Dietary zinc supplementation inhibits bacterial plasmid conjugation in vitro by regulating plasmid replication (rep) and transfer (tra) genes.

Humans use dietary supplements for several intended effects, such as supplementing malnutrition. While these compounds have been developed for host end benefits, their ancillary impact on the gut microbiota remains unclear. The human gut has been proposed as a reservoir for the prevalent lateral transfer of antimicrobial resistance and virulence genes in bacteria through plasmid conjugation. Here, we studied the effect of dietary zinc supplements on the incidence of plasmid conjugation in vitro. Supplement effects were analyzed through standardized broth conjugation assays. The avian pathogenic Escherichia coli (APEC) strain APEC-O2-211 was a donor of the multidrug resistance plasmid pAPEC-O2-211A-ColV, and the human commensal isolate E. coli HS-4 was the plasmid-free recipient. Bacterial strains were standardized and mixed 1:1 and supplemented 1:10 with water, or zinc derived from either commercial zinc supplements or zinc gluconate reagent at varying concentrations. We observed a significant reduction in donors, recipients, and transconjugant populations in conjugations supplemented with zinc, with a dose-dependent relationship. Additionally, we observed a significant reduction (P < 0.05) in log conjugation efficiency in zinc-treated reactions. Upregulation of the mRNA for the plasmid replication initiation gene repA and the subset of transfer genes M, J, E, K, B, P, C, W, U, N, F, Q, D, I, and X was observed. Furthermore, we observed a downregulation of the conjugal propilin gene traA and the entry exclusion gene traS. This study demonstrates the effect of dietary zinc supplements on the conjugal transfer of a multidrug resistance plasmid between pathogenic and commensal bacteria during in vitro conditions.IMPORTANCEThis study identifies dietary zinc supplementation as a potential novel intervention for mitigating the emergence of multidrug resistance in bacteria, thus preventing antibiotic treatment failure and death in patients and animals. Further studies are required to determine the applicability of this approach in an in vivo model.

Comparative genomic analysis of Acanthamoeba from different sources and horizontal transfer events of antimicrobial resistance genes.

Acanthamoeba species are among the most common free-living amoeba and ubiquitous protozoa, mainly distributed in water and soil, and cause Acanthamoeba keratitis (AK) and severe visual impairment in patients. Although several studies have reported genomic characteristics of Acanthamoeba, limited sample sizes and sources have resulted in an incomplete understanding of the genetic diversity of Acanthamoeba from different sources. While endosymbionts exert a significant influence on the phenotypes of Acanthamoeba, including pathogenicity, virulence, and drug resistance, the species diversity and functional characterization remain largely unexplored. Herein, our study sequenced and analyzed the whole genomes of 19 Acanthamoeba pathogenic strains that cause AK, and by integrating publicly available genomes, we sampled 29 Acanthamoeba strains from ocular, environmental, and other sources. Combined pan-genomic and comparative functional analyses revealed genetic differences and evolutionary relationships among the different sources of Acanthamoeba, as well as classification into multiple functional groups, with ocular isolates in particular showing significant differences that may account for differences in pathogenicity. Phylogenetic and rhizome gene mosaic analyses of ocular Acanthamoeba strains suggested that genomic exchanges between Acanthamoeba and endosymbionts, particularly potential antimicrobial resistance genes trafficking including the adeF, amrA, and amrB genes exchange events, potentially contribute to Acanthamoeba drug resistance. In conclusion, this study elucidated the adaptation of Acanthamoeba to different ecological niches and the influence of gene exchange on the evolution of ocular Acanthamoeba genome, guiding the clinical diagnosis and treatment of AK and laying a theoretical groundwork for developing novel therapeutic approaches. IMPORTANCE: Acanthamoeba causes a serious blinding keratopathy, Acanthamoeba keratitis, which is currently under-recognized by clinicians. In this study, we analyzed 48 strains of Acanthamoeba using a whole-genome approach, revealing differences in pathogenicity and function between strains of different origins. Horizontal transfer events of antimicrobial resistance genes can help provide guidance as potential biomarkers for the treatment of specific Acanthamoeba keratitis cases.

Conjugal plasmid transfer in the plant rhizosphere in the One Health context.

