Mechanism Of Gene Transfer Research Articles

Multi-focused laboratory experiments based on Quorum Sensing and Quorum Quenching for acquiring Microbial Physiology concepts.

After a time away from the classrooms and laboratories due to the global pandemic, the return to teaching activities during the semester represented a challenge to both teachers and students. Our particular situation in a Microbial Physiology course was the necessity of imparting in shorter time, laboratory practices that usually take longer. This article describes a 2-week-long laboratory exercise that covers several concepts in an interrelated way: conjugation as a gene transfer mechanism, regulation of microbial physiology, production of secondary metabolites, degradation of macromolecules, and biofilm formation. Utilizing a Quorum Quenching (QQ) strategy, the Quorum Sensing (QS) system of Pseudomonas aeruginosa is first attenuated. Then, phenotypes regulated by QS are evidenced. QS is a regulatory mechanism of microbial physiology that relies on signal molecules. QS is related in P. aeruginosa to several virulence factors, some of which are exploited in the laboratory practices presented in this work. QQ is a phenomenon by which QS is interrupted or attenuated. We utilized a QQ approach based on the enzymatic degradation of the P. aeruginosa QS signals to evidence QS-regulated traits that are relevant to our Microbial Physiology course. Results obtained with the same test performed by a random group of students before and after the activities show the positive effectiveness of the approach presented in this work.

Enhancing Maternal Health: Cost-effective Alternatives in High Pressure Processing of Fruit Products

The search for efficacious Alternatives to the Current Standard Procedure in the Food Manufacturing Industry is a public health imperative. Recent advances and rapid adoption of high-pressure processing units in food manufacturing is gaining momentum across various industry sectors. The momentum of industrial importance across various sectors of food manufacturing, has led to requiring extensive microbiological hurdle validation studies for efficacious and feasible utilization of the technology. Fruit juices such as apple juice are an important component of maternal and child health diets. In regards to, microorganisms moving through vertical and horizontal gene transfer mechanisms, these systems work in the prevention of natural and anthropogenic pathogens of public health concern. As a result, adapting High Pressure Processing (HPP) in the inactivation of the pathogens is important. In this study, the protocol involves exposure to various times and intensity levels of elevated hydrostatic pressure. HPP is being used to identify the most effective conditions for vector (microorganism) inactivation. There was a large area of effectiveness of the HPP technology eradicating microorganisms in toxin-producing Escherichia coli O157:H7 (STEC), Non-O157 Shiga toxin-producing Escherichia coli (nSTEC), Salmonella serovars, and Listeria monocytogenes. Each were effectively eradicated utilizing this HPP technology. These specific microorganisms were selected as they are some of the most common ones that are involved in foodborne illness. Elevated hydrostatic pressure is a non-thermal procedure that exposes pathogens to pressures of up to 80,000 PSI (>550 MPa). Various times (3, 4, and 5 minutes) at pressure intensity levels of 600 MPa, (87K PSI), 550 MPa (79K PSI), 480 MPa (70K PSI), 415 MPa (60K PSI), and 345 MPa (50K PSI) of elevated hydrostatic pressure were investigated at 4°C and for 45°C. This research measured the effect of HPP treatment in eradicating the microbial load with nominal effects on organoleptic and nutritional quality of fruit juices. The results of this study provide support of cost effective and healthy fruit juice options to mothers and their children.

Genomic Analysis of a Community-Acquired Methicillin-Resistant Staphylococcus aureus Sequence Type 1 Associated with Caprine Mastitis.

This study aimed to investigate the genomic and epidemiological features of a methicillin-resistant Staphylococcus aureus sequence type 1 (MRSA ST1) strain associated with caprine subclinical mastitis. An S. aureus strain was isolated from goat's milk with subclinical mastitis in Paraiba, Northeastern Brazil, by means of aseptic procedures and tested for antimicrobial susceptibility using the disk-diffusion method. Whole genome sequencing was performed using the Illumina MiSeq platform. After genome assembly and annotation, in silico analyses, including multilocus sequence typing (MLST), antimicrobial resistance and stress-response genes, virulence factors, and plasmids detection were performed. A comparative SNP-based phylogenetic analysis was performed using publicly available MRSA genomes. The strain showed phenotypic resistance to cefoxitin, penicillin, and tetracycline and was identified as sequence type 1 (ST1) and spa type 128 (t128). It harbored the SCCmec type IVa (2B), as well as the lukF-PV and lukS-PV genes. The strain was phylogenetically related to six community-acquired MRSA isolates (CA-MRSA) strains associated with human clinical disease in North America, Europe, and Australia. This is the first report of a CA-MRSA strain associated with milk in the Americas. The structural and epidemiologic features reported in the MRSA ST1 carrying a mecA-SCCmec type IVa suggest highly complex mechanisms of horizontal gene transfer in MRSA. The SNP-based phylogenetic analysis suggests a zooanthroponotic transmission, i.e., a strain of human origin.

