are apparently vast and gene specific. Interestingly, a number of genes are found in both B3 and Gordonia DR phages.},
}

@article {pmid39117207,
year = {2024},
author = {Erler, T and Droop, F and Lübbert, C and Knobloch, JK and Carlsen, L and Papan, C and Schwanz, T and Zweigner, J and Dengler, J and Hoffmann, M and Mutters, NT and Savin, M},
title = {Analysing carbapenemases in hospital wastewater: Insights from intracellular and extracellular DNA using qPCR and digital PCR.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {175344},
doi = {10.1016/j.scitotenv.2024.175344},
pmid = {39117207},
issn = {1879-1026},
abstract = {The widespread dissemination of carbapenem-resistant bacteria in wastewater systems, particularly from clinical sources, poses a significant public health risk. This study assessed the concentrations and distributions of extracellular DNA (exDNA) and intracellular DNA (iDNA) harboring carbapenemase genes in wastewater from six tertiary care hospitals in Germany. We collected a total of 36 samples, comprising six biological replicates from each hospital, and analysed them using quantitative real-time PCR (qPCR) and digital PCR (dPCR). The analysis targeted seven carbapenemase genes: blaNDM, blaKPC, blaIMP, blaVIM, blaOXA-23-like, blaOXA-48-like, and blaOXA-58-like across both DNA fractions. Our results revealed significant variability in the concentrations of exDNA and iDNA across the sampling sites, with iDNA typically present at higher concentrations. Using NanoDrop One spectrophotometry and the Qubit dsDNA kit, exDNA concentrations ranged from 2.7 to 7.7 ng/mL, while Qubit recorded lower values between 1.1 and 4.0 ng/mL. Conversely, iDNA concentrations were markedly higher, spanning from 42.3 to 191.7 ng/mL with NanoDrop and 12.0 to 46.5 ng/mL with Qubit, highlighting the variability between DNA types and quantification methods. Despite its lower concentrations, exDNA comprised up to 18.2 % of total DNA, highlighting its potential role in the horizontal transfer of antimicrobial resistance genes (ARGs). The study detected target ARGs in both DNA fractions at all sites, with notable differences in their concentrations; iDNA consistently exhibited higher levels of ARGs, with the highest concentrations reaching 10.57 ± 0.20 log gene copies per liter (GC/L) for blaVIM in iDNA and 6.96 ± 0.72 log GC/L for blaIMP in exDNA. dPCR demonstrated greater sensitivity than qPCR, especially effective for detecting low-abundance targets like blaOXA-23-like in the exDNA fraction. Additionally, qPCR's susceptibility to inhibition and contamination emphasizes the superior robustness of dPCR. This research highlights the need for improved monitoring and the implementation of advanced treatment technologies to mitigate ARG dissemination in wastewater.},
}

@article {pmid39113256,
year = {2024},
author = {Hossain, AKMZ and Chowdhury, AMMA},
title = {Understanding the Evolution and Transmission Dynamics of Antibiotic Resistance Genes: A Comprehensive Review.},
journal = {Journal of basic microbiology},
volume = {},
number = {},
pages = {e2400259},
doi = {10.1002/jobm.202400259},
pmid = {39113256},
issn = {1521-4028},
abstract = {Antibiotic resistance poses a formidable challenge to global public health, necessitating comprehensive understanding and strategic interventions. This review explores the evolution and transmission dynamics of antibiotic resistance genes, with a focus on Bangladesh. The indiscriminate use of antibiotics, compounded by substandard formulations and clinical misdiagnosis, fuels the emergence and spread of resistance in the country. Studies reveal high resistance rates among common pathogens, emphasizing the urgent need for targeted interventions and rational antibiotic use. Molecular assessments uncover a diverse array of antibiotic resistance genes in environmental reservoirs, highlighting the complex interplay between human activities and resistance dissemination. Horizontal gene transfer mechanisms, particularly plasmid-mediated conjugation, facilitate the exchange of resistance determinants among bacterial populations, driving the evolution of multidrug-resistant strains. The review discusses clinical implications, emphasizing the interconnectedness of environmental and clinical settings in resistance dynamics. Furthermore, bioinformatic and experimental evidence elucidates novel mechanisms of resistance gene transfer, underscoring the dynamic nature of resistance evolution. In conclusion, combating antibiotic resistance requires a multifaceted approach, integrating surveillance, stewardship, and innovative research to preserve the efficacy of antimicrobial agents and safeguard public health.},
}