Introduction: Horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs) is one of the primary routes of antimicrobial resistance (AMR) dissemination. In the One Health context, tracking the spread of mobile genetic elements (MGEs) carrying ARGs in agri-food ecosystems is pivotal in understanding AMR diffusion and estimating potential risks for human health. So far, little attention has been devoted to plant niches; hence, this study aimed to evaluate the conjugal transfer of ARGs to the bacterial community associated with the plant rhizosphere, a hotspot for microbial abundance and activity in the soil. We simulated a source of AMR determinants that could enter the food chain via plants through irrigation. Methods: Among the bacterial strains isolated from treated wastewater, the strain Klebsiella variicola EEF15 was selected as an ARG donor because of the relevance of Enterobacteriaceae in the AMR context and the One Health framework. The strain ability to recolonize lettuce, chosen as a model for vegetables that were consumed raw, was assessed by a rifampicin resistant mutant. K. variicola EEF15 was genetically manipulated to track the conjugal transfer of the broad host range plasmid pKJK5 containing a fluorescent marker gene to the natural rhizosphere microbiome obtained from lettuce plants. Transconjugants were sorted by fluorescent protein expression and identified through 16S rRNA gene amplicon sequencing. Results and discussion: K. variicola EEF15 was able to colonize the lettuce rhizosphere and inhabit its leaf endosphere 7 days past bacterial administration. Fluorescence stereomicroscopy revealed plasmid transfer at a frequency of 10-3; cell sorting allowed the selection of the transconjugants. The conjugation rates and the strain's ability to colonize the plant rhizosphere and leaf endosphere make strain EEF15::lacIq-pLpp-mCherry-gmR with pKJK5::Plac::gfp an interesting candidate to study ARG spread in the agri-food ecosystem. Future studies taking advantage of additional environmental donor strains could provide a comprehensive snapshot of AMR spread in the One Health context.

Chlomito: a novel tool for precise elimination of organelle genome contamination from nuclear genome assembly.

Introduction: Accurate reference genomes are fundamental to understanding biological evolution, biodiversity, hereditary phenomena and diseases. However, many assembled nuclear chromosomes are often contaminated by organelle genomes, which will mislead bioinformatic analysis, and genomic and transcriptomic data interpretation. Methods: To address this issue, we developed a tool named Chlomito, aiming at precise identification and elimination of organelle genome contamination from nuclear genome assembly. Compared to conventional approaches, Chlomito utilized new metrics, alignment length coverage ratio (ALCR) and sequencing depth ratio (SDR), thereby effectively distinguishing true organelle genome sequences from those transferred into nuclear genomes via horizontal gene transfer (HGT). Results: The accuracy of Chlomito was tested using sequencing data from Plum, Mango and Arabidopsis. The results confirmed that Chlomito can accurately detect contigs originating from the organelle genomes, and the identified contigs covered most regions of the organelle reference genomes, demonstrating efficiency and precision of Chlomito. Considering user convenience, we further packaged this method into a Docker image, simplified the data processing workflow. Discussion: Overall, Chlomito provides an efficient, accurate and convenient method for identifying and removing contigs derived from organelle genomes in genomic assembly data, contributing to the improvement of genome assembly quality.

Genomes of nitrogen-fixing eukaryotes reveal a non-canonical model of organellogenesis.

Endosymbiont gene transfer and import of host-encoded proteins are considered hallmarks of organelles necessary for stable integration of two cells. However, newer endosymbiotic models have challenged the origin and timing of such genetic integration during organellogenesis. Epithemia diatoms contain diazoplasts, closely related to recently-described nitrogen-fixing organelles, that are also stably integrated and co-speciating with their host algae. We report genomic analyses of two species, freshwater E.clementina and marine E.pelagica, which are highly divergent but share a common endosymbiotic origin. We found minimal evidence of genetic integration: nonfunctional diazoplast-to-nuclear DNA transfers in the E.clementina genome and 6 host-encoded proteins of unknown function in the E.clementina diazoplast proteome, far fewer than in other recently-acquired organelles. Epithemia diazoplasts are a valuable counterpoint to existing organellogenesis models, demonstrating that endosymbionts can be stably integrated and inherited absent significant genetic integration. The minimal genetic integration makes diazoplasts valuable blueprints for bioengineering endosymbiotic compartments de novo.