Structure of the Portal Complex from Staphylococcus aureus Pathogenicity Island 1 Transducing Particles In Situ and In Isolation

Staphylococcus aureus is an important human pathogen, and the prevalence of antibiotic resistance is a major public health concern. The evolution of pathogenicity and resistance in S. aureus often involves acquisition of mobile genetic elements (MGEs). Bacteriophages play an especially important role, since transduction represents the main mechanism for horizontal gene transfer. S. aureus pathogenicity islands (SaPIs), including SaPI1, are MGEs that carry genes encoding virulence factors, and are mobilized at high frequency through interactions with specific “helper” bacteriophages, such as 80α, leading to packaging of the SaPI genomes into virions made from structural proteins supplied by the helper. Among these structural proteins is the portal protein, which forms a ring-like portal at a fivefold vertex of the capsid, through which the DNA is packaged during virion assembly and ejected upon infection of the host. We have used high-resolution cryo-electron microscopy to determine structures of the S. aureus bacteriophage 80α portal itself, produced by overexpression, and in situ in the empty and full SaPI1 virions, and show how the portal interacts with the capsid. These structures provide a basis for understanding portal and capsid assembly and the conformational changes that occur upon DNA packaging and ejection.

Electric organ discharge from electric eel facilitates DNA transformation into teleost larvae in laboratory conditions

Background Electric eels (Electrophorus sp.) are known for their ability to produce electric organ discharge (EOD) reaching voltages of up to 860 V. Given that gene transfer via intense electrical pulses is a well-established technique in genetic engineering, we hypothesized that electric eels could potentially function as a gene transfer mechanism in their aquatic environment. Methods To investigate this hypothesis, we immersed zebrafish larvae in water containing DNA encoding the green fluorescent protein (GFP) and exposed them to electric eel’s EOD. Results and Discussion Some embryos exhibited a mosaic expression of green fluorescence, in contrast to the control group without electrical stimulation, which showed little distinct fluorescence. This suggests that electric eel EOD has the potential to function as an electroporator for the transfer of DNA into eukaryotic cells. While electric eel EOD is primarily associated with behaviors related to sensing, predation, and defense, it may incidentally serve as a possible mechanism for gene transfer in natural environment. This investigation represents the initial exploration of the uncharted impact of electric eel EOD, but it does not directly establish its significance within the natural environment. Further research is required to understand the ecological implications of this phenomenon.

Antibiotic Resistance Genes (ARGs) in the Environment of Saudi Aquaculture as a New Class of Pollutants

Aquaculture is a productive sector that will be instrumental in addressing the challenges of the forthcoming generation, including the demand for proteins endorsing humans and environmental stewardship. Saudi Arabia (SA) economy heavily depends on aquaculture. However, aquaculture practices, which encompass applying antibiotics for both prophylaxis and treatment, impose a significant impact. Applying antibiotics in aquaculture causes the neighboring microorganisms in the water column, soil particles, and aquaculture-related bacterium species to become resistant to antibiotics. Bacteria can spread antibiotic resistance genes (ARGs) through gene transfer mechanisms, further distributing genetic determinants in aquatic habitats. SA is one of the nations with the highest projected relative growth in aquaculture antibiotic consumption. There have been reports of numerous antibiotic-resistant microorganisms in SA, but the majority of studies focused on isolates from human samples. Several ARGs developing resistance to aminoglycosides, carbapenems, tetracyclines, and beta-lactams were reported in clinical samples in SA; however, limited reviews about aquaculture-related antibiotic resistance genes (AARGs) have been published in SA. In this article, the main drivers of increasing the dissemination of AARGs were poor sanitation systems, human clinical antibiotic resistance (AR), antibiotic misuse, aquatic feed-containing antibiotics, and lack of awareness regarding antibiotics use in both clinical and (AR) aquaculture systems. Saudi national corporations are required to combat AARGs, including reiterating the threat of AR and looking for more cutting-edge knowhows or efficient administration choices to regulate it. It is necessary to educate the general population alongside organizations about AARG dissemination so as to increase understanding and alter the existing circumstances.

