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Bibliography on: Horizontal Gene Transfer

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ESP: PubMed Auto Bibliography 28 Mar 2024 at 01:30 Created: 

Horizontal Gene Transfer

The pathology-inducing genes of O157:H7 appear to have been acquired, likely via prophage, by a nonpathogenic E. coli ancestor, perhaps 20,000 years ago. That is, horizontal gene transfer (HGT) can lead to the profound phenotypic change from benign commensal to lethal pathogen. "Horizontal" in this context refers to the lateral or "sideways" movement of genes between microbes via mechanisms not directly associated with reproduction. HGT among prokaryotes can occur between members of the same "species" as well as between microbes separated by vast taxonomic distances. As such, much prokaryotic genetic diversity is both created and sustained by high levels of HGT. Although HGT can occur for genes in the core-genome component of a pan-genome, it occurs much more frequently among genes in the optional, flex-genome component. In some cases, HGT has become so common that it is possible to think of some "floating" genes more as attributes of the environment in which they are useful rather than as attributes of any individual bacterium or strain or "species" that happens to carry them. For example, bacterial plasmids that occur in hospitals are capable of conferring pathogenicity on any bacterium that successfully takes them up. This kind of genetic exchange can occur between widely unrelated taxa.

Created with PubMed® Query: ( "horizontal gene transfer" OR "lateral gene transfer") NOT pmcbook NOT ispreviousversion

Citations The Papers (from PubMed®)

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RevDate: 2024-03-27

Duwor S, Brites D, P Mäser (2024)

Phylogenetic Analysis of Pyruvate-Ferredoxin Oxidoreductase, a Redox Enzyme Involved in the Pharmacological Activation of Nitro-Based Prodrugs in Bacteria and Protozoa.

Biology, 13(3): pii:biology13030178.

The present frontrunners in the chemotherapy of infections caused by protozoa are nitro-based prodrugs that are selectively activated by PFOR-mediated redox reactions. This study seeks to analyze the distribution of PFOR in selected protozoa and bacteria by applying comparative genomics to test the hypothesis that PFOR in eukaryotes was acquired through horizontal gene transfer (HGT) from bacteria. Furthermore, to identify other putatively acquired genes, proteome-wide and gene enrichment analyses were used. A plausible explanation for the patchy occurrence of PFOR in protozoa is based on the hypothesis that bacteria are potential sources of genes that enhance the adaptation of protozoa in hostile environments. Comparative genomics of Entamoeba histolytica and the putative gene donor, Desulfovibrio vulgaris, identified eleven candidate genes for HGT involved in intermediary metabolism. If these results can be reproduced in other PFOR-possessing protozoa, it would provide more validated evidence to support the horizontal transfer of pfor from bacteria.

RevDate: 2024-03-27

Peng D, Wang Z, Tian J, et al (2024)

Phyllosphere bacterial community dynamics in response to bacterial wildfire disease: succession and interaction patterns.

Frontiers in plant science, 15:1331443.

Plants interact with complex microbial communities in which microorganisms play different roles in plant development and health. While certain microorganisms may cause disease, others promote nutrient uptake and resistance to stresses through a variety of mechanisms. Developing plant protection measures requires a deeper comprehension of the factors that influence multitrophic interactions and the organization of phyllospheric communities. High-throughput sequencing was used in this work to investigate the effects of climate variables and bacterial wildfire disease on the bacterial community's composition and assembly in the phyllosphere of tobacco (Nicotiana tabacum L.). The samples from June (M1), July (M2), August (M3), and September (M4) formed statistically separate clusters. The assembly of the whole bacterial population was mostly influenced by stochastic processes. PICRUSt2 predictions revealed genes enriched in the M3, a period when the plant wildfire disease index reached climax, were associated with the development of the wildfire disease (secretion of virulence factor), the enhanced metabolic capacity and environmental adaption. The M3 and M4 microbial communities have more intricate molecular ecological networks (MENs), bursting with interconnections within a densely networked bacterial population. The relative abundances of plant-beneficial and antagonistic microbes Clostridiales, Bacillales, Lactobacillales, and Sphingobacteriales, showed significant decrease in severally diseased sample (M3) compared to the pre-diseased samples (M1/M2). Following the results of MENs, we further test if the correlating bacterial pairs within the MEN have the possibility to share functional genes and we have unraveled 139 entries of such horizontal gene transfer (HGT) events, highlighting the significance of HGT in shaping the adaptive traits of plant-associated bacteria across the MENs, particularly in relation to host colonization and pathogenicity.

RevDate: 2024-03-26

Nasser F, Gaudreau A, Lubega S, et al (2024)

Characterization of the diversity of type IV secretion system-encoding plasmids in Acinetobacter.

Emerging microbes & infections, 13(1):2320929.

The multi-drug resistant pathogen Acinetobacter baumannii has gained global attention as an important clinical challenge. Owing to its ability to survive on surfaces, its capacity for horizontal gene transfer, and its resistance to front-line antibiotics, A. baumannii has established itself as a successful pathogen. Bacterial conjugation is a central mechanism for pathogen evolution. The epidemic multidrug-resistant A. baumannii ACICU harbours a plasmid encoding a Type IV Secretion System (T4SS) with homology to the E. coli F-plasmid, and plasmids with homologous gene clusters have been identified in several A. baumannii sequence types. However the genetic and host strain diversity, global distribution, and functional ability of this group of plasmids is not fully understood. Using systematic analysis, we show that pACICU2 belongs to a group of almost 120 T4SS-encoding plasmids within four different species of Acinetobacter and one strain of Klebsiella pneumoniae from human and environmental origin, and globally distributed across 20 countries spanning 4 continents. Genetic diversity was observed both outside and within the T4SS-encoding cluster, and 47% of plasmids harboured resistance determinants, with two plasmids harbouring eleven. Conjugation studies with an extensively drug-resistant (XDR) strain showed that the XDR plasmid could be successfully transferred to a more divergent A. baumanii, and transconjugants exhibited the resistance phenotype of the plasmid. Collectively, this demonstrates that these T4SS-encoding plasmids are globally distributed and more widespread among Acinetobacter than previously thought, and that they represent an important potential reservoir for future clinical concern.

RevDate: 2024-03-27
CmpDate: 2024-03-27

Crowley C, Selvaraj A, Hariharan A, et al (2024)

Fusobacterium nucleatum subsp. polymorphum recovered from malignant and potentially malignant oral disease exhibit heterogeneity in adhesion phenotypes and adhesin gene copy number, shaped by inter-subspecies horizontal gene transfer and recombination-derived mosaicism.

Microbial genomics, 10(3):.

Fusobacterium nucleatum is an anaerobic commensal of the oral cavity associated with periodontitis and extra-oral diseases, including colorectal cancer. Previous studies have shown an increased relative abundance of this bacterium associated with oral dysplasia or within oral tumours. Using direct culture, we found that 75 % of Fusobacterium species isolated from malignant or potentially malignant oral mucosa were F. nucleatum subsp. polymorphum. Whole genome sequencing and pangenome analysis with Panaroo was carried out on 76 F. nucleatum subsp. polymorphum genomes. F. nucleatum subsp. polymorphum was shown to possesses a relatively small core genome of 1604 genes in a pangenome of 7363 genes. Phylogenetic analysis based on the core genome shows the isolates can be separated into three main clades with no obvious genotypic associations with disease. Isolates recovered from healthy and diseased sites in the same patient are generally highly related. A large repertoire of adhesins belonging to the type V secretion system (TVSS) could be identified with major variation in repertoire and copy number between strains. Analysis of intergenic recombination using fastGEAR showed that adhesin complement is shaped by horizontal gene transfer and recombination. Recombination events at TVSS adhesin genes were not only common between lineages of subspecies polymorphum, but also between different subspecies of F. nucleatum. Strains of subspecies polymorphum with low copy numbers of TVSS adhesin encoding genes tended to have the weakest adhesion to oral keratinocytes. This study highlights the genetic heterogeneity of F. nucleatum subsp. polymorphum and provides a new framework for defining virulence in this organism.

RevDate: 2024-03-25

Ferilli F, Lione G, Gonthier P, et al (2024)

First detection of mycoviruses in Gnomoniopsis castaneae suggests a putative horizontal gene transfer event between negative-sense and double-strand RNA viruses.

Virology, 594:110057 pii:S0042-6822(24)00078-3 [Epub ahead of print].

Gnomoniopsis castaneae is an ascomycetous fungus mainly known as a major pathogen of chestnut causing nut rots, although it is often found as an endophyte in chestnut tissues. To date, no virus has been reported as associated with to this fungus. Here, a collection of G. castaneae isolates from several European countries was screened to detect mycoviruses infecting the fungus: for the first time we report the identification and prevalence of mitovirus Gnomoniopsis castaneae mitovirus 1 (GcMV1) and the chrysovirus Gnomoniopsis castaneae chrysovirus 1 (GcCV1). Interestingly, we provide evidence supporting a putative horizontal gene transfer between members of the phyla Negarnaviricota and Duplornaviricota: a small putative protein of unknown function encoded on the RNA3 of GcCV1 (Chrysoviridae) has homologs in the genome of viruses of the family Mymonaviridae.

RevDate: 2024-03-26
CmpDate: 2024-03-25

Asad A, Jahan I, Munni MA, et al (2024)

Multidrug-resistant conjugative plasmid carrying mphA confers increased antimicrobial resistance in Shigella.

Scientific reports, 14(1):6947.

Shigellosis remains a common gastrointestinal disease mostly in children < 5 years of age in developing countries. Azithromycin (AZM), a macrolide, is currently the first-line treatment for shigellosis in Bangladesh; ciprofloxacin (CIP) and ceftriaxone (CRO) are also used frequently. We aimed to evaluate the current epidemiology of antimicrobial resistance (AMR) and mechanism(s) of increasing macrolide resistance in Shigella in Bangladesh. A total of 2407 clinical isolates of Shigella from 2009 to 2016 were studied. Over the study period, Shigella sonnei was gradually increasing and become predominant (55%) over Shigella flexneri (36%) by 2016. We used CLSI-guided epidemiological cut-off value (ECV) for AZM in Shigella to set resistance breakpoints (zone-diameter ≤ 15 mm for S. flexneri and ≤ 11 mm for S. sonnei). Between 2009 and 2016, AZM resistance increased from 22% to approximately 60%, CIP resistance increased by 40%, and CRO resistance increased from zero to 15%. The mphA gene was the key macrolide resistance factor in Shigella; a 63MDa conjugative middle-range plasmid was harboring AZM and CRO resistance factors. Our findings show that, especially after 2014, there has been a rapid increase in resistance to the three most effective antibiotics. The rapid spread of macrolide (AZM) resistance genes among Shigella are driven by horizontal gene transfer rather than direct lineage.

RevDate: 2024-03-23

Liu Q, Peng Y, Liao J, et al (2024)

Broad-spectrum hydrocarbon-degrading microbes in the global ocean metagenomes.

The Science of the total environment pii:S0048-9697(24)01889-8 [Epub ahead of print].

Understanding the diversity and functions of hydrocarbon-degrading microorganisms in marine environments is crucial for both advancing knowledge of biogeochemical processes and improving bioremediation methods. In this study, we leveraged nearly 20,000 metagenome-assembled genomes (MAGs), recovered from a wide array of marine samples across the global oceans, to map the diversity of aerobic hydrocarbon-degrading microorganisms. A broad bacterial diversity was uncovered, with a notable preference for degrading aliphatic hydrocarbons over aromatic ones, primarily within Proteobacteria and Actinobacteriota. Three types of broad-spectrum hydrocarbon-degrading bacteria were identified for their ability to degrade various hydrocarbons and possession of multiple copies of hydrocarbon biodegradation genes. These bacteria demonstrate extensive metabolic versatility, aiding their survival and adaptability in diverse environmental conditions. Evidence of gene duplication and horizontal gene transfer in these microbes suggests a potential enhancement in the diversity of hydrocarbon-degrading bacteria. Positive correlations were observed between the abundances of hydrocarbon-degrading genes and environmental parameters such as temperature (-5 to 35 °C) and salinity (20 to 42 PSU). Overall, our findings offer valuable insights into marine hydrocarbon-degrading microorganisms and suggest considerations for selecting microbial strains for oil pollution remediation.

RevDate: 2024-03-23

Baker BA, Gutiérrez-Preciado A, Rodríguez Del Río Á, et al (2024)

Expanded phylogeny of extremely halophilic archaea shows multiple independent adaptations to hypersaline environments.

Nature microbiology [Epub ahead of print].

Extremely halophilic archaea (Haloarchaea, Nanohaloarchaeota, Methanonatronarchaeia and Halarchaeoplasmatales) thrive in saturating salt concentrations where they must maintain osmotic equilibrium with their environment. The evolutionary history of adaptations enabling salt tolerance remains poorly understood, in particular because the phylogeny of several lineages is conflicting. Here we present a resolved phylogeny of extremely halophilic archaea obtained using improved taxon sampling and state-of-the-art phylogenetic approaches designed to cope with the strong compositional biases of their proteomes. We describe two uncultured lineages, Afararchaeaceae and Asbonarchaeaceae, which break the long branches at the base of Haloarchaea and Nanohaloarchaeota, respectively. We obtained 13 metagenome-assembled genomes (MAGs) of these archaea from metagenomes of hypersaline aquatic systems of the Danakil Depression (Ethiopia). Our phylogenomic analyses including these taxa show that at least four independent adaptations to extreme halophily occurred during archaeal evolution. Gene-tree/species-tree reconciliation suggests that gene duplication and horizontal gene transfer played an important role in this process, for example, by spreading key genes (such as those encoding potassium transporters) across extremely halophilic lineages.

RevDate: 2024-03-22

Gàlvez-Morante A, Guéguen L, Natsidis P, et al (2024)

Dollo parsimony overestimates ancestral gene content reconstructions.

Genome biology and evolution pii:7633882 [Epub ahead of print].