Advances in CRISPR-Cas systems for gut microbiome.

CRISPR-Cas technology has revolutionized microbiome research by enabling precise genetic manipulation of microbial communities. This review explores its diverse applications in gut microbiome studies, probiotic development, microbiome diagnostics, pathogen targeting, and microbial community engineering. Engineered bacteriophages and conjugative probiotics exemplify CRISPR-Cas's capability for targeted bacterial manipulation, offering promising strategies against antibiotic-resistant infections and other gut-related disorders. CRISPR-Cas systems also enhance probiotic efficacy by improving stress tolerance and colonization in the gastrointestinal tract. CRISPR-based techniques in diagnostics enable early intervention by enabling fast and sensitive pathogen identification. Furthermore, CRISPR-mediated gene editing allows tailored modification of microbial populations, mitigating risks associated with horizontal gene transfer and enhancing environmental and health outcomes. Despite its transformative potential, ethical and regulatory challenges loom large, demanding robust frameworks to guide its responsible application. This chapter highlights CRISPR-Cas's pivotal role in advancing microbiome research toward personalized medicine and microbial therapeutics while emphasizing the imperative of balanced ethical deliberations and comprehensive regulatory oversight.

Reticulate evolution: Detection and utility in the phylogenomics era.

Phylogenomics has enriched our understanding that the Tree of Life can have network-like or reticulate structures among some taxa and genes. Two non-vertical modes of evolution - hybridization/introgression and horizontal gene transfer - deviate from a strictly bifurcating tree model, causing non-treelike patterns. However, these reticulate processes can produce similar patterns to incomplete lineage sorting or recombination, potentially leading to ambiguity. Here, we present a brief overview of a phylogenomic workflow for inferring organismal histories and compare methods for distinguishing modes of reticulate evolution. We discuss how the timing of coalescent events can help disentangle introgression from incomplete lineage sorting and how horizontal gene transfer events can help determine the relative timing of speciation events. In doing so, we identify pitfalls of certain methods and discuss how to extend their utility across the Tree of Life. Workflows, methods, and future directions discussed herein underscore the need to embrace reticulate evolutionary patterns for understanding the timing and rates of evolutionary events, providing a clearer view of life's history.

Characteristics of tetracycline antibiotic resistance gene enrichment and migration in soil-plant system.

Tetracycline Resistance Genes (TRGs) have received widespread attention in recent years, as they are a novel environmental pollutant that can rapidly accumulate and migrate in soil plant systems through horizontal gene transfer (HGT), posing a potential threat to food safety and public health. This article systematically reviews the pollution sources, enrichment, and migration characteristics of TRGs in soil. The main sources of TRGs include livestock manure and contaminated wastewater, especially in intensive farming environments where TRGs pollution is more severe. In soil, TRGs diffuse horizontally between bacteria and migrate to plant tissues through mechanisms such as plasmid conjugation, integron mediation, and phage transduction. The migration of TRGs is not limited to the soil interior, and increasing evidence suggests that they can also enter the plant system through plant root absorption and the HGT pathway of endophytic bacteria, ultimately accumulating in plant roots, stems, leaves, fruits, and other parts. This process has a direct impact on human health, especially when TRGs are found in crops such as vegetables, which may be transmitted to the human body through the food chain. In addition, this article also deeply analyzed various factors that affect the migration of TRGs, including the residual level of tetracycline in soil, the type and concentration of microorganisms, heavy metal pollution, and the presence of new pollutants such as microplastics. These factors significantly affect the enrichment rate and migration mode of TRGs in soil. In addition, two technologies that can effectively eliminate TRGs in livestock breeding environments were introduced, providing reference for healthy agricultural production. The article concludes by summarizing the shortcomings of current research on TRGs, particularly the limited understanding of TRG migration pathways and their impact mechanisms. Future research should focus on revealing the migration mechanisms of TRGs in soil plant systems and developing effective control and governance measures to reduce the environmental transmission risks of TRGs and ensure the safety of ecosystems and human health.

Crouching bacteria, hidden tetA genes in natural waters: Intracellular damage via double persulfate activation (UVA/Fe2+/PDS) effectively alleviates the spread of antibiotic resistance.