Systematic investigation of recipient cell genetic requirements reveals important surface receptors for conjugative transfer of IncI2 plasmids

Bacterial conjugation is a major horizontal gene transfer mechanism. While the functions encoded by many conjugative plasmids have been intensively studied, the contribution of recipient chromosome-encoded genes remains largely unknown. Here, we analyzed the genetic requirement of recipient cells for conjugation of IncI2 plasmid TP114, which was recently shown to transfer at high rates in the gut microbiota. We performed transfer assays with ~4,000 single-gene deletion mutants of Escherichia coli. When conjugation occurs on a solid medium, we observed that recipient genes impairing transfer rates were not associated with a specific cellular function. Conversely, transfer assays performed in broth were largely dependent on the lipopolysaccharide biosynthesis pathway. We further identified specific structures in lipopolysaccharides used as recipient cell surface receptors by PilV adhesins associated with the type IVb accessory pilus of TP114. Our strategy is applicable to study other mobile genetic elements and understand important host cell factors for their dissemination.

Characteristics of chloroplast and mitochondrial genomes and intracellular gene transfer in the Korean endemic shrub, Sophora koreensis Nakai (Fabaceae)

Sophora koreensis Nakai, an endemic species distributed only in the Korean Peninsula, is of great geographical, economic, and taxonomic importance. Although its complete chloroplast (cp) genome sequence has been reported, its mitochondrial (mt) genome sequence has not yet been studied. Therefore, in this study, we aimed to investigate its mt genome sequence and compare it with those reported for other Fabaceae species. Total genomic DNA was extracted from fresh S. koreensis leaves collected from natural habitats in Gangwon-do Province, South Korea. This was followed by polymerase chain reaction (PCR) amplification of cpDNA insertions in the mt genome and the detection of microsatellites and dispersed repeats in the cp and mt genomes. Finally, the cp and mt genomes of S. koreensis were compared with those reported for other Fabaceae species. The cp sequence of S. koreensis showed identical gene orders and contents as those previously reported. Only six substitutions and one deletion were detected with 99 % homology. Conversely, the complete mt genome sequence, which was 517,845 bp in length and encoded 61 genes, including 43 protein-coding, 15 transfer RNAs, and 3 ribosomal RNA genes, was considerably different from that of S. japonica in terms of gene order and composition. Further, the mt genome of S. koreensis included ca. 7 and 3 kb insertions, representing an intracellular gene transfer (IGT) event, and the regions with these insertions were determined to be originally present in the cp genome. This IGT event was also confirmed via PCR amplification. IGT events can be induced via biological gene expression control or the use of repetitive sequences, and they provide important insights into the evolutionary lineage of S. koreensis. However, further studies are needed to clarify the gene transfer mechanisms between the two organelles.

Diversity and evolution of an abundant ICEclc family of integrative and conjugative elements in Pseudomonas aeruginosa.

Microbial populations swiftly adapt to changing environments through horizontal gene transfer. While the mechanisms of gene transfer are well known, the impact of environmental conditions on the selection of transferred gene functions remains less clear. We investigated ICEs, specifically the ICEclc-type, in Pseudomonas aeruginosa clinical isolates. Our findings revealed co-evolution between ICEs and their hosts, with ICE transfers occurring within strains. Gene functions carried by ICEs are positively selected, including potential virulence factors and heavy metal resistance. Comparison to publicly available P. aeruginosa genomes unveiled widespread antibiotic-resistance determinants within ICEclc clades. Thus, the ubiquitous ICEclc family significantly contributes to P. aeruginosa's adaptation and fitness in diverse environments.

Restriction-methylation systems regulate transformation in Acinetobacter baumannii.

Antimicrobial resistance in Acinetobacter baumannii is a major concern. Natural transformation remains understudied as a horizontal gene transfer (HGT) mechanism for the spread of resistance genes. Recent work (Vesel et al.) reveals a profound impact of the state of donor DNA methylation with strong implications for HGT of resistance determinants in this worrisome pathogen.