Ancestral reconstruction is a widely-used technique that has been applied to understand the evolutionary history of gain and loss of gene families. Ancestral gene content can be reconstructed via different phylogenetic methods, but many current and previous studies employ Dollo parsimony. We hypothesize that Dollo parsimony is not appropriate for ancestral gene content reconstruction inferences based on sequence homology, as Dollo parsimony is derived from the assumption that a complex character cannot be regained. This premise does not accurately model molecular sequence evolution, in which false orthology can result from sequence convergence or lateral gene transfer. The aim of this study is to test Dollo parsimony's suitability for ancestral gene content reconstruction and to compare its inferences with a maximum likelihood-based approach which allows a gene family to be gained more than once within a tree. We first compared the performance of the two approaches on a series of artificial datasets each of 5,000 genes that were simulated according to a spectrum of evolutionary rates without gene gain or loss, so that inferred deviations from the true gene count would arise only from errors in orthology inference and ancestral reconstruction. Next, we reconstructed protein domain evolution on a phylogeny representing known eukaryotic diversity. We observed that Dollo parsimony produced numerous ancestral gene content overestimations, especially at nodes closer to the root of the tree. These observations led us to the conclusion that, confirming our hypothesis, Dollo parsimony is not an appropriate method for ancestral reconstruction studies based on sequence homology.

RevDate: 2024-03-22

Sheinman M, Arndt PF, F Massip (2024)

Modeling the mosaic structure of bacterial genomes to infer their evolutionary history.

Proceedings of the National Academy of Sciences of the United States of America, 121(13):e2313367121.

The chronology and phylogeny of bacterial evolution are difficult to reconstruct due to a scarce fossil record. The analysis of bacterial genomes remains challenging because of large sequence divergence, the plasticity of bacterial genomes due to frequent gene loss, horizontal gene transfer, and differences in selective pressure from one locus to another. Therefore, taking advantage of the rich and rapidly accumulating genomic data requires accurate modeling of genome evolution. An important technical consideration is that loci with high effective mutation rates may diverge beyond the detection limit of the alignment algorithms used, biasing the genome-wide divergence estimates toward smaller divergences. In this article, we propose a novel method to gain insight into bacterial evolution based on statistical properties of genome comparisons. We find that the length distribution of sequence matches is shaped by the effective mutation rates of different loci, by the horizontal transfers, and by the aligner sensitivity. Based on these inputs, we build a model and show that it accounts for the empirically observed distributions, taking the Enterobacteriaceae family as an example. Our method allows to distinguish segments of vertical and horizontal origins and to estimate the time divergence and exchange rate between any pair of taxa from genome-wide alignments. Based on the estimated time divergences, we construct a time-calibrated phylogenetic tree to demonstrate the accuracy of the method.

RevDate: 2024-03-21

Fogg PCM (2024)

Gene transfer agents: The ambiguous role of selfless viruses in genetic exchange and bacterial evolution.

Molecular microbiology [Epub ahead of print].

Gene transfer agents (GTAs) are genetic elements derived from ancestral bacteriophages that have become domesticated by the host. GTAs are present in diverse prokaryotic organisms, where they can facilitate horizontal gene transfer under certain conditions. Unlike typical bacteriophages, GTAs do not exhibit any preference for the replication or transfer of the genes encoding them; instead, they exhibit a remarkable capacity to package chromosomal, and sometimes extrachromosomal, DNA into virus-like capsids and disseminate it to neighboring cells. Because GTAs resemble defective prophages, identification of novel GTAs is not trivial. The detection of candidates relies on the genetic similarity to known GTAs, which has been fruitful in α-proteobacterial lineages but challenging in more distant bacteria. Here we consider several fundamental questions: What is the true prevalence of GTAs in prokaryote genomes? Given there are high costs for GTA production, what advantage do GTAs provide to the bacterial host to justify their maintenance? How is the bacterial chromosome recognized and processed for inclusion in GTA particles? This article highlights the challenges in comprehensively understanding GTAs' prevalence, function and DNA packaging method. Going forward, broad study of atypical GTAs and use of ecologically relevant conditions are required to uncover their true impact on bacterial chromosome evolution.

RevDate: 2024-03-22

Liu X, Zhao H, A Wong (2024)

Accounting for the health risk of probiotics.

Heliyon, 10(6):e27908.

Probiotics have long been associated with a myriad of health benefits, so much so that their adverse effects whether mild or severe, are often neglected or overshadowed by the enormous volume of articles describing their beneficial effects in the current literature. Recent evidence has demonstrated several health risks of probiotics that warrant serious reconsideration of their applications and further investigations. This review aims to highlight studies that report on how probiotics might cause opportunistic systemic and local infections, detrimental immunological effects, metabolic disturbance, allergic reactions, and facilitating the spread of antimicrobial resistance. To offer a recent account of the literature, articles within the last five years were prioritized. The narration of these evidence was based on the nature of the studies in the following order of preference: clinical studies or human samples, in vivo or animal models, in situ, in vitro and/or in silico. We hope that this review will inform consumers, food scientists, and medical practitioners, on the health risks, while also encouraging research that will focus on and clarify the adverse effects of probiotics.

RevDate: 2024-03-22
CmpDate: 2024-03-22

Kehlet-Delgado H, Montoya AP, Jensen KT, et al (2024)

The evolutionary genomics of adaptation to stress in wild rhizobium bacteria.

Proceedings of the National Academy of Sciences of the United States of America, 121(13):e2311127121.

Microbiota comprise the bulk of life's diversity, yet we know little about how populations of microbes accumulate adaptive diversity across natural landscapes. Adaptation to stressful soil conditions in plants provides seminal examples of adaptation in response to natural selection via allelic substitution. For microbes symbiotic with plants however, horizontal gene transfer allows for adaptation via gene gain and loss, which could generate fundamentally different evolutionary dynamics. We use comparative genomics and genetics to elucidate the evolutionary mechanisms of adaptation to physiologically stressful serpentine soils in rhizobial bacteria in western North American grasslands. In vitro experiments demonstrate that the presence of a locus of major effect, the nre operon, is necessary and sufficient to confer adaptation to nickel, a heavy metal enriched to toxic levels in serpentine soil, and a major axis of environmental soil chemistry variation. We find discordance between inferred evolutionary histories of the core genome and nreAXY genes, which often reside in putative genomic islands. This suggests that the evolutionary history of this adaptive variant is marked by frequent losses, and/or gains via horizontal acquisition across divergent rhizobium clades. However, different nre alleles confer distinct levels of nickel resistance, suggesting allelic substitution could also play a role in rhizobium adaptation to serpentine soil. These results illustrate that the interplay between evolution via gene gain and loss and evolution via allelic substitution may underlie adaptation in wild soil microbiota. Both processes are important to consider for understanding adaptive diversity in microbes and improving stress-adapted microbial inocula for human use.

RevDate: 2024-03-20

Adeyelu OO, Essien EN, Adebote V, et al (2024)

Antimicrobial resistance genetic determinants and susceptibility profile of Pseudomonas aeruginosa isolated from clinical samples in a tertiary hospital in Ogun State, Nigeria.

Transactions of the Royal Society of Tropical Medicine and Hygiene pii:7632340 [Epub ahead of print].

BACKGROUND: Genetic determinants are known to promote antibiotic resistance through horizontal gene transfer.

METHODS: We molecularly characterized integrons, plasmid replicon types and metallo-β-lactamase-encoding genes of 38 Pseudomonas aeruginosa strains isolated from clinical samples.

RESULTS: The P. aeruginosa isolates displayed high resistance (97.4%) to β-lactams. Seventeen (44.74%) of them possessed plasmids. Of the 17 isolates that possessed plasmids, 11 (64.7%) of them harboured IncFIA plasmid replicon type, while 6 (35.3%), 5 (29.4%) and 5 (29.4%) were of the IncFIB, IncF and IncW types, respectively. The intI1 gene was detected in 19 (50%) of the isolates. The blaNDM-A, blaNDM-B and blaVIM genes were detected in 14 (35.9%), 4 (10.3%) and 5 (12.8%) of the isolates, respectively.

CONCLUSIONS: High resistance to β-lactams was observed among P. aeruginosa strains of clinical origin in this study. They possessed transmissible genetic elements indicating the potential for continuous dissemination, thus continuous surveillance is advocated.

RevDate: 2024-03-20

Tekle YI, H Tefera (2024)

A Small Genome Amidst the Giants: Evidence of Genome Reduction in a Small Tubulinid Free-Living Amoeba.

Genome biology and evolution pii:7632165 [Epub ahead of print].

This study investigates the genomic characteristics of Echinamoeba silvestris, a small-sized amoeba within the Tubulinea clade of the Amoebozoa supergroup. Despite Tubulinea's significance in various fields, genomic data for this clade have been scarce. E. silvestris presents the smallest free-living amoeba genome within Tubulinea and Amoebozoa to date. Comparative analysis reveals intriguing parallels with parasitic lineages in terms of genome size and predicted gene numbers, emphasizing the need to understand the consequences of reduced genomes in free-living amoebae. Functional categorization of predicted genes in E. silvestris shows similar percentages of ortholog groups to other amoebae in various categories, but a distinctive feature is the extensive gene contraction in orphan (ORFan) genes and those involved in biological processes. Notably, among the few genes that underwent expansion, none are related to cellular components, suggesting adaptive processes that streamline biological processes and cellular components for efficiency and energy conservation. Additionally, our investigation into non-coding and repetitive elements sheds light on the evolution of genome size in amoebae, with E. silvestris distinguished by low percentage of repetitive elements. Furthermore, the analysis reveals that E. silvestris has the lowest mean number of introns per gene among the species studied, providing further support for its observed compact genome. Overall, this research underscores the diversity within Tubulinea, highlights knowledge gaps in Amoebozoa genomics, and positions E. silvestris as a valuable addition to genomic datasets, prompting further exploration of complexities in Amoebozoa diversity and genome evolution.

RevDate: 2024-03-20
CmpDate: 2024-03-20

Bernabeu M, Manzano-Morales S, T Gabaldón (2024)

On the impact of incomplete taxon sampling on the relative timing of gene transfer events.

PLoS biology, 22(3):e3002460.

A recent study questioned the use of branch length methods to assess the relative timing of horizontal gene transfers because of the effects of so-called "ghost" lineages. This Formal Comment discusses key considerations regarding the potential effect of missing lineages when assessing relative timing of evolutionary events.

RevDate: 2024-03-18

Wang P, Du X, Zhao Y, et al (2024)

Combining CRISPR/Cas9 and natural excision for the precise and complete removal of mobile genetic elements in bacteria.

Applied and environmental microbiology [Epub ahead of print].

Horizontal gene transfer, facilitated by mobile genetic elements (MGEs), is an adaptive evolutionary process that contributes to the evolution of bacterial populations and infectious diseases. A variety of MGEs not only can integrate into the bacterial genome but also can survive or even replicate like plasmids in the cytoplasm, thus requiring precise and complete removal for studying their strategies in benefiting host cells. Existing methods for MGE removal, such as homologous recombination-based deletion and excisionase-based methods, have limitations in effectively eliminating certain MGEs. To overcome these limitations, we developed the Cas9-NE method, which combines the CRISPR/Cas9 system with the natural excision of MGEs. In this approach, a specialized single guide RNA (sgRNA) element is designed with a 20-nucleotide region that pairs with the MGE sequence. This sgRNA is expressed from a plasmid that also carries the Cas9 gene. By utilizing the Cas9-NE method, both the integrative and circular forms of MGEs can be precisely and completely eliminated through Cas9 cleavage, generating MGE-removed cells. We have successfully applied the Cas9-NE method to remove four representative MGEs, including plasmids, prophages, and genomic islands, from Vibrio strains. This new approach not only enables various investigations on MGEs but also has significant implications for the rapid generation of strains for commercial purposes.IMPORTANCEMobile genetic elements (MGEs) are of utmost importance for bacterial adaptation and pathogenicity, existing in various forms and multiple copies within bacterial cells. Integrated MGEs play dual roles in bacterial hosts, enhancing the fitness of the host by delivering cargo genes and potentially modifying the bacterial genome through the integration/excision process. This process can lead to alterations in promoters or coding sequences or even gene disruptions at integration sites, influencing the physiological functions of host bacteria. Here, we developed a new approach called Cas9-NE, allowing them to maintain the natural sequence changes associated with MGE excision. Cas9-NE allows the one-step removal of integrated and circular MGEs, addressing the challenge of eliminating various MGE forms efficiently. This approach simplifies MGE elimination in bacteria, expediting research on MGEs.

RevDate: 2024-03-17

Xu H, Tan C, Li C, et al (2024)

ESBL- E. coli extracellular vesicles mediate bacterial resistance to β-lactam and mediate horizontal transfer of blaCTX-M-55.

International journal of antimicrobial agents pii:S0924-8579(24)00063-3 [Epub ahead of print].

Extracellular vesicles (EVs) have become the focus of research as an emerging method of horizontal gene transfer. In recent years, studies on the association between EVs and the spread of bacterial resistance have emerged, but there is a lack of research on the role of EVs secreted by ESBL-producing E. coli in the spread of β-lactam resistance. Therefore, in this study, the role of EVs secreted by ESBL-E. coli in the transmission of β-lactam resistance in E. coli was evaluated. The results showed that ESBL-EVs were protective against β-lactam antibiotic-susceptible bacteria, and this protective effect was dependent on the integrity of the EVs and showed dose- and time-dependent effects. At the same time, ESBL-EVs can also mediate the horizontal transmission of blaCTX-M-55, and EVs-mediated gene transfer is selective, preferring to transfer in more closely related species. In this study, we demonstrated the important role of EVs in the transmission of β-lactam resistance in chicken ESBL-E. coli, and evaluated the risk of EVs-mediated horizontal gene transfer, which provided a theoretical basis for elucidating the mechanism of EVs-mediated resistance transmission.

RevDate: 2024-03-19

You Z, Wang C, Yang X, et al (2024)

Effects of eutrophication on the horizontal transfer of antibiotic resistance genes in microalgal-bacterial symbiotic systems.

Environmental research, 251(Pt 2):118692 pii:S0013-9351(24)00596-6 [Epub ahead of print].

Overloading of nutrients such as nitrogen causes eutrophication of freshwater bodies. The spread of antibiotic resistance genes (ARGs) poses a threat to ecosystems. However, studies on the enrichment and spread of ARGs from increased nitrogen loading in algal-bacterial symbiotic systems are limited. In this study, the transfer of extracellular kanamycin resistance (KR) genes from large (RP4) small (pEASY-T1) plasmids into the intracellular and extracellular DNA (iDNA, eDNA) of the inter-algal environment of Chlorella pyrenoidosa was investigated, along with the community structure of free-living (FL) and particle-attached (PA) bacteria under different nitrogen source concentrations (0-2.5 g/L KNO3). The results showed that KR gene abundance in the eDNA adsorbed on solid particles (D-eDNA) increased initially and then decreased with increasing nitrogen concentration, while the opposite was true for the rest of the free eDNA (E-eDNA). Medium nitrogen concentrations promoted the transfer of extracellular KR genes into the iDNA attached to algal microorganisms (A-iDNA), eDNA attached to algae (B-eDNA), and the iDNA of free microorganisms (C-iDNA); high nitrogen contributed to the transfer of KR genes into C-iDNA. The highest percentage of KR genes was found in B-eDNA with RP4 plasmid treatment (66.2%) and in C-iDNA with pEASY-T1 plasmid treatment (86.88%). In addition, dissolved oxygen (DO) significantly affected the bacterial PA and FL community compositions. Nephelometric turbidity units (NTU) reflected the abundance of ARGs in algae. Proteobacteria, Cyanobacteria, Bacteroidota, and Actinobacteriota were the main potential hosts of ARGs. These findings provide new insights into the distribution and dispersal of ARGs in the phytoplankton inter-algal environment.