In this study, we elucidated the chemical and biological inactivation mechanisms of peroxydisulfate (PDS) activated by UVA and Fe2+ (UVA/Fe2+/PDS) in wild-type antibiotic-resistant bacteria (ARB) isolated from a river in Inner Mongolia. Among the screened wild-type ARB, the relative abundance of unidentified Enterobacteriaceae, Stenotrophomonas, and Ralstonia was high. A ratio of 1:1 for Fe2+ and PDS under 18 W·m-2 UVA radiation (sunny days) completely inactivated the environmental ARB isolates. In the macro view of the inactivation process, Fe2+ first activates PDS rapidly, and later the UVA energy accumulated starts to activate PDS; HO• then becomes the main active species at a rate-limiting step. From a micro perspective, damage to the cell wall, intracellular proteins, inactivation of antioxidant enzymes, and genetic material degradation are the inactivation series of events by UVA/Fe2+/PDS, contributing to the 97.8 % inactivation of ARB at the initial stage. No regrowth of sublethal ARBs was observed. The transfer of tetracycline resistance genes from ARB to lab E. coli was evaluated by horizontal gene transfer (HGT), in which no HGT occurred when ARB was eliminated by UVA/Fe2+/PDS. Moreover, the sulfate and iron residuals in the effluents of treated water were lower than the drinking water standards. In summary, PDS, UVA, and Fe2+ activation effectively inactivated wild ARB with a low concentration of reagents, while inhibiting their regrowth and spread of resistance due to the contribution of intracellular inactivation pathways.

Outer membrane vesicles secreted from Actinobacillus pleuropneumoniae isolate disseminating the floR resistance gene to Enterobacteriaceae.

Actinobacillus pleuropneumoniae, a significant respiratory pig pathogen, is causing substantial losses in the global swine industry. The resistance spectrum of A. pleuropneumoniae is expanding, and multidrug resistance is a severe issue. Horizontal gene transfer (HGT) plays a crucial role in the development of the bacterial genome by facilitating the dissemination of resistance determinants. However, the horizontal transfer of resistance genes via A. pleuropneumoniae-derived outer membrane vesicles (OMVs) has not been previously reported. In this study, we used Illumina NovaSeq and PacBio SequeI sequencing platforms to determine the whole genome sequence of A. pleuropneumoniae GD2107, a multidrug-resistant (MDR) isolate from China. We detected a plasmid in the isolate named pGD2107-1; the plasmid was 5,027 bp in size with 7 putative open reading frames (ORF) and included the floR resistance genes. The carriage of resistance genes in A. pleuropneumoniae OMVs was identified using a polymerase chain reaction (PCR) assay, and then we thoroughly evaluated the influence of OMVs on the horizontal transfer of drug-resistant plasmids. The transfer of the plasmid to recipient bacteria via OMVs was confirmed by PCR. In growth competition experiments, all recipients carrying the pGD2107-1 plasmid exhibited a fitness cost compared to the corresponding original recipients. This study revealed that OMVs could mediate interspecific horizontal transfer of the resistance plasmid pGD2107-1 into Escherichia coli recipient strains and significantly enhance the resistance of the transformants. In summary, A. pleuropneumoniae-OMVs play the pivotal role of vectors for dissemination of the floR gene spread and may contribute to more antimicrobial resistance gene transfer in other Enterobacteriaceae.

Nanoscale zero-valent iron alleviated horizontal transfer of antibiotic resistance genes in soil: The important role of extracellular polymeric substances.

Extracellular polymeric substances (EPS) are tightly related to the horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs), but often neglected in soil. In this study, nanoscale zero-valent iron (nZVI) was utilized for attenuation of ARGs in contaminated soil, with an emphasis on its effects on EPS secretion and HGT. Results showed during soil microbe cultivation exposed to tetracycline, more EPS was secreted and significant increase of tet was observed due to facilitated HGT. Notably, copies of EPS-tet accounted for 71.39 % of the total tet, implying vital effects of EPS on ARGs proliferation. When co-exposed to nZVI, EPS secretion was decreased by 38.36-71.46 %, for that nZVI could alleviate the microbial oxidative stress exerted by tetracycline resulting in downregulation of genes expression related to the c-di-GMP signaling system. Meanwhile, the abundance of EPS-tet was obviously reduced from 7.04 to 5.12-6.47 log unit, directly causing decrease of total tet from 7.19 to 5.68-6.69 log unit. For the reduced tet, it was mainly due to decreased EPS secretion induced by nZVI resulting in inhibition of HGT especially transformation of the EPS-tet. This work gives an inspiration for attenuation of ARGs dissemination in soil through an EPS regulation strategy.