Occurrence and Role of Bacterial Biofilms in Different Systems

Bacterial biofilms are complex communities of bacteria that adhere to surfaces, including living tissues, and form a protective matrix of extracellular polymeric substances (EPS). Biofilms are widespread and play crucial roles in various processes, such as nutrient cycling, bioremediation, and biofouling. They have significant implications for public health. Biofilms provide an ideal environment for bacteria to exchange genetic material, including resistance genes, via horizontal gene transfer mechanisms such as conjugation, transformation, and transduction. Moreover, biofilms can protect bacteria from antibiotics and host immune responses, enabling them to persist and cause chronic infections. The EPS matrix, which can act as a physical barrier, limits the penetration of antibiotics into the biofilm, and the slow-growing or dormant cells within the biofilm are less susceptible to antibiotics than their planktonic counterparts. The significance of bacterial biofilms in the development of antibiotic resistance has prompted research efforts to understand their formation and mechanisms of resistance. Novel strategies to prevent or disrupt biofilm formation are also being explored, including the development of antibiofilm agents and biofilm-disrupting enzymes. Understanding the role of biofilms in the spread of antibiotic resistance is crucial for the development of effective treatment and prevention strategies to combat the chronic infections associated with biofilm-producing bacteria.

Association between Phenotypes of Antimicrobial Resistance, ESBL Resistance Genes, and Virulence Genes of Salmonella Isolated from Chickens in Sichuan, China.

The aim of this study was to explore the association between antimicrobial resistance, ESBL genes, and virulence genes of Salmonella isolates. From 2019 to 2021, a total of 117 Salmonella isolates were obtained from symptomatic chickens in Sichuan Province, China. The strains were tested for antimicrobial resistance and the presence of ESBL according to the Clinical and Laboratory Standards Institute (CLSI) instructions. The presence of ESBL genes and genes for virulence was determined using Polymerase Chain Reaction (PCR). In addition, Multilocus Sequence Typing (MLST) was applied to confirm the molecular genotyping. Moreover, the mechanism of ESBL and virulence gene transfer and the relationships between the resistance phenotype, ESBL genes, and virulence genes were explored. The isolates exhibited different frequencies of resistance to antibiotics (resistance rates ranged from 21.37% to 97.44%), whereas 68.38% and 41.03% of isolates were multi-drug resistance (MDR) and ESBL-producers, respectively. In the PCR analysis, blaCTX-M was the most prevalent ESBL genotype (73.42%, 58/79), and blaCTX-M-55 showed the most significant effect on the resistance to cephalosporins as tested by logistic regression analysis. Isolates showed a high carriage rate of invA, avrA, sopB, sopE, ssaQ, spvR, spvB, spvC, stn, and bcfC (ranged from 51.28% to 100%). MLST analysis revealed that the 117 isolates were divided into 11 types, mainly ST92, ST11, and ST3717. Of 48 ESBL-producers, 21 transconjugants were successfully obtained by conjugation. Furthermore, ESBL and spv virulence genes were obtained simultaneously in 15 transconjugants. These results highlighted that Salmonella isolates were common carriers of ESBLs and multiple virulence genes. Horizontal transfer played a key role in disseminating antimicrobial resistance and pathogenesis. Therefore, it is necessary to continuously monitor the use of antimicrobials and the prevalence of AMR and virulence in Salmonella from food animals and to improve the antibiotic stewardship for salmonellosis.

Molecular characterization of methicilin-resistant Staphylococcus aureus strain BM85 isolated from a Vietnamese patient with bloodstream infection

Methicillin-resistant Staphylococcus aureus (MRSA) is a threat to global health due to its resistance to β-lactam antibiotics and many other antibiotic classes developed via both intrinsic and acquired mechanisms. In this study, molecular characteristics related to antibiotic resistance of MRSA strain BM85 were investigated by whole-genome sequencing of a sample isolated from a patient with bloodstream infection at Bach Mai Hospital, Vietnam. Antibiotic susceptibility testing was also performed to determine the correlation between the presence of antibiotic-resistant genes and resistance phenotypes. Genomic analyses showed that the MRSA strain BM85 belonged to the major community-acquired (CA)-MRSA lineage ST59 originating from Taiwan. The strain harbored Staphylococcal Cassette Chromosome mec (SCCmec) type Vb (5C2&5) and Panton-Valentine leukocidin (PVL). Additionally, MRSA strain BM85 also possessed various antibiotic-resistant genes including tet38, tetK, blaZ, mecA, aph(3')-IIIa, aacA-aphD, and ermB which were located on mobile genetic elements MESPM1, Tn553-Tn4001 transposon, and a plasmid carrying the tetK gene, which was responsible for tetracycline resistance. The genotypic-resistant results were concordant with the phenotypic-resistant profile in which MRSA strain BM85 was resistant to penicillin, cefoxitin, gentamicin, kanamycin, tobramycin, erythromycin, and tetracycline. The sequencing data for the MRSA strain BM85 was deposited in GenBank, NCBI under accession number: BioProject PRJNA857185. In conclusion, the acquisition of the foreign genetic elements associated with antibiotic resistances through horizontal gene transfer mechanisms was the key driver of multidrug resistance in the multidrug-resistant MRSA strain BM85.