RevDate: 2024-03-16

Novikova PV, Bhanu Busi S, Probst AJ, et al (2024)

Functional prediction of proteins from the human gut archaeome.

ISME communications, 4(1):ycad014.

The human gastrointestinal tract contains diverse microbial communities, including archaea. Among them, Methanobrevibacter smithii represents a highly active and clinically relevant methanogenic archaeon, being involved in gastrointestinal disorders, such as inflammatory bowel disease and obesity. Herein, we present an integrated approach using sequence and structure information to improve the annotation of M. smithii proteins using advanced protein structure prediction and annotation tools, such as AlphaFold2, trRosetta, ProFunc, and DeepFri. Of an initial set of 873 481 archaeal proteins, we found 707 754 proteins exclusively present in the human gut. Having analysed archaeal proteins together with 87 282 994 bacterial proteins, we identified unique archaeal proteins and archaeal-bacterial homologs. We then predicted and characterized functional domains and structures of 73 unique and homologous archaeal protein clusters linked the human gut and M. smithii. We refined annotations based on the predicted structures, extending existing sequence similarity-based annotations. We identified gut-specific archaeal proteins that may be involved in defense mechanisms, virulence, adhesion, and the degradation of toxic substances. Interestingly, we identified potential glycosyltransferases that could be associated with N-linked and O-glycosylation. Additionally, we found preliminary evidence for interdomain horizontal gene transfer between Clostridia species and M. smithii, which includes sporulation Stage V proteins AE and AD. Our study broadens the understanding of archaeal biology, particularly M. smithii, and highlights the importance of considering both sequence and structure for the prediction of protein function.

RevDate: 2024-03-15

Liu H, Zhang Z, Li X, et al (2024)

Temperature-phased anaerobic sludge digestion effectively removes antibiotic resistance genes in a full-scale wastewater treatment plant.

The Science of the total environment, 924:171555 pii:S0048-9697(24)01696-6 [Epub ahead of print].

Sludge is a major by-product and the final reservoir of antibiotic resistance genes (ARGs) in wastewater treatment plants (WWTPs). Temperature-phased anaerobic digestion (TPAD), consisting of thermophilic anaerobic digestion (AD) (55 °C) and mesophilic AD processes (37 °C), has been implemented in WWTPs for sludge reduction while improving the biomethane production. However, the impact of TPAD on the ARGs' fate is still undiscovered in lab-scale experiments and full-scale WWTPs. This study, for the first time, investigated the fate of ARGs during the TPAD process across three seasons in a full-size WWTP. Ten typical ARGs and one integrase gene of class 1 integron (intI1) involving ARGs horizontal gene transfer were examined in sludge before and after each step of the TPAD process. TPAD reduced aac(6')-Ib-cr, blaTEM, drfA1, sul1, sul2, ermb, mefA, tetA, tetB and tetX by 87.3-100.0 %. TPAD reduced the overall average absolute abundance of targeted ARGs and intI1 by 92.39 % and 92.50 %, respectively. The abundance of targeted ARGs in sludge was higher in winter than in summer and autumn before and after TPAD. During the TPAD processes, thermophilic AD played a major role in the removal of ARGs, contributing to >60 % removal of ARGs, while the subsequent mesophilic AD contributed to a further 31 % removal of ARGs. The microbial community analysis revealed that thermophilic AD reduced the absolute abundance of ARGs hosts, antibiotic resistant bacteria. In addition, thermophilic AD reduced the abundance of the intI1, while the intI1 did not reproduce during the mesophilic AD, also contributing to a decline in the absolute abundance of ARGs in TPAD. This study demonstrates that TPAD can effectively reduce the abundance of ARGs in sludge, which will suppress the transmission of ARGs from sludge into the natural environment and deliver environmental and health benefits to our society.

RevDate: 2024-03-15
CmpDate: 2024-03-15

Keith M, Park de la Torriente A, Chalka A, et al (2024)

Predictive phage therapy for Escherichia coli urinary tract infections: Cocktail selection for therapy based on machine learning models.

Proceedings of the National Academy of Sciences of the United States of America, 121(12):e2313574121.

This study supports the development of predictive bacteriophage (phage) therapy: the concept of phage cocktail selection to treat a bacterial infection based on machine learning (ML) models. For this purpose, ML models were trained on thousands of measured interactions between a panel of phage and sequenced bacterial isolates. The concept was applied to Escherichia coli associated with urinary tract infections. This is an important common infection in humans and companion animals from which multidrug-resistant (MDR) bloodstream infections can originate. The global threat of MDR infection has reinvigorated international efforts into alternatives to antibiotics including phage therapy. E. coli exhibit extensive genome-level variation due to horizontal gene transfer via phage and plasmids. Associated with this, phage selection for E. coli is difficult as individual isolates can exhibit considerable variation in phage susceptibility due to differences in factors important to phage infection including phage receptor profiles and resistance mechanisms. The activity of 31 phage was measured on 314 isolates with growth curves in artificial urine. Random Forest models were built for each phage from bacterial genome features, and the more generalist phage, acting on over 20% of the bacterial population, exhibited F1 scores of >0.6 and could be used to predict phage cocktails effective against previously untested strains. The study demonstrates the potential of predictive ML models which integrate bacterial genomics with phage activity datasets allowing their use on data derived from direct sequencing of clinical samples to inform rapid and effective phage therapy.

RevDate: 2024-03-13

Shang Y, Zhang Y, Wang R, et al (2024)

Deciphering the molecular and functional basis of TMexCD1: the plasmid-encoded efflux pump of resistance-nodulation-division superfamily.

Antimicrobial agents and chemotherapy [Epub ahead of print].

Horizontal gene transfer has been demonstrated to be an important driver for the emergency of multidrug-resistant pathogens. Recently, a transferable gene cluster tmexCD1-toprJ1 of the resistance-nodulation-division (RND) superfamily was identified in the plasmids of animal-derived Klebsiella pneumoniae strains, with a higher efflux capacity for various drugs than the Escherichia coli AcrAB-TolC homolog system. In this study, we focused on the differences in the inner membrane pump of these two systems and identified some key residues that contribute to the robust efflux activity of the TMexCD1 system. With the aid of homologous modeling and molecular docking, eight residues from the proximal binding pocket (PBP) and nine from the distal binding pocket (DBP) were selected and subjected to site-directed mutagenesis. Several of them, such as S134, I139, D181, and A290, were shown to be important for substrate binding in the DBP region, and all residues in PBP and DBP showed certain substrate preferences. Apart from the conservative switch loop (L613-623[TMexD1]) previously identified in the E. coli AcrB (EcAcrB), a relatively unconservative loop (L665-675[TMexD1]) at the bottom of PBP was proposed as a critical element for the robust activity of TMexD1, due to variations at sites E669, G670, N673, and S674 compared to EcAcrAB, and the significantly altered efflux activity due to their mutations. The conservation and flexibility of these key factors can contribute to the evolution of the RND efflux pumps and thus serve as potential targets for developing inhibitors to block the widespread of the TMexCD1 system.

RevDate: 2024-03-12

Li J, Liao Q, Wang Y, et al (2024)

Involvement of functional metabolism promotes the enrichment of antibiotic resistome in drinking water: Based on the PICRUSt2 functional prediction.

Journal of environmental management, 356:120544 pii:S0301-4797(24)00530-9 [Epub ahead of print].

Biofilters are the important source and sink of antibiotic resistance genes (ARGs) and antibiotic resistance bacteria (ARB) in the drinking water. Current studies generally ascribed the prevalence of BAR in biofilter from the perspective of gene behavior, i.e. horizontal gene transfer (HGT), little attentions have been paid on the ARGs carrier- ARB. In this study, we proposed the hypothesis that ARB participating in pollutant metabolism processes and becoming dominant is an important way for the enrichment of ARGs. To verify this, the antibiotic resistome and bacterial functional metabolic pathways of a sand filter was profiled using heterotrophic bacterial plate counting method (HPC), high-throughput qPCR, Illumina Hiseq sequencing and PICRUSt2 functional prediction. The results illustrated a significant leakage of ARB in the effluent of the sand filter with an average absolute abundance of approximately 10[2]-10[3] CFU/mL. Further contribution analysis revealed that the dominant genera, such as Acinetobacter spp., Aeromonas spp., Elizabethkingia spp., and Bacillus spp., were primary ARGs hosts, conferring resistance to multiple antibiotics including sulfamethoxazole, tetracycline and β-lactams. Notably, these ARGs hosts were involved in nitrogen metabolism, including extracellular nitrate/nitrite transport and nitrite reduction, which are crucial in nitrification and denitrification in biofilters. For example, Acinetobacter spp., the dominant bacteria in the filter (relative abundance 69.97 %), contributed the majority of ARGs and 53.79 % of nitrite reduction function. That is, ARB can predominate by participating in the nitrogen metabolism pathways, facilitating the enrichment of ARGs. These findings provide insights into the stable presence of ARGs in biofilters from a functional metabolism perspective, offering a significant supplementary to the mechanisms of the emergence, maintenance, and transmission of BARin drinking water.

RevDate: 2024-03-12

Beck C, Krusche J, Notaro A, et al (2024)

Wall teichoic acid substitution with glucose governs phage susceptibility of Staphylococcus epidermidis.

mBio [Epub ahead of print].

The species- and clone-specific susceptibility of Staphylococcus cells for bacteriophages is governed by the structures and glycosylation patterns of wall teichoic acid (WTA) glycopolymers. The glycosylation-dependent phage-WTA interactions in the opportunistic pathogen Staphylococcus epidermidis and in other coagulase-negative staphylococci (CoNS) have remained unknown. We report a new S. epidermidis WTA glycosyltransferase TagE whose deletion confers resistance to siphoviruses such as ΦE72 but enables binding of otherwise unbound podoviruses. S. epidermidis glycerolphosphate WTA was found to be modified with glucose in a tagE-dependent manner. TagE is encoded together with the enzymes PgcA and GtaB providing uridine diphosphate-activated glucose. ΦE72 transduced several other CoNS species encoding TagE homologs, suggesting that WTA glycosylation via TagE is a frequent trait among CoNS that permits interspecies horizontal gene transfer. Our study unravels a crucial mechanism of phage-Staphylococcus interaction and horizontal gene transfer, and it will help in the design of anti-staphylococcal phage therapies.IMPORTANCEPhages are highly specific for certain bacterial hosts, and some can transduce DNA even across species boundaries. How phages recognize cognate host cells remains incompletely understood. Phages infecting members of the genus Staphylococcus bind to wall teichoic acid (WTA) glycopolymers with highly variable structures and glycosylation patterns. How WTA is glycosylated in the opportunistic pathogen Staphylococcus epidermidis and in other coagulase-negative staphylococci (CoNS) species has remained unknown. We describe that S. epidermidis glycosylates its WTA backbone with glucose, and we identify a cluster of three genes responsible for glucose activation and transfer to WTA. Their inactivation strongly alters phage susceptibility patterns, yielding resistance to siphoviruses but susceptibility to podoviruses. Many different CoNS species with related glycosylation genes can exchange DNA via siphovirus ΦE72, suggesting that glucose-modified WTA is crucial for interspecies horizontal gene transfer. Our finding will help to develop antibacterial phage therapies and unravel routes of genetic exchange.

RevDate: 2024-03-11

Kim YH, Lee DH, Seo HS, et al (2024)

Genome-based taxonomic identification and safety assessment of an Enterococcus strain isolated from a homemade dairy product.

International microbiology : the official journal of the Spanish Society for Microbiology [Epub ahead of print].

The aim of this study was to explore the taxonomic identification and evaluate the safety of a bacterium, Enterococcus lactis IDCC 2105, isolated from homemade cheese in Korea, using whole genome sequence (WGS) analysis. It sought to identify the species level of this Enterococcus spp., assess its antibiotic resistance, and evaluate its virulence potential. WGS analysis confirmed the bacterial strain IDCC 2105 as E. lactis and identified genes responsible for resistance to erythromycin and clindamycin, specifically msrC, and eatAv, which are chromosomally located, indicating a minimal risk for horizontal gene transfer. The absence of plasmids in E. lactis IDCC 2105 further diminishes the likelihood of resistance gene dissemination. Additionally, our investigation into seven virulence factors, including hemolysis, platelet aggregation, biofilm formation, hyaluronidase, gelatinase, ammonia production, and β-glucuronidase activity, revealed no detectable virulence traits. Although bioinformatic analysis suggested the presence of collagen adhesion genes acm and scm, these were not corroborated by phenotypic virulence assays. Based on these findings, E. lactis IDCC 2105 presents as a safe strain for potential applications, contributing valuable information on its taxonomy, antibiotic resistance profile, and lack of virulence factors, supporting its use in food products.

RevDate: 2024-03-12

Simón D, Ramos N, Lamolle G, et al (2024)

Two decades ago, giant viruses were discovered: the fall of an old paradigm.

Frontiers in microbiology, 15:1356711.

RevDate: 2024-03-12
CmpDate: 2023-09-01

Pereira L, LT Dunning (2023)

Extrachromosomal circular DNA as a vehicle to gene transfer in plants.

Plant physiology, 193(1):172-173.

RevDate: 2024-03-11
CmpDate: 2024-03-11

Colombi E, Bertels F, Doulcier G, et al (2024)

Rapid dissemination of host metabolism-manipulating genes via integrative and conjugative elements.

Proceedings of the National Academy of Sciences of the United States of America, 121(11):e2309263121.