Genomic insights into symbiosis and host adaptation of sponge-associated novel bacterium, Rossellomorea orangium sp. nov.

Sponge-associated microorganisms play vital roles in marine sponge ecology. This study presents a genomic investigation of Rossellomorea sp. MCCB 382, isolated from Stelletta sp., reveals insights into its adaptations and symbiotic roles. Phylogenomic study and Overall Genomic Relatedness Index (OGRI) classify MCCB 382 as a novel species, Rossellomorea orangium sp. nov. The genome encodes numerous carbohydrate metabolism enzymes (CAZymes), likely aiding nutrient cycling in the sponge host. Unique eukaryotic-like protein domains hint at potential mechanisms of symbiosis. Defense mechanisms include CRISPR, restriction modification systems, DNA phosphorothioation, toxin-antitoxin systems, and heavy metal and multidrug resistance genes, indicating adaptation to challenging marine environments. Unlike obligate mutualists, MCCB 382 shows no genome reduction. Furthermore, the presence of mobile genetic elements, horizontal gene transfer, and prophages suggest genetic versatility, implying flexible metabolic potential and capacity for rapid adaptation and symbiosis shifts. MCCB 382 possesses six biosynthetic gene clusters for secondary metabolites, including both type II and III polyketide synthases (PKS), terpenes, (NRPS), NRPS-independent-siderophore, and lassopeptide. Further genome mining using BiGScape revealed four distinct gene cluster families, T2PKS, NRPS-independent-siderophore, lasso peptide, and terpene, presenting opportunities for novel compound elucidation. Our study reveals a symbiotic lifestyle of MCCB 382 with the host sponge, highlighting symbiont factors that aid in establishing and sustaining this relationship. This is the pioneering genomic characterisation of a novel Rossellomorea sp. within the sponge Stelletta sp. holobiont.

Unnoticed antimicrobial resistance risk in Tibetan cities unveiled by sewage metagenomic surveillance: Compared to the eastern Chinese cities.

Sewage surveillance is a cost-effective tool for assessing antimicrobial resistance (AMR) in urban populations. However, research on sewage AMR in remote areas is still limited. Here, we used shotgun metagenomic sequencing to profile antibiotic resistance genes (ARGs) and ARG-carrying pathogens (APs) across 15 cities in Tibetan Plateau (TP) and the major cities in eastern China. Notable regional disparities in sewage ARG composition were found, with a significantly higher ARG abundance in TP (2.97 copies/cell). A total of 542 and 545 APs were identified in sewage from TP and the East, respectively, while more than 40 % carried mobile genetic elements (MGEs). Moreover, 65 MGEs-carrying APs were identified as World Health Organization (WHO) priority-like bacterial and fungal pathogens. Notably, a fungal zoonotic pathogen, Enterocytozoon bieneusi, was found for the first time to carry a nitroimidazole resistance gene (nimJ). Although distinct in AP compositions, the relative abundances of APs were comparable in these two regions. Furthermore, sewage in TP was found to be comparable to the cities in eastern China in terms of ARG mobility and AMR risks. These findings provide insights into ARGs and APs distribution in Chinese sewage and stress the importance of AMR surveillance and management strategies in remote regions.

Horizontal gene transfer from chloroplast to mitochondria of seagrasses in the yellow-Bohai seas.