Dual pathogenicity island transfer by piggybacking lateral transduction

Lateral transduction (LT) is the process by which temperate phages mobilize large sections of bacterial genomes. Despite its importance, LT has only been observed during prophage induction. Here, we report that superantigen-carrying staphylococcal pathogenicity islands (SaPIs) employ a related but more versatile and complex mechanism of gene transfer to drive chromosomal hypermobility while self-transferring with additional virulence genes from the host. We found that after phage infection or prophage induction, activated SaPIs form concatamers in the bacterial chromosome by switching between parallel genomic tracks in replication bubbles. This dynamic life cycle enables SaPIbov1 to piggyback its LT of staphylococcal pathogenicity island vSaα, which encodes an array of genes involved in host-pathogen interactions, allowing both islands to be mobilized intact and transferred in a single infective particle. Our findings highlight previously unknown roles of pathogenicity islands in bacterial virulence and show that their evolutionary impact extends beyond the genes they carry.

Inhibition of Plasmid Conjugation in Escherichia coli by Targeting rbsB Gene Using CRISPRi System.

Bacterial conjugation constitutes a major horizontal gene transfer mechanism for the dissemination of antibiotic-resistant genes (ARGs) among human pathogens. The spread of ARGs can be halted or diminished by interfering with the conjugation process. In this study, we explored the possibility of using an rbsB gene as a single target to inhibit plasmid-mediated horizontal gene transfer in Escherichia coli by CRISPR interference (CRISPRi) system. Three single-guide RNAs (sgRNAs) were designed to target the rbsB gene. The transcriptional levels of the rbsB gene, the conjugation-related genes, and the conjugation efficiency in the CRISPRi strain were tested. We further explored the effect of the repressed expression of the rbsB gene on the quorum sensing (QS) system and biofilm formation. The results showed that the constructed CRISPRi system was effective in repressing the transcriptional level of the rbsB gene at a rate of 66.4%. The repressed expression of the rbsB gene resulted in the reduced conjugation rate of RP4 plasmid by 88.7%, which significantly inhibited the expression of the conjugation-related genes (trbBp, trfAp, traF and traJ) and increased the global regulator genes (korA, korB and trbA). The repressed rbsB gene expression reduced the depletion of autoinducer 2 signals (AI-2) by 12.8% and biofilm formation by a rate of 68.2%. The results of this study indicated the rbsB gene could be used as a universal target for the inhibition of conjugation. The constructed conjugative CRISPRi system has the potential to be used in ARG high-risk areas.

Agrobacterium tumefaciens-Mediated Plant Transformation: A Review.

Agrobacterium tumefaciens-mediated plant transformation is the most dominant technique for the transformation of plants. It is used to transform monocotyledonous and dicotyledonous plants. A. tumefaciens apply for stable and transient transformation, random and targeted integration of foreign genes, as well as genome editing of plants. The Advantages of this method include cheapness, uncomplicated operation, high reproducibility, a low copy number of integrated transgenes, and the possibility of transferring larger DNA fragments. Engineered endonucleases such as CRISPR/Cas9 systems, TALENs, and ZFNs can be delivered with this method. Nowadays, Agrobacterium-mediated transformation is used for the Knock in, Knock down, and Knock out of genes. The transformation effectiveness of this method is not always desirable. Researchers applied various strategies to improve the effectiveness of this method. Here, a general overview of the characteristics and mechanism of gene transfer with Agrobacterium is presented. Advantages, updated data on the factors involved in optimizing this method, and other useful materials that lead to maximum exploitation as well as overcoming obstacles of this method are discussed. Moreover, the application of this method in the generation of genetically edited plants is stated. This review can help researchers to establish a rapid and highly effective Agrobacterium-mediated transformation protocol for any plant species.