Integrative and conjugative elements (ICEs) are self-transmissible mobile elements that transfer functional genetic units across broad phylogenetic distances. Accessory genes shuttled by ICEs can make significant contributions to bacterial fitness. Most ICEs characterized to date encode readily observable phenotypes contributing to symbiosis, pathogenicity, and antimicrobial resistance, yet the majority of ICEs carry genes of unknown function. Recent observations of rapid acquisition of ICEs in a pandemic lineage of Pseudomonas syringae pv. actinidae led to investigation of the structural and functional diversity of these elements. Fifty-three unique ICE types were identified across the P. syringae species complex. Together they form a distinct family of ICEs (PsICEs) that share a distant relationship to ICEs found in Pseudomonas aeruginosa. PsICEs are defined by conserved backbone genes punctuated by an array of accessory cargo genes, are highly recombinogenic, and display distinct evolutionary histories compared to their bacterial hosts. The most common cargo is a recently disseminated 16-kb mobile genetic element designated Tn6212. Deletion of Tn6212 did not alter pathogen growth in planta, but mutants displayed fitness defects when grown on tricarboxylic acid (TCA) cycle intermediates. RNA-seq analysis of a set of nested deletion mutants showed that a Tn6212-encoded LysR regulator has global effects on chromosomal gene expression. We show that Tn6212 responds to preferred carbon sources and manipulates bacterial metabolism to maximize growth.

RevDate: 2024-03-11
CmpDate: 2024-03-11

Hayashi N, Lai Y, Fuerte-Stone J, et al (2024)

Cas9-assisted biological containment of a genetically engineered human commensal bacterium and genetic elements.

Nature communications, 15(1):2096.

Sophisticated gene circuits built by synthetic biology can enable bacteria to sense their environment and respond predictably. Engineered biosensing bacteria outfitted with such circuits can potentially probe the human gut microbiome to prevent, diagnose, or treat disease. To provide robust biocontainment for engineered bacteria, we devised a Cas9-assisted auxotrophic biocontainment system combining thymidine auxotrophy, an Engineered Riboregulator (ER) for controlled gene expression, and a CRISPR Device (CD). The CD prevents the engineered bacteria from acquiring thyA via horizontal gene transfer, which would disrupt the biocontainment system, and inhibits the spread of genetic elements by killing bacteria harboring the gene cassette. This system tunably controlled gene expression in the human gut commensal bacterium Bacteroides thetaiotaomicron, prevented escape from thymidine auxotrophy, and blocked transgene dissemination. These capabilities were validated in vitro and in vivo. This biocontainment system exemplifies a powerful strategy for bringing genetically engineered microorganisms safely into biomedicine.

RevDate: 2024-03-07

Wang YC, Mao Y, Fu HM, et al (2024)

New insights into functional divergence and adaptive evolution of uncultured bacteria in anammox community by complete genome-centric analysis.

The Science of the total environment pii:S0048-9697(24)01671-1 [Epub ahead of print].

Anaerobic ammonium-oxidation (anammox) bacteria play a crucial role in global nitrogen cycling and wastewater nitrogen removal, but they share symbiotic relationships with various other microorganisms. Functional divergence and adaptive evolution of uncultured bacteria in anammox community remain underexplored. Although shotgun metagenomics based on short reads has been widely used in anammox research, metagenome-assembled genomes (MAGs) are often discontinuous and highly contaminated, which limits in-depth analyses of anammox communities. Here, for the first time, we performed Pacific Biosciences high-fidelity (HiFi) long-read sequencing on the anammox granule sludge sample from a lab-scale bioreactor, and obtained 30 accurate and complete metagenome-assembled genomes (cMAGs). These cMAGs were obtained by selecting high-quality circular contigs from initial assemblies of long reads generated by HiFi sequencing, eliminating the need for Illumina short reads, binning, and reassembly. One new anammox species affiliated with Candidatus Jettenia and three species affiliated with novel families were found in this anammox community. cMAG-centric analysis revealed functional divergence in general and nitrogen metabolism among the anammox community members, and they might adopt a cross-feeding strategy in organic matter, cofactors, and vitamins. Furthermore, we identified 63 mobile genetic elements (MGEs) and 50 putative horizontal gene transfer (HGT) events within these cMAGs. The results suggest that HGT events and MGEs related to phage and integration or excision, particularly transposons containing tnpA in anammox bacteria, might play important roles in the adaptive evolution of this anammox community. The cMAGs generated in the present study could be used to establish of a comprehensive database for anammox bacteria and associated microorganisms. Our findings highlight the advantages of HiFi sequencing for the studies of complex mixed cultures and advance our understanding of anammox communities.

RevDate: 2024-03-07

Xie X, Chen B, Zhu S, et al (2024)

Comparative analysis of characteristics of antibiotic resistomes between Arctic soils and representative contaminated samples using metagenomic approaches.

Journal of hazardous materials, 469:133943 pii:S0304-3894(24)00522-3 [Epub ahead of print].

Antibiotic resistance is one of the most concerned global health issues. However, comprehensive profiles of antibiotic resistance genes (ARGs) in various environmental settings are still needed to address modern antibiotic resistome. Here, Arctic soils and representative contaminated samples from ARG pollution sources were analyzed using metagenomic approaches. The diversity and abundance of ARGs in Arctic soils were significantly lower than those in contaminated samples (p < 0.01). ARG profiles in Arctic soils were featured with the dominance of vanF, ceoB, and bacA related to multidrug and bacitracin, whereas those from ARG pollution sources were characterized by prevalent resistance to anthropogenic antibiotics such as sulfonamides, tetracyclines, and beta-lactams. Mobile genetic elements (MGEs) were found in all samples, and their abundance and relatedness to ARGs were both lower in Arctic soils than in polluted samples. Significant relationships between bacterial communities and ARGs were observed (p < 0.01). Cultural bacteria in Arctic soils had clinically-concerned resistance to erythromycin, vancomycin, ampicillin, etc., but ARGs relevant to those antibiotics were undetectable in their genomes. Our results suggested that Arctic environment could be an important reservoir of novel ARGs, and antibiotic stresses could cause ARG pollution via horizontal gene transfer and enrichment of resistant bacteria.

RevDate: 2024-03-07

Franceus J, Rivas-Fernández JP, Lormans J, et al (2024)

Evolution of Phosphorylase Activity in an Ancestral Glycosyltransferase.

ACS catalysis, 14(5):3103-3114.

The reconstruction of ancestral sequences can offer a glimpse into the fascinating process of molecular evolution by exposing the adaptive pathways that shape the proteins found in nature today. Here, we track the evolution of the carbohydrate-active enzymes responsible for the synthesis and turnover of mannogen, a critical carbohydrate reserve in Leishmania parasites. Biochemical characterization of resurrected enzymes demonstrated that mannoside phosphorylase activity emerged in an ancestral bacterial mannosyltransferase, and later disappeared in the process of horizontal gene transfer and gene duplication in Leishmania. By shuffling through plausible historical sequence space in an ancestral mannosyltransferase, we found that mannoside phosphorylase activity could be toggled on through various combinations of mutations at positions outside of the active site. Molecular dynamics simulations showed that such mutations can affect loop rigidity and shield the active site from water molecules that disrupt key interactions, allowing α-mannose 1-phosphate to adopt a catalytically productive conformation. These findings highlight the importance of subtle distal mutations in protein evolution and suggest that the vast collection of natural glycosyltransferases may be a promising source of engineering templates for the design of tailored phosphorylases.

RevDate: 2024-03-06

Haudiquet M, Le Bris J, Nucci A, et al (2024)

Capsules and their traits shape phage susceptibility and plasmid conjugation efficiency.

Nature communications, 15(1):2032.

Bacterial evolution is affected by mobile genetic elements like phages and conjugative plasmids, offering new adaptive traits while incurring fitness costs. Their infection is affected by the bacterial capsule. Yet, its importance has been difficult to quantify because of the high diversity of confounding mechanisms in bacterial genomes such as anti-viral systems and surface receptor modifications. Swapping capsule loci between Klebsiella pneumoniae strains allowed us to quantify their impact on plasmid and phage infection independently of genetic background. Capsule swaps systematically invert phage susceptibility, revealing serotypes as key determinants of phage infection. Capsule types also influence conjugation efficiency in both donor and recipient cells, a mechanism shaped by capsule volume and conjugative pilus structure. Comparative genomics confirmed that more permissive serotypes in the lab correspond to the strains acquiring more conjugative plasmids in nature. The least capsule-sensitive pili (F-like) are the most frequent in the species' plasmids, and are the only ones associated with both antibiotic resistance and virulence factors, driving the convergence between virulence and antibiotics resistance in the population. These results show how traits of cellular envelopes define slow and fast lanes of infection by mobile genetic elements, with implications for population dynamics and horizontal gene transfer.

RevDate: 2024-03-06

Shi X, Shen Z, Shao B, et al (2024)

Antibiotic resistant genes profile in the surface sediments of typical aquaculture areas across 15 major lakes in China.

Environmental pollution (Barking, Essex : 1987) pii:S0269-7491(24)00423-8 [Epub ahead of print].

Aquatic farming is considered as a major source of antibiotic resistant bacteria (ARB) and antibiotic-resistance genes (ARGs) for the natural environment of the lakes. ARB and ARGs in the natural environment have increased quickly because of the human activities. Here, we have profiled the diversity and abundance of ARGs in sediments from the typical aquaculture areas around 15 major lakes in China using PCR and qPCR, and further assessed the risk factor shaping the occurrence and distribution of ARGs. And class 1, 2 and 3 integrons were initially detected by PCR with specific primers. ARGs were widely distributed in the lakes: Weishan Lake and Poyang Lake showed high diversity of ARGs, followed by Dongting Lake, Chao Lake and Tai Lake. Generally, the ARGs in the Middle-Lower Yangtze Plain were more abundant than those in the Qinghai-Tibet Plateau. Tetracycline resistance genes (tet(C), tet(A) &tet(M)) were prominent in sediments, and the next was AmpC β-lactamase gene group BIL/LAT/CMY, and the last was the genes resistance to aminoglycosides (strA-strB). Partial least squares path modeling analysis (PLS-PMA) revealed that livestock had a significant direct effect on the distribution of ARGs in lakes, and population might indirectly influence the profiles of ARGs by affecting the scale of livestock and aquaculture. The detectable rate of class 1, 2 and 3 integrons were 80%, 100% and 46.67%, respectively. The prevalence of integrons might play a key role in promoting more frequent horizontal gene transfer (HGT) events, resulting in the environmental mobilization and dissemination of ARGs between bacteria.

RevDate: 2024-03-06

Wang Y, Zhang Z, Kang J, et al (2024)

Phages in different habitats and their ability to carry antibiotic resistance genes.

Journal of hazardous materials, 469:133941 pii:S0304-3894(24)00520-X [Epub ahead of print].

As the most abundant organisms on Earth, phages play a key role in the evolution of bacterial antibiotic resistance. Although previous studies have demonstrated the molecular mechanisms of horizontal gene transfer mediated by mobile genetic elements, our understanding of the intertwined relationships between antibiotic resistance genes (ARGs) and phages is limited. In this study, we analysed 2781 metagenomic samples to reveal the composition and species interactions of phage communities in different habitats as well as their capacity to carry ARGs with health risks. The composition of phage communities varies in different habitats and mainly depends on environmental conditions. Terrestrial habitats display more complex and robust interactions between phages than aquatic and human-associated habitats, resulting in the highest biodiversity of phages. Several types of phages in certain taxa (4.95-7.67%, mainly belonging to Caudoviricetes) have the capacity to carry specific ARGs and display a high potential risk to human health, especially in human-associated habitats. Overall, our results provide insights into the assembly mechanisms of phage communities and their effects on the dissemination of antibiotic resistance.

RevDate: 2024-03-06

Sharma DK, YS Rajpurohit (2024)

Multitasking functions of bacterial extracellular DNA in biofilms.

Journal of bacteriology [Epub ahead of print].

Bacterial biofilms are intricate ecosystems of microbial communities that adhere to various surfaces and are enveloped by an extracellular matrix composed of polymeric substances. Within the context of bacterial biofilms, extracellular DNA (eDNA) originates from cell lysis or is actively secreted, where it exerts a significant influence on the formation, stability, and resistance of biofilms to environmental stressors. The exploration of eDNA within bacterial biofilms holds paramount importance in research, with far-reaching implications for both human health and the environment. An enhanced understanding of the functions of eDNA in biofilm formation and antibiotic resistance could inspire the development of strategies to combat biofilm-related infections and improve the management of antibiotic resistance. This comprehensive review encapsulates the latest discoveries concerning eDNA, encompassing its origins, functions within bacterial biofilms, and significance in bacterial pathogenesis.

RevDate: 2024-03-05

Dmitrijeva M, Tackmann J, Matias Rodrigues JF, et al (2024)

A global survey of prokaryotic genomes reveals the eco-evolutionary pressures driving horizontal gene transfer.

Nature ecology & evolution [Epub ahead of print].

Horizontal gene transfer, the exchange of genetic material through means other than reproduction, is a fundamental force in prokaryotic genome evolution. Genomic persistence of horizontally transferred genes has been shown to be influenced by both ecological and evolutionary factors. However, there is limited availability of ecological information about species other than the habitats from which they were isolated, which has prevented a deeper exploration of ecological contributions to horizontal gene transfer. Here we focus on transfers detected through comparison of individual gene trees to the species tree, assessing the distribution of gene-exchanging prokaryotes across over a million environmental sequencing samples. By analysing detected horizontal gene transfer events, we show distinct functional profiles for recent versus old events. Although most genes transferred are part of the accessory genome, genes transferred earlier in evolution tend to be more ubiquitous within present-day species. We find that co-occurring, interacting and high-abundance species tend to exchange more genes. Finally, we show that host-associated specialist species are most likely to exchange genes with other host-associated specialist species, whereas species found across different habitats have similar gene exchange rates irrespective of their preferred habitat. Our study covers an unprecedented scale of integrated horizontal gene transfer and environmental information, highlighting broad eco-evolutionary trends.

RevDate: 2024-03-05

Zhang Y, Li W, Wu Y, et al (2024)

Chitosan oligosaccharide accelerates the dissemination of antibiotic resistance genes through promoting conjugative plasmid transfer.

Journal of hazardous materials, 469:133922 pii:S0304-3894(24)00501-6 [Epub ahead of print].