@article {pmid39103341,
year = {2024},
author = {Hu, K and Chou, CW and Wilke, CO and Finkelstein, IJ},
title = {Distinct horizontal transfer mechanisms for type I and type V CRISPR-associated transposons.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {6653},
pmid = {39103341},
issn = {2041-1723},
support = {R01 GM124141/GM/NIGMS NIH HHS/United States ; R01GM088344//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; R01 GM088344/GM/NIGMS NIH HHS/United States ; F-1808//Welch Foundation/ ; R01GM124141//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; },
mesh = {*DNA Transposable Elements/genetics ; *Escherichia coli/genetics/metabolism ; *CRISPR-Cas Systems ; *Clustered Regularly Interspaced Short Palindromic Repeats ; *Gene Transfer, Horizontal ; *CRISPR-Associated Proteins/metabolism/genetics ; Escherichia coli Proteins/genetics/metabolism ; },
abstract = {CASTs use both CRISPR-associated proteins and Tn7-family transposons for RNA-guided vertical and horizontal transmission. CASTs encode minimal CRISPR arrays but can't acquire new spacers. Here, we report that CASTs can co-opt defense-associated CRISPR arrays for horizontal transmission. A bioinformatic analysis shows that CASTs co-occur with defense-associated CRISPR systems, with the highest prevalence for type I-B and type V CAST sub-types. Using an E. coli quantitative transposition assay and in vitro reconstitution, we show that CASTs can use CRISPR RNAs from these defense systems. A high-resolution structure of the type I-F CAST-Cascade in complex with a type III-B CRISPR RNA reveals that Cas6 recognizes direct repeats via sequence-independent π - π interactions. In addition to using heterologous CRISPR arrays, type V CASTs can also transpose via an unguided mechanism, even when the S15 co-factor is over-expressed. Over-expressing S15 and the trans-activating CRISPR RNA or a single guide RNA reduces, but does not abrogate, off-target integration for type V CASTs. Our findings suggest that some CASTs may exploit defense-associated CRISPR arrays and that this fact must be considered when porting CASTs to heterologous bacterial hosts. More broadly, this work will guide further efforts to engineer the activity and specificity of CASTs for gene editing applications.},
}

*DNA Transposable Elements/genetics
*Escherichia coli/genetics/metabolism
*CRISPR-Cas Systems
*Clustered Regularly Interspaced Short Palindromic Repeats
*Gene Transfer, Horizontal
*CRISPR-Associated Proteins/metabolism/genetics
Escherichia coli Proteins/genetics/metabolism

@article {pmid39102038,
year = {2024},
author = {Olanrewaju, OS and Molale-Tom, LG and Bezuidenhout, CC},
title = {Genomic diversity, antibiotic resistance, and virulence in South African Enterococcus faecalis and Enterococcus lactis isolates.},
journal = {World journal of microbiology & biotechnology},
volume = {40},
number = {10},
pages = {289},
pmid = {39102038},
issn = {1573-0972},
mesh = {South Africa ; *Genome, Bacterial ; *Enterococcus faecalis/genetics/drug effects/pathogenicity/isolation & purification ; Virulence/genetics ; *Genetic Variation ; *Anti-Bacterial Agents/pharmacology ; *Virulence Factors/genetics ; Humans ; Drug Resistance, Bacterial/genetics ; Genomic Islands/genetics ; Gram-Positive Bacterial Infections/microbiology ; Enterococcus/genetics/drug effects/pathogenicity/isolation & purification/classification ; Phylogeny ; Gene Transfer, Horizontal ; Genomics ; Microbial Sensitivity Tests ; },
abstract = {This study presents the empirical findings of an in-depth genomic analysis of Enterococcus faecalis and Enterococcus lactis isolates from South Africa. It offers valuable insights into their genetic characteristics and their significant implications for public health. The study uncovers nuanced variations in the gene content of these isolates, despite their similar GC contents, providing a comprehensive view of the evolutionary diversity within the species. Genomic islands are identified, particularly in E. faecalis, emphasizing its propensity for horizontal gene transfer and genetic diversity, especially in terms of antibiotic resistance genes. Pangenome analysis reveals the existence of a core genome, accounting for a modest proportion of the total genes, with 2157 core genes, 1164 shell genes, and 4638 cloud genes out of 7959 genes in 52 South African E. faecalis genomes (2 from this study, 49 south Africa genomes downloaded from NCBI, and E. faecalis reference genome). Detecting large-scale genomic rearrangements, including chromosomal inversions, underscores the dynamic nature of bacterial genomes and their role in generating genetic diversity. The study uncovers an array of antibiotic resistance genes, with trimethoprim, tetracycline, glycopeptide, and multidrug resistance genes prevalent, raising concerns about the effectiveness of antibiotic treatment. Virulence gene profiling unveils a diverse repertoire of factors contributing to pathogenicity, encompassing adhesion, biofilm formation, stress resistance, and tissue damage. These empirical findings provide indispensable insights into these bacteria's genomic dynamics, antibiotic resistance mechanisms, and virulence potential, underlining the pressing need to address antibiotic resistance and implement robust control measures.},
}