Seagrasses are ideal for studying plant adaptation to marine environments. In this study, the mitochondrial (mt) and chloroplast (cp) genomes of Ruppia sinensis were sequenced. The results showed an extensive gene loss in seagrasses, including a complete loss of cp-rpl19 genes in Zosteraceae, most cp-ndh genes in Hydrocharitaceae, and mt-rpl and mt-rps genes in all seagrasses, except for the mt-rpl16 gene in Phyllospadix iwatensis. Notably, most ribosomal protein genes were lost in the mt and cp genomes. The deleted cp genes were not transferred to the mt genomes through horizontal gene transfer. Additionally, a significant DNA transfer between seagrass organelles was found, with the mt genomes of Zostera containing numerous sequences from the cp genome. Rearrangement analyses revealed an unreported inversion of the cp genome in R. sinensis. Moreover, four positively selected genes (atp8, nad5, atp4, and ccmFn) and five variable regions (matR, atp4, atp8, rps7, and ccmFn) were identified.

Why do mobile genetic elements transfer DNA of their hosts?

The prokaryote world is replete with mobile genetic elements (MGEs) - self-replicating entities that can move within and between their hosts. Many MGEs not only transfer their own DNA to new hosts but also transfer host DNA located elsewhere on the chromosome in the process. This could potentially lead to indirect benefits to the host when the resulting increase in chromosomal variation results in more efficient natural selection. We review the diverse ways in which MGEs promote the transfer of host DNA and explore the benefits and costs to MGEs and hosts. In many cases, MGE-mediated transfer of host DNA might not be selected for because of a sex function, but evidence of MGE domestication suggests that there may be host benefits of MGE-mediated sex.

Genomic analysis of conjugative and chromosomally integrated mobile genetic elements in oral streptococci.

This study aimed to investigate the diversity of conjugative and chromosomally integrated mobile genetic elements (cciMGEs) within six oral streptococci species. cciMGEs, including integrative and conjugative elements (ICEs) and integrative and mobilizable elements (IMEs), are stably maintained on the host cell chromosome; however, under certain conditions, they are able to excise, form extrachromosomal circles, and transfer via a conjugation apparatus. Many cciMGEs encode "cargo" functions that aid survival in new niches and evolve new antimicrobial resistance or virulence properties, whereas others have been shown to influence host bacterial physiology. Here, using a workflow employing preexisting bioinformatics tools, we analyzed 551 genomes for the presence of cciMGEs across six common health- and disease-associated oral streptococci. We identified 486 cciMGEs, 173 of which were ICEs and 233 of which were IMEs. The cciMGEs were diverse in size, cargo genes, and relaxase types. We identified several novel relaxase proteins and a widespread IME carrying a small multidrug resistance transporter. Additionally, we provide evidence that several of the bioinformatically predicted cciMGEs encoded within various Streptococcus mutans strains are capable of excision and circularization, a critical step for cciMGE conjugative transfer. These findings highlight the significance and potential impact of MGEs in shaping the genetic landscape, pathogenicity, and antimicrobial resistance profiles of the oral microbiota.IMPORTANCEOral streptococci are important players in the oral microbiome, influencing both health and disease states within dental bacterial communities. Evolutionary adaptation, shaped in a major part by the horizontal transfer of genes, is essential for their survival in the oral cavity and within new environments. Conjugation is a significant driver of horizontal gene transfer; however, there is limited information regarding this process in oral bacteria. This study utilizes publicly available genome sequences to identify conjugative and chromosomally integrated mobile genetic elements (cciMGEs) across several species of oral streptococci and presents the preliminary characterization of these elements. Our findings significantly enhance our understanding of the mobile genomic landscape of oral streptococci critical for human health, with valuable insights into how cciMGEs might influence the survival and pathogenesis of these bacteria in the oral microbiome.

Spatiotemporal profiles and underlying mechanisms of the antibiotic resistome in two water-diversion lakes.