The dissemination of antibiotic resistance genes (ARGs), especially via plasmid-mediated horizontal gene transfer, poses a pervasive threat to global health. Chitosan-oligosaccharide (COS) is extensively utilized in medicine, plant and animal husbandry. However, their impact on microflora implies the potential to exert selective pressure on plasmid transfer. To explore the role of COS in facilitating the dissemination of ARGs via plasmid conjugation, we established in vitro mating models. The addition of COS to conjugation mixtures significantly enhanced the transfer of RP4 plasmid and mcr-1 positive IncX4 plasmid in both intra- and inter-specific. Phenotypic and transcriptome analysis revealed that COS enhanced intercellular contact by neutralizing cell surface charge and increasing cell surface hydrophobicity. Additionally, COS increased membrane permeability by inhibiting the Tol-Pal system, thereby facilitating plasmid conjugative transfer. Furthermore, COS served as the carbon source and was metabolized by E. coli, providing energy for plasmid conjugation through regulating the expression of ATPase and global repressor factor-related genes in RP4 plasmid. Overall, these findings improve our awareness of the potential risks associated with the presence of COS and the spread of bacterial antibiotic resistance, emphasizing the need to establish guidelines for the prudent use of COS and its discharge into the environment.

RevDate: 2024-03-05

Gschwind R, Petitjean M, Fournier C, et al (2024)

Inter-phylum circulation of a beta-lactamase-encoding gene: a rare but observable event.

Antimicrobial agents and chemotherapy [Epub ahead of print].

Beta-lactamase-mediated degradation of beta-lactams is the most common mechanism of beta-lactam resistance in Gram-negative bacteria. Beta-lactamase-encoding genes can be transferred between closely related bacteria, but spontaneous inter-phylum transfers (between distantly related bacteria) have never been reported. Here, we describe an extended-spectrum beta-lactamase (ESBL)-encoding gene (blaMUN-1) shared between the Pseudomonadota and Bacteroidota phyla. An Escherichia coli strain was isolated from a patient in Münster (Germany). Its genome was sequenced. The ESBL-encoding gene (named blaMUN-1) was cloned, and the corresponding enzyme was characterized. The distribution of the gene among bacteria was investigated using the RefSeq Genomes database. The frequency and relative abundance of its closest homolog in the global microbial gene catalog (GMGC) were analyzed. The E. coli strain exhibited two distinct morphotypes. Each morphotype possessed two chromosomal copies of the blaMUN-1 gene, with one morphotype having two additional copies located on a phage-plasmid p0111. Each copy was located within a 7.6-kb genomic island associated with mobility. blaMUN-1 encoded for an extended-spectrum Ambler subclass A2 beta-lactamase with 43.0% amino acid identity to TLA-1. blaMUN-1 was found in species among the Bacteroidales order and in Sutterella wadsworthensis (Pseudomonadota). Its closest homolog in GMGC was detected frequently in human fecal samples. This is, to our knowledge, the first reported instance of inter-phylum transfer of an ESBL-encoding gene, between the Bacteroidota and Pseudomonadota phyla. Although the gene was frequently detected in the human gut, inter-phylum transfer was rare, indicating that inter-phylum barriers are effective in impeding the spread of ESBL-encoding genes, but not entirely impenetrable.

RevDate: 2024-03-04

van der Gulik PTS, Hoff WD, D Speijer (2024)

The contours of evolution: In defence of Darwin's tree of life paradigm.

BioEssays : news and reviews in molecular, cellular and developmental biology [Epub ahead of print].

Both the concept of a Darwinian tree of life (TOL) and the possibility of its accurate reconstruction have been much criticized. Criticisms mostly revolve around the extensive occurrence of lateral gene transfer (LGT), instances of uptake of complete organisms to become organelles (with the associated subsequent gene transfer to the nucleus), as well as the implications of more subtle aspects of the biological species concept. Here we argue that none of these criticisms are sufficient to abandon the valuable TOL concept and the biological realities it captures. Especially important is the need to conceptually distinguish between organismal trees and gene trees, which necessitates incorporating insights into widely occurring LGT into modern evolutionary theory. We demonstrate that all criticisms, while based on important new findings, do not invalidate the TOL. After considering the implications of these new insights, we find that the contours of evolution are best represented by a TOL.

RevDate: 2024-03-05

Satija K, VP Anjankar (2024)

Molecular Characterization of Multidrug-Resistant Shigella flexneri.

Cureus, 16(1):e53276.

Due to their propensity for causing diarrheal illnesses and their rising susceptibility to antimicrobials, Shigella infections constitute a serious threat to global public health. This extensive study explores the frequency, antibiotic resistance, genetic evolution, and effects of Shigella infections on vulnerable groups. The research covers a wide range of geographical areas and sheds information on how the prevalence of Shigella species is evolving. Shigella strain antimicrobial resistance patterns are thoroughly examined. Multidrug resistance (MDR) has been found to often occur in investigations, especially when older antimicrobials are used. The improper use of antibiotics in China is blamed for the quick emergence of resistance, and variations in resistance rates have been seen across different geographical areas. Shigella strains' genetic makeup can be used to identify emerging trends and horizontal gene transfer's acquisition of resistance genes. Notably, S. sonnei exhibits the capacity to obtain resistance genes from nearby bacteria, increasing its capacity for infection. The study also emphasizes the difficulties in accurately serotyping Shigella strains due to inconsistencies between molecular and conventional serology. These results highlight the necessity of reliable diagnostic methods for monitoring Shigella infections. In conclusion, this study emphasizes how dynamic Shigella infections are, with varying patterns of occurrence, changing resistance landscapes, and genetic adaptability. In addition to tackling the rising problem of antibiotic resistance in Shigella infections, these findings are essential for guiding efforts for disease surveillance, prevention, and treatment.

RevDate: 2024-03-04

Xiao Y, Zhang S, Li H, et al (2024)

Metagenomic insights into the response of soil microbial communities to pathogenic Ralstonia solanacearum.

Frontiers in plant science, 15:1325141.

Understanding the response of soil microbial communities to pathogenic Ralstonia solanacearum is crucial for preventing bacterial wilt outbreaks. In this study, we investigated the soil physicochemical and microbial community to assess their impact on the pathogenic R.solanacearum through metagenomics. Our results revealed that certain archaeal taxa were the main contributors influencing the health of plants. Additionally, the presence of the pathogen showed a strong negative correlation with soil phosphorus levels, while soil phosphorus was significantly correlated with bacterial and archaeal communities. We found that the network of microbial interactions in healthy plant rhizosphere soils was more complex compared to diseased soils. The diseased soil network had more linkages, particularly related to the pathogen occurrence. Within the network, the family Comamonadaceae, specifically Ramlibacter_tataouinensis, was enriched in healthy samples and showed a significantly negative correlation with the pathogen. In terms of archaea, Halorubrum, Halorussus_halophilus (family: Halobacteriaceae), and Natronomonas_pharaonis (family: Haloarculaceae) were enriched in healthy plant rhizosphere soils and showed negative correlations with R.solanacearum. These findings suggested that the presence of these archaea may potentially reduce the occurrence of bacterial wilt disease. On the other hand, Halostagnicola_larseniia and Haloterrigena_sp._BND6 (family: Natrialbaceae) had higher relative abundance in diseased plants and exhibited significantly positive correlations with R.solanacearum, indicating their potential contribution to the pathogen's occurrence. Moreover, we explored the possibility of functional gene sharing among the correlating bacterial pairs within the Molecular Ecological Network. Our analysis revealed 468 entries of horizontal gene transfer (HGT) events, emphasizing the significance of HGT in shaping the adaptive traits of plant-associated bacteria, particularly in relation to host colonization and pathogenicity. Overall, this work revealed key factors, patterns and response mechanisms underlying the rhizosphere soil microbial populations. The findings offer valuable guidance for effectively controlling soil-borne bacterial diseases and developing sustainable agriculture practices.

RevDate: 2024-03-02

Huang HJ, Li LL, Ye ZX, et al (2024)

Salivary proteins potentially derived from horizontal gene transfer are critical for salivary sheath formation and other feeding processes.

Communications biology, 7(1):257.

Herbivorous insects employ an array of salivary proteins to aid feeding. However, the mechanisms behind the recruitment and evolution of these genes to mediate plant-insect interactions remain poorly understood. Here, we report a potential horizontal gene transfer (HGT) event from bacteria to an ancestral bug of Eutrichophora. The acquired genes subsequently underwent duplications and evolved through co-option. We annotated them as horizontal-transferred, Eutrichophora-specific salivary protein (HESPs) according to their origin and function. In Riptortus pedestris (Coreoidea), all nine HESPs are secreted into plants during feeding. The RpHESP4 to RpHESP8 are recently duplicated and found to be indispensable for salivary sheath formation. Silencing of RpHESP4-8 increases the difficulty of R. pedestris in probing the soybean, and the treated insects display a decreased survivability. Although silencing the other RpHESPs does not affect the salivary sheath formation, negative effects are also observed. In Pyrrhocoris apterus (Pyrrhocoroidea), five out of six PaHESPs are secretory salivary proteins, with PaHESP3 being critical for insect survival. The PaHESP5, while important for insects, no longer functions as a salivary protein. Our results provide insight into the potential origin of insect saliva and shed light on the evolution of salivary proteins.

RevDate: 2024-03-02

Wiśniewski P, Zakrzewski A, Chajęcka-Wierzchowska W, et al (2024)

Possibility of transfer and activation of 'silent' tetracycline resistance genes among Enterococcus faecalis under high-pressure processing.

Food microbiology, 120:104481.

In this study, the tetracycline resistance of Enterococcus faecalis strains isolated from food was determined and molecular analyses of the resistance background were performed by determining the frequency of selected tetracycline resistance genes. In addition, the effect of high-pressure stress (400 and 500 MPa) on the expression of selected genes encoding tetracycline resistance was determined, as well as changes in the frequency of transfer of these genes in isolates showing sensitivity to tetracyclines. In our study, we observed an increase in the expression of genes encoding tetracyclines, especially the tet(L) gene, mainly under 400 MPa pressure. The study confirmed the possibility of transferring genes encoding tetracyclines such as tet(M), tet(L), tet(K), tet(W) and tet(O) by horizontal gene transfer in both control strains and exposed to high-pressure. Exposure of the strains to 400 MPa pressure had a greater effect on the possibility of gene transfer and expression than the application of a higher-pressure. To our knowledge, this study for the first time determined the effect of high-pressure stress on the expression of selected genes encoding tetracycline resistance, as well as the possibility and changes in the frequency of transfer of these genes in Enterococcus faecalis isolates showing sensitivity to tetracyclines and possessing silent genes. Due to the observed possibility of increased expression of some of the genes encoding tetracycline resistance and the possibility of their spread by horizontal gene transfer to other microorganisms in the food environment, under the influence of high-pressure processing in strains phenotypically susceptible to this antibiotic, it becomes necessary to monitor this ability in isolates derived from foods.

RevDate: 2024-03-01

Fogarty EC, Schechter MS, Lolans K, et al (2024)

A cryptic plasmid is among the most numerous genetic elements in the human gut.

Cell, 187(5):1206-1222.e16.

Plasmids are extrachromosomal genetic elements that often encode fitness-enhancing features. However, many bacteria carry "cryptic" plasmids that do not confer clear beneficial functions. We identified one such cryptic plasmid, pBI143, which is ubiquitous across industrialized gut microbiomes and is 14 times as numerous as crAssphage, currently established as the most abundant extrachromosomal genetic element in the human gut. The majority of mutations in pBI143 accumulate in specific positions across thousands of metagenomes, indicating strong purifying selection. pBI143 is monoclonal in most individuals, likely due to the priority effect of the version first acquired, often from one's mother. pBI143 can transfer between Bacteroidales, and although it does not appear to impact bacterial host fitness in vivo, it can transiently acquire additional genetic content. We identified important practical applications of pBI143, including its use in identifying human fecal contamination and its potential as an alternative approach to track human colonic inflammatory states.

RevDate: 2024-03-01

Workman RE, Stoltzfus MJ, Keith NC, et al (2024)

Anti-CRISPR proteins trigger a burst of CRISPR-Cas9 expression that enhances phage defense.

Cell reports, 43(3):113849 pii:S2211-1247(24)00177-3 [Epub ahead of print].

CRISPR-Cas immune systems provide bacteria with adaptive immunity against bacteriophages, but they are often transcriptionally repressed to mitigate auto-immunity. In some cases, CRISPR-Cas expression increases in response to a phage infection, but the mechanisms of induction are largely unknown, and it is unclear whether induction occurs strongly and quickly enough to benefit the bacterial host. In S. pyogenes, Cas9 is both an immune effector and auto-repressor of CRISPR-Cas expression. Here, we show that phage-encoded anti-CRISPR proteins relieve Cas9 auto-repression and trigger a rapid increase in CRISPR-Cas levels during a single phage infective cycle. As a result, fewer cells succumb to lysis, leading to a striking survival benefit after multiple rounds of infection. CRISPR-Cas induction also reduces lysogeny, thereby limiting a route for horizontal gene transfer. Altogether, we show that Cas9 is not only a CRISPR-Cas effector and repressor but also a phage sensor that can mount an anti-anti-CRISPR transcriptional response.

RevDate: 2024-02-29

Wong TKF, Cherryh C, Rodrigo AG, et al (2024)

MAST: Phylogenetic Inference with Mixtures Across Sites and Trees.

Systematic biology pii:7616281 [Epub ahead of print].

Hundreds or thousands of loci are now routinely used in modern phylogenomic studies. Concatenation approaches to tree inference assume that there is a single topology for the entire dataset, but different loci may have different evolutionary histories due to incomplete lineage sorting, introgression, and/or horizontal gene transfer; even single loci may not be treelike due to recombination. To overcome this shortcoming, we introduce an implementation of a multi-tree mixture model that we call MAST. This model extends a prior implementation by Boussau et al. (2009) by allowing users to estimate the weight of each of a set of pre-specified bifurcating trees in a single alignment. The MAST model allows each tree to have its own weight, topology, branch lengths, substitution model, nucleotide or amino acid frequencies, and model of rate heterogeneity across sites. We implemented the MAST model in a maximum-likelihood framework in the popular phylogenetic software, IQ-TREE. Simulations show that we can accurately recover the true model parameters, including branch lengths and tree weights for a given set of tree topologies, under a wide range of biologically realistic scenarios. We also show that we can use standard statistical inference approaches to reject a single-tree model when data are simulated under multiple trees (and vice versa). We applied the MAST model to multiple primate datasets and found that it can recover the signal of incomplete lineage sorting in the Great Apes, as well as the asymmetry in minor trees caused by introgression among several macaque species. When applied to a dataset of four Platyrrhine species for which standard concatenated maximum likelihood and gene tree approaches disagree, we observe that MAST gives the highest weight (i.e. the largest proportion of sites) to the tree also supported by gene tree approaches. These results suggest that the MAST model is able to analyse a concatenated alignment using maximum likelihood, while avoiding some of the biases that come with assuming there is only a single tree. We discuss how the MAST model can be extended in the future.