South Africa
*Genome, Bacterial
*Enterococcus faecalis/genetics/drug effects/pathogenicity/isolation & purification
Virulence/genetics
*Genetic Variation
*Anti-Bacterial Agents/pharmacology
*Virulence Factors/genetics
Humans
Drug Resistance, Bacterial/genetics
Genomic Islands/genetics
Gram-Positive Bacterial Infections/microbiology
Enterococcus/genetics/drug effects/pathogenicity/isolation & purification/classification
Phylogeny
Gene Transfer, Horizontal
Genomics
Microbial Sensitivity Tests

@article {pmid39101807,
year = {2024},
author = {Dhurve, G and Behera, SR and Kodetham, G and Siddavattam, D},
title = {Outer membrane vesicles of Acinetobacter baumannii DS002 carry circular DNA similar to bovine meat and milk factors (BMMFs) and SPHINX 2.36 and probably play a role in interdomain lateral gene transfer.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0081724},
doi = {10.1128/spectrum.00817-24},
pmid = {39101807},
issn = {2165-0497},
abstract = {UNLABELLED: The discovery of Replication Competent Circular DNA molecules in mammalian cells and tissues is being linked to debilitating diseases, such as multiple sclerosis (MS), bovine spongiform encephalopathy (BSE), and colorectal cancer (CRC). These circular DNA molecules, otherwise known as bovine meat and milk factors (BMMFs) and Slow Progressive Hidden INfections of variable (X) latency (SPHINX), bear significant (80%) sequence similarity with the plasmids of Acinetobacter baumannii strains. Nanostructures, such as bacterial outer membrane vesicles (OMVs) serve as vehicles for transporting biomolecular cargo and have the potential to facilitate interkingdom lateral mobility of DNA. Strengthening the proposed hypothesis, this study demonstrates that OMVs derived from A. baumannii DS002 carrying four plasmids and genome (pTS236) of phage, AbDs1, successfully reached different parts of the body, including the central nervous system, following the injection of fluorescein isothiocyanate (FITC)-labeled OMVs into experimental mice. Out of the four OMV-associated plasmids, three (pTS4586, pTS9900, and pTS134338) were identified within the lumen, and the fourth one (pTS11291) was found on the surface of OMVs. In addition to the indigenous plasmids, the phage-encoded protein, Orf96, anchored on the surface of the OMVs by establishing a strong interaction with the OMV-associated porin, OmpA. Intriguingly, a subset of labeled OMVs, when incubated with Neuro2A cells, translocated across the membrane and reached to the cytoplasmic space of the cells. Collectively, the experimental evidence presented herein underscores the promising potential of OMVs as vehicles for delivering molecular cargo containing plasmids and phage genomes to diverse mammalian tissues and cells.

IMPORTANCE: Several independent studies have demonstrated the existence of replication competent circular DNA molecules of bacterial and viral origin in mammalian cells and tissues. However, studies about their origin and lateral mobility to mammalian cells are scarce. Our work describes the existence of circular DNA, similar to that of DNA molecules identified in mammalian cells, OMVs derived from soil isolate of A. baumannii DS002. Furthermore, the work also provides visual evidence that demonstrates the passage of labeled OMVs to different organs of experimental mice within hours after intravenously administering OMVs into experimental mice. Some of the labeled OMVs have even crossed the membrane of Neuro2A, suggesting the existence of interkingdom horizontal mobility between bacteria and mammals.},
}