Characterization and fitness cost analysis of two plasmids carrying different subtypes of blaNDM in aquaculture farming

In recent years, the blaNDM gene, which mediate resistance to carbapenems, has disseminated all over the world, and has also been detected in animals. Understanding the dissemination and accumulation of antibiotic resistance genes (ARGs) in a human-impacted environment is essential to solve the food safety problems caused by antibiotics. In this study, two strains of carbapenem bacteria carrying blaNDM were screened from 244 strains isolated from two T. sinensis farms in Zhejiang province, China. After their plasmids were isolated and sequenced, their structure and gene environment were analyzed and the mechanism of blaNDM gene transfer was explored. The study measured the fitness cost of plasmids carrying different blaNDM subtypes by four biological characteristics experiments. The results showed that the fitness cost of IncC plasmid carrying blaNDM-1 was higher than that of IncX3 plasmid carrying blaNDM-5. Furthermore, the real-time PCR showed that the decrease of transcription level of fitness-related genes lead to the different fitness cost of plasmids carrying different blaNDM subtypes. Fitness of many blaNDM-harboring plasmids enhanced the further dissemination of this gene and increase the risk of blaNDM gene spreading in aquatic environment, and thus further investigation of carbapenem-resistant bacterias among food animals are in urgent need.

Detecting patterns of accessory genome coevolution in Staphylococcus aureus using data from thousands of genomes

Bacterial genomes exhibit widespread horizontal gene transfer, resulting in highly variable genome content that complicates the inference of genetic interactions. In this study, we develop a method for detecting coevolving genes from large datasets of bacterial genomes based on pairwise comparisons of closely related individuals, analogous to a pedigree study in eukaryotic populations. We apply our method to pairs of genes from the Staphylococcus aureus accessory genome of over 75,000 annotated gene families using a database of over 40,000 whole genomes. We find many pairs of genes that appear to be gained or lost in a coordinated manner, as well as pairs where the gain of one gene is associated with the loss of the other. These pairs form networks of rapidly coevolving genes, primarily consisting of genes involved in virulence, mechanisms of horizontal gene transfer, and antibiotic resistance, particularly the SCCmec complex. While we focus on gene gain and loss, our method can also detect genes that tend to acquire substitutions in tandem, or genotype-phenotype or phenotype-phenotype coevolution. Finally, we present the R package DeCoTUR that allows for the computation of our method.

The complex regulation of competence in Staphylococcus aureus under microaerobic conditions

To perform natural transformation, one of the three main Horizontal Gene Transfer mechanisms, bacteria need to enter a physiological differentiated state called genetic competence. Interestingly, new bacteria displaying such aptitude are often discovered, and one of the latest is the human pathogen Staphylococcus aureus.Here, we show an optimized protocol, based on planktonic cells cultures, leading to a large percentage of the population activating the development of competence and a significant improvement of S. aureus natural transformation efficiencies. Taking advantage of these conditions, we perform transcriptomics analyses to characterize the regulon of each central competence regulator. SigH and ComK1 are both found essential for activating natural transformation genes but also important for activation or repression of peripheral functions. Even though ComK2 is not found important for the control of transformation genes, its regulon shows an important overlap with that of SigH and ComK1. Finally, we propose that microaerobic conditions, sensed by the SrrAB two-component system, are key to activate competence in S. aureus.

Catch me if you can: capturing microbial community transformation by extracellular DNA using Hi-C sequencing

The transformation of environmental microorganisms by extracellular DNA is an overlooked mechanism of horizontal gene transfer and evolution. It initiates the acquisition of exogenous genes and propagates antimicrobial resistance alongside vertical and conjugative transfers. We combined mixed-culture biotechnology and Hi-C sequencing to elucidate the transformation of wastewater microorganisms with a synthetic plasmid encoding GFP and kanamycin resistance genes, in the mixed culture of chemostats exposed to kanamycin at concentrations representing wastewater, gut and polluted environments (0.01–2.5–50–100 mg L−1). We found that the phylogenetically distant Gram-negative Runella (102 Hi-C links), Bosea (35), Gemmobacter (33) and Zoogloea (24) spp., and Gram-positive Microbacterium sp. (90) were transformed by the foreign plasmid, under high antibiotic exposure (50 mg L−1). In addition, the antibiotic pressure shifted the origin of aminoglycoside resistance genes from genomic DNA to mobile genetic elements on plasmids accumulating in microorganisms. These results reveal the power of Hi-C sequencing to catch and surveil the transfer of xenogenetic elements inside microbiomes.