RevDate: 2024-02-28

Jeong GJ, Khan F, Tabassum N, et al (2024)

Bacterial extracellular vesicles: modulation of biofilm formation and virulence.

Acta biomaterialia pii:S1742-7061(24)00100-4 [Epub ahead of print].

Microbial pathogens cause persistent infections by forming biofilms and producing numerous virulence factors. Bacterial extracellular vesicles (BEVs) are nanostructures produced by various bacterial species vital for molecular transport. BEVs include various components, including lipids (glycolipids, LPS, and phospholipids), nucleic acids (genomic DNA, plasmids, and short RNA), proteins (membrane proteins, enzymes, and toxins), and quorum-sensing signaling molecules. BEVs play a major role in forming extracellular polymeric substances (EPS) in biofilms by transporting EPS components such as extracellular polysaccharides, proteins, and extracellular DNA. BEVs have been observed to carry various secretory virulence factors. Thus, BEVs play critical roles in cell-to-cell communication, biofilm formation, virulence, disease progression, and resistance to antimicrobial treatment. In contrast, BEVs have been shown to impede early-stage biofilm formation, disseminate mature biofilms, and reduce virulence. This review summarizes the current status in the literature regarding the composition and role of BEVs in microbial infections. Furthermore, the dual functions of BEVs in eliciting and suppressing biofilm formation and virulence in various microbial pathogens are thoroughly discussed. This review is expected to improve our understanding of the use of BEVs in determining the mechanism of biofilm development in pathogenic bacteria and in developing drugs to inhibit biofilm formation by microbial pathogens. STATEMENT OF SIGNIFICANCE: Bacterial extracellular vesicles (BEVs) are nanostructures formed by membrane blebbing and explosive cell lysis. It is essential for transporting lipids, nucleic acids, proteins, and quorum-sensing signaling molecules. BEVs play an important role in the formation of the biofilm's extracellular polymeric substances (EPS) by transporting its components, such as extracellular polysaccharides, proteins, and extracellular DNA. Furthermore, BEVs shield genetic material from nucleases and thermodegradation by packaging it during horizontal gene transfer, contributing to the transmission of bacterial adaptation determinants like antibiotic resistance. Thus, BEVs play a critical role in cell-to-cell communication, biofilm formation, virulence enhancement, disease progression, and drug resistance. In contrast, BEVs have been shown to prevent early-stage biofilm, disperse mature biofilm, and reduce virulence characteristics.

RevDate: 2024-02-28

Kfoury B, Rodrigues WFC, Kim SJ, et al (2024)

Multiple horizontal gene transfer events have shaped plant glycosyl hydrolase diversity and function.

The New phytologist [Epub ahead of print].

Plant glycosyl hydrolases (GHs) play a crucial role in selectively breaking down carbohydrates and glycoconjugates during various cellular processes, such as reserve mobilization, pathogen defense, and modification/disassembly of the cell wall. In this study, we examined the distribution of GH genes in the Archaeplastida supergroup, which encompasses red algae, glaucophytes, and green plants. We identified that the GH repertoire expanded from a few tens of genes in early archaeplastidians to over 400 genes in modern angiosperms, spanning 40 GH families in land plants. Our findings reveal that major evolutionary transitions were accompanied by significant changes in the GH repertoire. Specifically, we identified at least 23 GH families acquired by green plants through multiple horizontal gene transfer events, primarily from bacteria and fungi. We found a significant shift in the subcellular localization of GH activity during green plant evolution, with a marked increase in extracellular-targeted GH proteins associated with the diversification of plant cell wall polysaccharides and defense mechanisms against pathogens. In conclusion, our study sheds light on the macroevolutionary processes that have shaped the GH repertoire in plants, highlighting the acquisition of GH families through horizontal transfer and the role of GHs in plant adaptation and defense mechanisms.

RevDate: 2024-02-28

Sun L, David KT, Wolters JF, et al (2024)

Functional and evolutionary integration of a fungal gene with a bacterial operon.

Molecular biology and evolution pii:7615510 [Epub ahead of print].

Siderophores are crucial for iron-scavenging in microorganisms. While many yeasts can uptake siderophores produced by other organisms, they are typically unable to synthesize siderophores themselves. In contrast, Wickerhamiella/Starmerella (W/S) clade yeasts gained the capacity to make the siderophore enterobactin following the remarkable horizontal acquisition of a bacterial operon enabling enterobactin synthesis. Yet, how these yeasts absorb the iron bound by enterobactin remains unresolved. Here, we demonstrate that Enb1 is the key enterobactin importer in the W/S-clade species Starmerella bombicola. Through phylogenomic analyses, we show that ENB1 is present in all W/S clade yeast species that retained the enterobactin biosynthetic genes. Conversely, it is absent in species that lost the ent genes, except for Starmerella stellata, making this species the only cheater in the W/S clade that can utilize enterobactin without producing it. Through phylogenetic analyses, we infer that ENB1 is a fungal gene that likely existed in the W/S clade prior to the acquisition of the ent genes and subsequently experienced multiple gene losses and duplications. Through phylogenetic topology tests, we show that ENB1 likely underwent horizontal gene transfer from an ancient W/S clade yeast to the order Saccharomycetales, which includes the model yeast Saccharomyces cerevisiae, followed by extensive secondary losses. Taken together, these results suggest that the fungal ENB1 and bacterial ent genes were cooperatively integrated into a functional unit within the W/S clade that enabled adaptation to iron-limited environments. This integrated fungal-bacterial circuit and its dynamic evolution determines the extant distribution of yeast enterobactin producers and cheaters.

RevDate: 2024-02-27

Wang H, Xia F, Xia Y, et al (2024)

Pangenome analysis of Shewanella xiamenensis revealed important genetic traits concerning genetic diversity, pathogenicity and antibiotic resistance.

BMC genomics, 25(1):216.

BACKGROUND: Shewanella xiamenensis, widely distributed in natural environments, has long been considered as opportunistic pathogen. Recently, significant changes in the resistance spectrum have been observed in S. xiamenensis, due to acquired antibiotic resistance genes. Therefore, a pan-genome analysis was conducted to illuminate the genomic changes in S. xiamenensis.

RESULTS: Phylogenetic analysis revealed three major clusters and three singletons, among which close relationship between several strains was discovered, regardless of their host and niches. The "open" genomes with diversity of accessory and strain-specific genomes took advantage towards diversity environments. The purifying selection pressure was the main force on genome evolution, especially in conservative genes. Only 53 gene families were under positive selection pressure. Phenotypic resistance analysis revealed 21 strains were classified as multi-drug resistance (MDR). Ten types of antibiotic resistance genes and two heavy metal resistance operons were discovered in S. xiamenensis. Mobile genetic elements and horizontal gene transfer increased genome diversity and were closely related to MDR strains. S. xiamenensis carried a variety of virulence genes and macromolecular secretion systems, indicating their important roles in pathogenicity and adaptability. Type IV secretion system was discovered in 15 genomes with various sequence structures, indicating it was originated from different donors through horizontal gene transfer.

CONCLUSIONS: This study provided with a detailed insight into the changes in the pan-genome of S. xiamenensis, highlighting its capability to acquire new mobile genetic elements and resistance genes for its adaptation to environment and pathogenicity to human and animals.

RevDate: 2024-02-27

Dewar AE, Belcher LJ, Scott TW, et al (2024)

Genes for cooperation are not more likely to be carried by plasmids.

Proceedings. Biological sciences, 291(2017):20232549.

Cooperation is prevalent across bacteria, but risks being exploited by non-cooperative cheats. Horizontal gene transfer, particularly via plasmids, has been suggested as a mechanism to stabilize cooperation. A key prediction of this hypothesis is that genes which are more likely to be transferred, such as those on plasmids, should be more likely to code for cooperative traits. Testing this prediction requires identifying all genes for cooperation in bacterial genomes. However, previous studies used a method which likely misses some of these genes for cooperation. To solve this, we used a new genomics tool, SOCfinder, which uses three distinct modules to identify all kinds of genes for cooperation. We compared where these genes were located across 4648 genomes from 146 bacterial species. In contrast to the prediction of the hypothesis, we found no evidence that plasmid genes are more likely to code for cooperative traits. Instead, we found the opposite-that genes for cooperation were more likely to be carried on chromosomes. Overall, the vast majority of genes for cooperation are not located on plasmids, suggesting that the more general mechanism of kin selection is sufficient to explain the prevalence of cooperation across bacteria.

RevDate: 2024-02-27

Crippen TL, Sullivan JP, RC Anderson (2024)

Bacterial proximity effects on the transfer of antibiotic resistance genes within the alimentary tract of yellow mealworm larvae.

Journal of economic entomology pii:7615022 [Epub ahead of print].

The arthropod intestinal tract and other anatomical parts naturally carry microorganisms. Some of which are pathogens, secrete toxins, or carry transferable antibiotic-resistance genes. The risks associated with the production and consumption of edible arthropods are dependent on indigenous microbes, as well as microbes introduced during the processes of rearing. This mass arthropod production puts individual arthropods in close proximity, which increases the possibility of their exposure to antibiotic-resistant bacteria carried by bacteria from fellow insects, industry workers, or rearing hardware and substrates. The purpose of this study was to determine if the alimentary tract of the yellow mealworm provided an environment permitting horizontal gene transfer between bacteria. The effect of the concentration of bacterial exposure was also assessed. Antibiotic resistance gene transfer between marker Salmonella Lignières (Enterobacterales: Enterobacteriaceae) and Escherichia coli (Migula) (Enterobacterales: Enterobacteriaceae) introduced into the larval gut demonstrated that the nutrient-rich environment of the yellow mealworm gut provided favorable conditions for the transfer of antibiotic resistance genes. Conjugation frequencies were similar across inoculum concentrations; however, transconjugant production correlated positively to increased exposure concentration. The lowest concentration of bacterial exposure required enrichment to detect and thus may have been approaching a threshold level for the 2 bacteria to colocate within the expanse of the larval gut. While many factors can affect this transfer, the simple factor of the proximity of donor and recipient bacteria, as defined by the concentration of bacteria within the volume of the insect gut, likely primarily contributed to the efficiency of antibiotic gene transfer.

RevDate: 2024-02-27

Kogay R, Wolf YI, EV Koonin (2024)

Defense systems and horizontal gene transfer in bacteria.

bioRxiv : the preprint server for biology pii:2024.02.09.579689.

Horizontal gene transfer (HGT) is a fundamental process in the evolution of prokaryotes, making major contributions to diversification and adaptation. Typically, HGT is facilitated by mobile genetic elements (MGEs), such as conjugative plasmids and phages that generally impose fitness costs on their hosts. However, a substantial fraction of bacterial genes is involved in defense mechanisms that limit the propagation of MGEs, raising the possibility that they can actively restrict HGT. Here we examine whether defense systems curb HGT by exploring the connections between HGT rate and the presence of 73 defense systems in 12 bacterial species. We found that only 6 defense systems, 3 of which are different CRISPR-Cas subtypes, are associated with the reduced gene gain rate on the scale of species evolution. The hosts of such defense systems tend to have a smaller pangenome size and harbor fewer phage-related genes compared to genomes lacking these systems, suggesting that these defense mechanisms inhibit HGT by limiting the integration of prophages. We hypothesize that restriction of HGT by defense systems is species-specific and depends on various ecological and genetic factors, including the burden of MGEs and fitness effect of HGT in bacterial populations.

RevDate: 2024-02-25

Rzymski P, Gwenzi W, Poniedziałek B, et al (2024)

Climate warming, environmental degradation and pollution as drivers of antibiotic resistance.

Environmental pollution (Barking, Essex : 1987) pii:S0269-7491(24)00363-4 [Epub ahead of print].

Antibiotic resistance is a major challenge to public health, but human-caused environmental changes have not been widely recognized as its drivers. Here, we provide a comprehensive overview of the relationships between environmental degradation and antibiotic resistance, demonstrating that the former can potentially fuel the latter with significant public health outcomes. We describe that (i) global warming favors horizontal gene transfer, bacterial infections, the spread of drug-resistant pathogens due to water scarcity, and the release of resistance genes with wastewater; (ii) pesticide and metal pollution act as co-selectors of antibiotic resistance mechanisms; (iii) microplastics create conditions promoting and spreading antibiotic resistance and resistant bacteria; (iv) changes in land use, deforestation, and environmental pollution reduce microbial diversity, a natural barrier to antibiotic resistance spread. We argue that management of antibiotic resistance must integrate environmental goals, including mitigation of further increases in the Earth's surface temperature, better qualitative and quantitative protection of water resources, strengthening of sewage infrastructure, counteracting the microbial diversity loss, reduction of pesticide and metal emissions, and plastic use, improved waste recycling, and improved wastewater treatment. These actions should be accompanied by restricting antibiotic use only to clinically justified situations, developing novel treatments, and promoting prophylaxis. It is pivotal for health authorities and the medical community to adopt the protection of environmental quality as a part of public health measures, also in the context of antibiotic resistance management.

RevDate: 2024-02-27

Ishola OA, Kublik S, Durai Raj AC, et al (2024)

Comparative Metagenomic Analysis of Bacteriophages and Prophages in Gnotobiotic Mouse Models.

Microorganisms, 12(2):.

Gnotobiotic murine models are important to understand microbiota-host interactions. Despite the role of bacteriophages as drivers for microbiome structure and function, there is no information about the structure and function of the gut virome in gnotobiotic models and the link between bacterial and bacteriophage/prophage diversity. We studied the virome of gnotobiotic murine Oligo-MM12 (12 bacterial species) and reduced Altered Schaedler Flora (ASF, three bacterial species). As reference, the virome of Specific Pathogen-Free (SPF) mice was investigated. A metagenomic approach was used to assess prophages and bacteriophages in the guts of 6-week-old female mice. We identified a positive correlation between bacteria diversity, and bacteriophages and prophages. Caudoviricetes (82.4%) were the most prominent class of phages in all samples with differing relative abundance. However, the host specificity of bacteriophages belonging to class Caudoviricetes differed depending on model bacterial diversity. We further studied the role of bacteriophages in horizontal gene transfer and microbial adaptation to the host's environment. Analysis of mobile genetic elements showed the contribution of bacteriophages to the adaptation of bacterial amino acid metabolism. Overall, our results implicate virome "dark matter" and interactions with the host system as factors for microbial community structure and function which determine host health. Taking the importance of the virome in the microbiome diversity and horizontal gene transfer, reductions in the virome might be an important factor driving losses of microbial biodiversity and the subsequent dysbiosis of the gut microbiome.