Human-induced interventions have altered the local characteristics of the lake ecosystems through changes in hydraulic exchange, which in turn impacts the ecological processes of antibiotic resistance genes (ARGs) in the lakes. However, the current understanding of the spatiotemporal patterns and driving factors of ARGs in water-diversion lakes is still seriously insufficient. In the present study, we investigated antibiotic resistome in the main regulation and storage hubs, namely Nansi Lake and Dongping Lake, of the eastern part of the South-to-North Water Diversion project in Shandong Province (China) using a metagenomic-based approach. A total of 653 ARG subtypes belonging to 25 ARG types were detected with a total abundance of 0.125-0.390 copies/cell, with the dominance of bacitracin, multidrug, and macrolide-lincosamide streptogramin resistance genes. The ARG compositions were sensitive to seasonal variation and also interfered by artificial regulation structures along the way. Human pathogenic bacteria such as Acinetobacter calcoaceticus, Acinetobacter lwoffii, Klebsiella pneumoniae, along with the multidrug resistance genes they carried, were the focus of risk control in the two studied lakes, especially in summer. Plasmids were the key mobile genetic elements (MGEs) driving the horizontal gene transfer of ARGs, especially multidrug and sulfonamide resistance genes. The null model revealed that stochastic process was the main driver of ecological drift for ARGs in the lakes. The partial least squares structural equation model further determined that seasonal changes of pH and temperature drove a shift in the bacterial community, which in turn shaped the profile of ARGs by altering the composition of MGEs, antibacterial biocide- and metal-resistance genes (BMGs), and virulence factor genes (VFGs). Our results highlighted the importance of seasonal factors in determining the water transfer period. These findings can aid in a deeper understanding of the spatiotemporal variations of ARGs in lakes and their driving factors, offering a scientific basis for antibiotic resistance management.

Bronze Age cheese reveals human-Lactobacillus interactions over evolutionary history.

Despite the long history of consumption of fermented dairy, little is known about how the fermented microbes were utilized and evolved over human history. Here, by retrieving ancient DNA of Bronze Age kefir cheese (∼3,500 years ago) from the Xiaohe cemetery, we explored past human-microbial interactions. Although it was previously suggested that kefir was spread from the Northern Caucasus to Europe and other regions, we found an additional spreading route of kefir from Xinjiang to inland East Asia. Over evolutionary history, the East Asian strains gained multiple gene clusters with defensive roles against environmental stressors, which can be a result of the adaptation of Lactobacillus strains to various environmental niches and human selection. Overall, our results highlight the role of past human activities in shaping the evolution of human-related microbes, and such insights can, in turn, provide a better understanding of past human behaviors.

The Contribution of Dairy Bedding and Silage to the Dissemination of Genes Coding for Antimicrobial Resistance: A Narrative Review.

Antimicrobial resistance (AMR) is a concern in the dairy industry. Recent studies have indicated that bedding serves as a reservoir for antimicrobial-resistant bacteria and antimicrobial-resistance genes (ARGs), while silage has been proposed as another possible source. The impact of AMR in dairy farming can be significant, resulting in decreased productivity and economic losses for farmers. Several studies have highlighted the safety implications of AMR bacteria and genes in bedding and silage, emphasizing the need for further research on how housing, bedding, and silage management affect AMR in farm environments. Exposure to sub-lethal concentrations of antibiotics, such as those from contaminated bedding and silage, can prompt bacteria to develop resistance mechanisms. Thus, even if antimicrobial usage is diminished, ARGs may be maintained in the dairy farm environment. By implementing proactive measures to tackle AMR in dairy farming, we can take steps to preserve the health and productivity of dairy cattle while also protecting public health. This involves addressing the prudent use of antibiotics during production and promoting animal welfare, hygiene, and management practices in bedding and farm environments to minimize the risk of AMR development and spread. This narrative review compiles the growing research, positioning the contribution of bedding and silage to the prevalence and dissemination of AMR, which can elicit insights for researchers and policymakers.

Trends in horizontal gene transfer research in Salmonella antimicrobial resistance: a bibliometric analysis.

Horizontal gene transfer (HGT) favors the acquisition and spread of antimicrobial resistance (AMR) genes in Salmonella, making it a major public health concern. We performed a bibliometric analysis to provide the current landscape of HGT in research on Salmonella AMR and identify emerging trends and potential research directions for the future. Data were collected from the Web of Science Core Collection and limited to articles and reviews published between 1999 and 2024 in English. VOSviewer 1.6.19 and CiteSpace 6.2.R1 software were used to conduct bibliometric analysis and visualize co-occurring keywords. A total of 1,467 publications were retrieved for analysis. American researchers contributed the most articles (n = 310). In the meantime, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement have the highest citation/publication rate of 85.6. Recent studies have focused on the application of whole genome sequencing (WGS), Salmonella quinolone and colistin resistance, and the biocontrol of Salmonella AMR. These findings provide new insights into the role of HGT and help identify new targets for controlling the spread of AMR in Salmonella populations.