RevDate: 2024-02-24

Lerner A, Benzvi C, A Vojdani (2024)

The Potential Harmful Effects of Genetically Engineered Microorganisms (GEMs) on the Intestinal Microbiome and Public Health.

Microorganisms, 12(2):.

Gut luminal dysbiosis and pathobiosis result in compositional and biodiversified alterations in the microbial and host co-metabolites. The primary mechanism of bacterial evolution is horizontal gene transfer (HGT), and the acquisition of new traits can be achieved through the exchange of mobile genetic elements (MGEs). Introducing genetically engineered microbes (GEMs) might break the harmonized balance in the intestinal compartment. The present objectives are: 1. To reveal the role played by the GEMs' horizontal gene transfers in changing the landscape of the enteric microbiome eubiosis 2. To expand on the potential detrimental effects of those changes on the human genome and health. A search of articles published in PubMed/MEDLINE, EMBASE, and Scielo from 2000 to August 2023 using appropriate MeSH entry terms was performed. The GEMs' horizontal gene exchanges might induce multiple human diseases. The new GEMs can change the long-term natural evolution of the enteric pro- or eukaryotic cell inhabitants. The worldwide regulatory authority's safety control of GEMs is not enough to protect public health. Viability, biocontainment, and many other aspects are only partially controlled and harmful consequences for public health should be avoided. It is important to remember that prevention is the most cost-effective strategy and primum non nocere should be the focus.

RevDate: 2024-02-24

Valenzuela JA, Vázquez L, Rodríguez J, et al (2024)

Phenotypic, Technological, Safety, and Genomic Profiles of Gamma-Aminobutyric Acid-Producing Lactococcus lactis and Streptococcus thermophilus Strains Isolated from Cow's Milk.

International journal of molecular sciences, 25(4): pii:ijms25042328.

Gamma-aminobutyric acid (GABA)-producing lactic acid bacteria (LAB) can be used as starters in the development of GABA-enriched functional fermented foods. In this work, four GABA-producing strains each of Lactococcus lactis and Streptococcus thermophilus species were isolated from cow's milk, and their phenotypic, technological, and safety profiles determined. Genome analysis provided genetic support for the majority of the analyzed traits, namely, GABA production, growth in milk, and the absence of genes of concern. The operon harboring the glutamate decarboxylase gene (gadB) was chromosomally encoded in all strains and showed the same gene content and gene order as those reported, respectively, for L. lactis and S. thermophilus. In the latter species, the operon was flanked (as in most strains of this species) by complete or truncated copies of insertion sequences (IS), suggesting recent acquisition through horizontal gene transfer. The genomes of three L. lactis and two S. thermophilus strains showed a gene encoding a caseinolytic proteinase (PrtP in L. lactis and PrtS in S. thermophilus). Of these, all but one grew in milk, forming a coagulum of good appearance and an appealing acidic flavor and taste. They also produced GABA in milk supplemented with monosodium glutamate. Two L. lactis strains were identified as belonging to the biovar. diacetylactis, utilized citrate from milk, and produced significant amounts of acetoin. None of the strains showed any noticeable antibiotic resistance, nor did their genomes harbor transferable antibiotic resistance genes or genes involved in toxicity, virulence, or pathogenicity. Altogether these results suggest that all eight strains may be considered candidates for use as starters or components of mixed LAB cultures for the manufacture of GABA-enriched fermented dairy products.

RevDate: 2024-02-23

Wang H, Wu P, Xiong L, et al (2024)

Nuclear genome of dinoflagellates: Size variation and insights into evolutionary mechanisms.

European journal of protistology, 93:126061 pii:S0932-4739(24)00011-7 [Epub ahead of print].

Recent progress in high-throughput sequencing technologies has dramatically increased availability of genome data for prokaryotes and eukaryotes. Dinoflagellates have distinct chromosomes and a huge genome size, which make their genomic analysis complicated. Here, we reviewed the nuclear genomes of core dinoflagellates, focusing on the genome and cell size. Till now, the genome sizes of several dinoflagellates (more than 25) have been measured by certain methods (e.g., flow cytometry), showing a range of 3-250 pg of genomic DNA per cell. In contrast to their relatively small cell size, their genomes are huge (about 1-80 times the human haploid genome). In the present study, we collected the genome and cell size data of dinoflagellates and compared their relationships. We found that dinoflagellate genome size exhibits a positive correlation with cell size. On the other hand, we recognized that the genome size is not correlated with phylogenetic relatedness. These may be caused by genome duplication, increased gene copy number, repetitive non-coding DNA, transposon expansion, horizontal gene transfer, organelle-to-nucleus gene transfer, and/or mRNA reintegration into the genome. Ultimate verification of these factors as potential causative mechanisms would require sequencing of more dinoflagellate genomes in the future.

RevDate: 2024-02-23

Chen T, Mo C, Yuan Y, et al (2024)

Short-, long-read metagenome and virome reveal the profile of phage-mediated ARGs in anoxic-oxic processes for swine wastewater treatment.

Journal of hazardous materials, 468:133789 pii:S0304-3894(24)00368-6 [Epub ahead of print].

Phages are among the most widely spread viruses, but their profiles and the antibiotic resistance genes (ARGs) they carry in swine wastewater remain underexplored. The present study investigated the distribution characteristics of phages and their ARG risk in anoxic/oxic (A/O) wastewater treatment processes of swine farms using short- and long-read metagenome and virome. The results demonstrated that the virome could extract more phage sequences than the total metagenome; thus, it was more suited for studying phages in wastewater settings. Intriguingly, phages had significantly lower abundance of ARG than ARGs harbored by total microorganisms (P < 0.01). Eleven ARGs co-occurred with phages and bacteria (R > 0.6 and P < 0.05), with Siphoviridae being the phage co-occurring with the most ARGs (5). Horizontal gene transfer (HGT) events were observed between Proteobacteria and the major phyla except for Bacteroidota. Furthermore, there were prophage sequences and ARGs on the same contig in bacterial MAGs. These data strongly demonstrate that phages promote horizontal transfer of ARG between bacterial hosts in A/O processes for swine wastewater treatment. Therefore, the risk of phage-mediated horizontal transfer of ARGs cannot be overlooked despite the low abundance of phage ARGs (pARG).

RevDate: 2024-02-23

Jiang YN, Tamiya-Ishitsuka H, Aoi R, et al (2024)

MazEF Homologs in Symbiobacterium thermophilum Exhibit Cross-Neutralization with Non-Cognate MazEFs.

Toxins, 16(2): pii:toxins16020081.

Toxin-antitoxin systems are preserved by nearly every prokaryote. The type II toxin MazF acts as a sequence-specific endoribonuclease, cleaving ribonucleotides at specific sequences that vary from three to seven bases, as has been reported in different host organisms to date. The present study characterized the MazEF module (MazEF-sth) conserved in the Symbiobacterium thermophilum IAM14863 strain, a Gram-negative syntrophic bacterium that can be supported by co-culture with multiple bacteria, including Bacillus subtilis. Based on a method combining massive parallel sequencing and the fluorometric assay, MazF-sth was determined to cleave ribonucleotides at the UACAUA motif, which is markedly similar to the motifs recognized by MazF from B. subtilis (MazF-bs), and by several MazFs from Gram-positive bacteria. MazF-sth, with mutations at conserved amino acid residues Arg29 and Thr52, lost most ribonuclease activity, indicating that these residues that are crucial for MazF-bs also play significant roles in MazF-sth catalysis. Further, cross-neutralization between MazF-sth and the non-cognate MazE-bs was discovered, and herein, the neutralization mechanism is discussed based on a protein-structure simulation via AlphaFold2 and multiple sequence alignment. The conflict between the high homology shared by these MazF amino acid sequences and the few genetic correlations among their host organisms may provide evidence of horizontal gene transfer.

RevDate: 2024-02-24

Yaikhan T, Chukamnerd A, Singkhamanan K, et al (2024)

Genomic Characterization of Mobile Genetic Elements Associated with Multidrug-Resistant Acinetobacter Non-baumannii Species from Southern Thailand.

Antibiotics (Basel, Switzerland), 13(2):.

This study investigated the genetic diversity, antimicrobial resistance profiles, and virulence characteristics of Acinetobacter non-baumannii isolates obtained from four hospitals in southern Thailand. Clinical data, genome information, and average nucleotide identity (ANI) were analyzed for eight isolates, revealing diverse genetic profiles and novel sequence types (STs). Minimum spanning tree analysis indicated potential clonal spread of certain STs across different geographic regions. Antimicrobial resistance genes (ARGs) were detected in all isolates, with a high prevalence of genes conferring resistance to carbapenems, highlighting the challenge of antimicrobial resistance in Acinetobacter spp. infections. Mobile genetic elements (MGEs) carrying ARGs were also identified, emphasizing the role of horizontal gene transfer in spreading resistance. Evaluation of virulence-associated genes revealed a diverse range of virulence factors, including those related to biofilm formation and antibiotic resistance. However, no direct correlation was found between virulence-associated genes in Acinetobacter spp. and specific clinical outcomes, such as infection severity or patient mortality. This complexity suggests that factors beyond gene presence may influence disease progression and outcomes. This study emphasizes the importance of continued surveillance and molecular epidemiological studies to combat the spread of multidrug-resistant (MDR) Acinetobacter non-baumannii strains. The findings provide valuable insights into the epidemiology and genetic characteristics of this bacteria in southern Thailand, with implications for infection control and antimicrobial management efforts.

RevDate: 2024-02-22

Wu Z, C Solís-Lemus (2024)

Ultrafast learning of four-node hybridization cycles in phylogenetic networks using algebraic invariants.

Bioinformatics advances, 4(1):vbae014.

MOTIVATION: The abundance of gene flow in the Tree of Life challenges the notion that evolution can be represented with a fully bifurcating process which cannot capture important biological realities like hybridization, introgression, or horizontal gene transfer. Coalescent-based network methods are increasingly popular, yet not scalable for big data, because they need to perform a heuristic search in the space of networks as well as numerical optimization that can be NP-hard. Here, we introduce a novel method to reconstruct phylogenetic networks based on algebraic invariants. While there is a long tradition of using algebraic invariants in phylogenetics, our work is the first to define phylogenetic invariants on concordance factors (frequencies of four-taxon splits in the input gene trees) to identify level-1 phylogenetic networks under the multispecies coalescent model.

RESULTS: Our novel hybrid detection methodology is optimization-free as it only requires the evaluation of polynomial equations, and as such, it bypasses the traversal of network space, yielding a computational speed at least 10 times faster than the fastest-to-date network methods. We illustrate our method's performance on simulated and real data from the genus Canis.

We present an open-source publicly available Julia package PhyloDiamond.jl available at https://github.com/solislemuslab/PhyloDiamond.jl with broad applicability within the evolutionary community.

RevDate: 2024-02-21

Mori Y, Yamashita E, Nakagawa A, et al (2024)

Determination of the three-dimensional structure of bacteriophage Mu(-) tail fiber and its characterization.

Virology, 593:110017 pii:S0042-6822(24)00038-2 [Epub ahead of print].

Bacteriophage Mu is a temperate phage known to infect various species of Enterobacteria, playing a role in bacterial mutation induction and horizontal gene transfer. The phage possesses two types of tail fibers important for host recognition, which enable it to expand its range of hosts. The alternate tail fibers are formed through the action of genes 49-50 or 52-51, allowing the Mu phage to recognize different surfaces of host cells. In a previous study, we presented the X-ray crystal structure of the C-terminal lipopolysaccharide (LPS)-binding domain of gene product (gp) 49, one of the subunits comprising the Mu tail fiber. In this study, we have determined the structure of the alternative tail fiber subunit, gp52, and compared it with other tail fibers. The results revealed that Mu phage employs different structural motifs for two individual tail fibers for recognizing different hosts.

RevDate: 2024-02-21

Aggarwal R, Mahajan P, Pandiya S, et al (2024)

Antibiotic resistance: a global crisis, problems and solutions.

Critical reviews in microbiology [Epub ahead of print].

Healthy state is priority in today's world which can be achieved using effective medicines. But due to overuse and misuse of antibiotics, a menace of resistance has increased in pathogenic microbes. World Health Organization (WHO) has announced ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.) as the top priority pathogens as these have developed resistance against certain antibiotics. To combat such a global issue, it is utmost important to identify novel therapeutic strategies/agents as an alternate to such antibiotics. To name certain antibiotic adjuvants including: inhibitors of beta-lactamase, efflux pumps and permeabilizers for outer membrane can potentially solve the antibiotic resistance problems. In this regard, inhibitors of lytic domain of lytic transglycosylases provide a novel way to not only act as an alternate to antibiotics but also capable of restoring the efficiency of previously resistant antibiotics. Further, use of bacteriophages is another promising strategy to deal with antibiotic resistant pathogens. Taking in consideration the alternatives of antibiotics, a green synthesis nanoparticle-based therapy exemplifies a good option to combat microbial resistance. As horizontal gene transfer (HGT) in bacteria facilitates the evolution of new resistance strains, therefore identifying the mechanism of resistance and development of inhibitors against it can be a novel approach to combat such problems. In our perspective, host-directed therapy (HDT) represents another promising strategy in combating antimicrobial resistance (AMR). This approach involves targeting specific factors within host cells that pathogens rely on for their survival, either through replication or persistence. As many new drugs are under clinical trials it is advisable that more clinical data and antimicrobial stewardship programs should be conducted to fully assess the clinical efficacy and safety of new therapeutic agents.

RevDate: 2024-02-21

Unitt A, Maiden M, O Harrison (2024)

Characterizing the diversity and commensal origins of penA mosaicism in the genus Neisseria.

Microbial genomics, 10(2):.

Mosaic penA alleles formed through horizontal gene transfer (HGT) have been instrumental to the rising incidence of ceftriaxone-resistant gonococcal infections. Although interspecies HGT of regions of the penA gene between Neisseria gonorrhoeae and commensal Neisseria species has been described, knowledge concerning which species are the most common contributors to mosaic penA alleles is limited, with most studies examining only a small number of alleles. Here, we investigated the origins of recombinant penA alleles through in silico analyses that incorporated 1700 penA alleles from 35 513 Neisseria isolates, comprising 15 different Neisseria species. We identified Neisseria subflava and Neisseria cinerea as the most common source of recombinant sequences in N. gonorrhoeae penA. This contrasted with Neisseria meningitidis penA, for which the primary source of recombinant DNA was other meningococci, followed by Neisseria lactamica. Additionally, we described the distribution of polymorphisms implicated in antimicrobial resistance in penA, and found that these are present across the genus. These results provide insight into resistance-related changes in the penA gene across human-associated Neisseria species, illustrating the importance of genomic surveillance of not only the pathogenic Neisseria, but also of the oral niche-associated commensals from which these pathogens are sourcing key genetic variation.

RevDate: 2024-02-20

Pfeifer E, EPC Rocha (2024)

Phage-plasmids promote recombination and emergence of phages and plasmids.

Nature communications, 15(1):1545.

Phages and plasmids are regarded as distinct types of mobile genetic elements that drive bacterial evolution by horizontal gene transfer. However, the distinction between both types is blurred by the existence of elements known as prophage-plasmids or phage-plasmids, which transfer horizontally between cells as viruses and vertically within cellular lineages as plasmids. Here, we study gene flow between the three types of elements. We show that the gene repertoire of phage-plasmids overlaps with those of phages and plasmids. By tracking recent recombination events, we find that phage-plasmids exchange genes more frequently with plasmids than with phages, and that direct gene exchange between plasmids and phages is less frequent in comparison. The results suggest that phage-plasmids can mediate gene flow between plasmids and phages, including exchange of mobile element core functions, defense systems, and antibiotic resistance. Moreover, a combination of gene transfer and gene inactivation may result in the conversion of elements. For example, gene loss turns P1-like phage-plasmids into integrative prophages or into plasmids (that are no longer phages). Remarkably, some of the latter have acquired conjugation-related functions to became mobilisable by conjugation. Thus, our work indicates that phage-plasmids can play a key role in the transfer of genes across mobile elements within their hosts, and can act as intermediates in the conversion of one type of element into another.

RevDate: 2024-02-20

Saini P, Bandsode V, Singh A, et al (2024)

Genomic insights into virulence, antimicrobial resistance, and adaptation acumen of Escherichia coli isolated from an urban environment.

mBio [Epub ahead of print].

Populations of common commensal bacteria such as Escherichia coli undergo genetic changes by the acquisition of certain virulence and antimicrobial resistance (AMR) encoding genetic elements leading to the emergence of pathogenic strains capable of surviving in the previously uninhabited or protected niches. These bacteria are also reported to be prevalent in the environment where they survive by adopting various recombination strategies to counter microflora of the soil and water, under constant selection pressure(s). In this study, we performed molecular characterization, phenotypic AMR analysis, and whole genome sequencing (WGS) of E. coli (n = 37) isolated from soil and surface water representing the urban and peri-urban areas. The primary aim of this study was to understand the genetic architecture and pathogenic acumen exhibited by environmental E. coli. WGS-based analysis entailing resistome and virulome profiling indicated the presence of various virulence (adherence, iron uptake, and toxins) and AMR encoding genes, including blaNDM-5 in the environmental isolates. A majority of our isolates belonged to phylogroup B1 (73%). A few isolates in our collection were of sequence type(s) (ST) 58 and 224 that could have emerged recently as clonal lineages and might pose risk of infection/transmission. Mobile genetic elements (MGEs) such as plasmids (predominantly) of the IncF family, prophages, pipolins, and insertion elements such as IS1 and IS5 were also observed to exist, which may presumably aid in the propagation of genes encoding resistance against antimicrobial drugs. The observed high prevalence of MGEs associated with multidrug resistance in pathogenic E. coli isolates belonging to the phylogroup B1 underscores the need for extended surveillance to keep track of and prevent the transmission of the bacterium to certain vulnerable human and animal populations.IMPORTANCEEvolutionary patterns of E. coli bacteria convey that they evolve into highly pathogenic forms by acquiring fitness advantages, such as AMR, and various virulence factors through the horizontal gene transfer (HGT)-mediated acquisition of MGEs. However, limited research on the genetic profiles of environmental E. coli, particularly from India, hinders our understanding of their transition to pathogenic forms and impedes the adoption of a comprehensive approach to address the connection between environmentally dwelling E. coli populations and human and veterinary public health. This study focuses on high-resolution genomic analysis of the environmental E. coli isolates aiming to understand the genetic similarities and differences among isolates from different environmental niches and uncover the survival strategies employed by these bacteria to thrive in their surroundings. Our approach involved molecular characterization of environmental samples using PCR-based DNA fingerprinting and subsequent WGS analysis. This multidisciplinary approach is likely to provide valuable insights into the understanding of any potential spill-over to human and animal populations and locales. Investigating these environmental isolates has significant potential for developing epidemiological strategies against transmission and understanding niche-specific evolutionary patterns.

RevDate: 2024-02-21
CmpDate: 2024-02-21

Fox BW, Helf MJ, Burkhardt RN, et al (2024)

Evolutionarily related host and microbial pathways regulate fat desaturation in C. elegans.

Nature communications, 15(1):1520.

Fatty acid desaturation is central to metazoan lipid metabolism and provides building blocks of membrane lipids and precursors of diverse signaling molecules. Nutritional conditions and associated microbiota regulate desaturase expression, but the underlying mechanisms have remained unclear. Here, we show that endogenous and microbiota-dependent small molecule signals promote lipid desaturation via the nuclear receptor NHR-49/PPARα in C. elegans. Untargeted metabolomics of a β-oxidation mutant, acdh-11, in which expression of the stearoyl-CoA desaturase FAT-7/SCD1 is constitutively increased, revealed accumulation of a β-cyclopropyl fatty acid, becyp#1, that potently activates fat-7 expression via NHR-49. Biosynthesis of becyp#1 is strictly dependent on expression of cyclopropane synthase by associated bacteria, e.g., E. coli. Screening for structurally related endogenous metabolites revealed a β-methyl fatty acid, bemeth#1, which mimics the activity of microbiota-dependent becyp#1 but is derived from a methyltransferase, fcmt-1, that is conserved across Nematoda and likely originates from bacterial cyclopropane synthase via ancient horizontal gene transfer. Activation of fat-7 expression by these structurally similar metabolites is controlled by distinct mechanisms, as microbiota-dependent becyp#1 is metabolized by a dedicated β-oxidation pathway, while the endogenous bemeth#1 is metabolized via α-oxidation. Collectively, we demonstrate that evolutionarily related biosynthetic pathways in metazoan host and associated microbiota converge on NHR-49/PPARα to regulate fat desaturation.

RevDate: 2024-02-19

Zhao S, Rogers MJ, Ding C, et al (2024)

Interspecies Mobility of Organohalide Respiration Gene Clusters Enables Genetic Bioaugmentation.

Environmental science & technology [Epub ahead of print].

Anthropogenic organohalide pollutants pose a severe threat to public health and ecosystems. In situ bioremediation using organohalide respiring bacteria (OHRB) offers an environmentally friendly and cost-efficient strategy for decontaminating organohalide-polluted sites. The genomic structures of many OHRB suggest that dehalogenation traits can be horizontally transferred among microbial populations, but their occurrence among anaerobic OHRB has not yet been demonstrated experimentally. This study isolates and characterizes a novel tetrachloroethene (PCE)-dechlorinating Sulfurospirillum sp. strain SP, distinguishing itself among anaerobic OHRB by showcasing a mechanism essential for horizontal dissemination of reductive dehalogenation capabilities within microbial populations. Its genetic characterization identifies a unique plasmid (pSULSP), harboring reductive dehalogenase and de novo corrinoid biosynthesis operons, functions critical to organohalide respiration, flanked by mobile elements. The active mobility of these elements was demonstrated through genetic analyses of spontaneously emerging nondehalogenating variants of strain SP. More importantly, bioaugmentation of nondehalogenating microcosms with pSULSP DNA triggered anaerobic PCE dechlorination in taxonomically diverse bacterial populations. Our results directly support the hypothesis that exposure to anthropogenic organohalide pollutants can drive the emergence of dehalogenating microbial populations via horizontal gene transfer and demonstrate a mechanism by which genetic bioaugmentation for remediation of organohalide pollutants could be achieved in anaerobic environments.

RevDate: 2024-02-19

Lehnert T, MAM Gijs (2024)

Microfluidic systems for infectious disease diagnostics.

Lab on a chip [Epub ahead of print].

Microorganisms, encompassing both uni- and multicellular entities, exhibit remarkable diversity as omnipresent life forms in nature. They play a pivotal role by supplying essential components for sustaining biological processes across diverse ecosystems, including higher host organisms. The complex interactions within the human gut microbiota are crucial for metabolic functions, immune responses, and biochemical signalling, particularly through the gut-brain axis. Viruses also play important roles in biological processes, for example by increasing genetic diversity through horizontal gene transfer when replicating inside living cells. On the other hand, infection of the human body by microbiological agents may lead to severe physiological disorders and diseases. Infectious diseases pose a significant burden on global healthcare systems, characterized by substantial variations in the epidemiological landscape. Fast spreading antibiotic resistance or uncontrolled outbreaks of communicable diseases are major challenges at present. Furthermore, delivering field-proven point-of-care diagnostic tools to the most severely affected populations in low-resource settings is particularly important and challenging. New paradigms and technological approaches enabling rapid and informed disease management need to be implemented. In this respect, infectious disease diagnostics taking advantage of microfluidic systems combined with integrated biosensor-based pathogen detection offers a host of innovative and promising solutions. In this review, we aim to outline recent activities and progress in the development of microfluidic diagnostic tools. Our literature research mainly covers the last 5 years. We will follow a classification scheme based on the human body systems primarily involved at the clinical level or on specific pathogen transmission modes. Important diseases, such as tuberculosis and malaria, will be addressed more extensively.

RevDate: 2024-02-20

Han X, Zhou J, Yu L, et al (2024)

Genome sequencing unveils blaKPC-2-harboring plasmids as drivers of enhanced resistance and virulence in nosocomial Klebsiella pneumoniae.

mSystems, 9(2):e0092423.

The threat posed by Klebsiella pneumoniae in healthcare settings has worsened due to the evolutionary advantages conferred by blaKPC-2-harboring plasmids (pKPC-2). However, the specific evolutionary pathway of nosocomial K. pneumoniae carrying pKPC-2 and its transmission between patients and healthcare environments are not yet well understood. Between 1 August and 31 December 2019, 237 ST11 KPC-2-producing-carbapenem-resistant K. pneumoniae (CRKP) (KPC-2-CRKP) were collected from patient or ward environments in an intensive care unit and subjected to Illumina sequencing, of which 32 strains were additionally selected for Nanopore sequencing to obtain complete plasmid sequences. Bioinformatics analysis, conjugation experiments, antimicrobial susceptibility tests, and virulence assays were performed to identify the evolutionary characteristics of pKPC-2. The pKPC-2 plasmids were divided into three subgroups with distinct evolutionary events, including Tn3-mediated plasmid homologous recombination, IS26-mediated horizontal gene transfer, and dynamic duplications of antibiotic resistance genes (ARGs). Surprisingly, the incidence rates of multicopy blaKPC-2, blaSHV-12, and blaCTX-M-65 were quite high (ranging from 27.43% to 67.01%), and strains negative for extended-spectrum β-lactamase tended to develop multicopy blaKPC-2. Notably, the presence of multicopy blaSHV-12 reduced sensitivity to ceftazidime/avibactam (CZA), and the relative expression level of blaSHV-12 in the CZA-resistant group was 6.12 times higher than that in the sensitive group. Furthermore, a novel hybrid pKPC-2 was identified, presenting enhanced virulence levels and decreased susceptibility to CZA. This study emphasizes the notable prevalence of multicopy ARGs and provides a comprehensive insight into the intricate and diverse evolutionary pathways of resistant plasmids that disseminate among patients and healthcare environments.IMPORTANCEThis study is based on a CRKP screening program between patients and ward environments in an intensive care unit, describing the pKPC-2 (blaKPC-2-harboring plasmids) population structure and evolutionary characteristics in clinical settings. Long-read sequencing was performed in genetically closely related strains, enabling the high-resolution analysis of evolution pathway between or within pKPC-2 subgroups. We revealed the extremely high rates of multicopy antibiotic resistance genes (ARGs) in clinical settings and its effect on resistance profile toward novel β-lactam/β-lactamase inhibitor combinations, which belongs to the last line treatment choices toward CRKP infection. A novel hybrid pKPC-2 carrying CRKP with enhanced resistance and virulence level was captured during its clonal spread between patients and ward environment. These evidences highlight the threat of pKPC-2 to CRKP treatment and control. Thus, surveillance and timely disinfection in clinical settings should be practiced to prevent transmission of CRKP carrying threatful pKPC-2. And rational use of antibiotics should be called for to prevent inducing of pKPC-2 evolution, especially the multicopy ARGs.

RevDate: 2024-02-19

Yuan C, An T, Li X, et al (2023)

Genomic analysis of Ralstonia pickettii reveals the genetic features for potential pathogenicity and adaptive evolution in drinking water.

Frontiers in microbiology, 14:1272636.

Ralstonia pickettii, the most critical clinical pathogen of the genus Ralstonia, has been identified as a causative agent of numerous harmful infections. Additionally, Ralstonia pickettii demonstrates adaptability to extreme environmental conditions, such as those found in drinking water. In this study, we conducted a comprehensive genomic analysis to investigate the genomic characteristics related to potential pathogenicity and adaptive evolution in drinking water environments of Ralstonia pickettii. Through phylogenetic analysis and population genetic analysis, we divided Ralstonia pickettii into five Groups, two of which were associated with drinking water environments. The open pan-genome with a large and flexible gene repertoire indicated a high genetic plasticity. Significant differences in functional enrichment were observed between the core- and pan-genome of different groups. Diverse mobile genetic elements (MGEs), extensive genomic rearrangements, and horizontal gene transfer (HGT) events played a crucial role in generating genetic diversity. In drinking water environments, Ralstonia pickettii exhibited strong adaptability, and the acquisition of specific adaptive genes was potentially facilitated by genomic islands (GIs) and HGT. Furthermore, environmental pressures drove the adaptive evolution of Ralstonia pickettii, leading to the accumulation of unique mutations in key genes. These mutations may have a significant impact on various physiological functions, particularly carbon metabolism and energy metabolism. The presence of virulence-related elements associated with macromolecular secretion systems, virulence factors, and antimicrobial resistance indicated the potential pathogenicity of Ralstonia pickettii, making it capable of causing multiple nosocomial infections. This study provides comprehensive insights into the potential pathogenicity and adaptive evolution of Ralstonia pickettii in drinking water environments from a genomic perspective.

RevDate: 2024-02-18

Wang T, Xu Y, Ling W, et al (2024)

Dissemination of antibiotic resistance genes is regulated by iron oxides: Insight into the influence on bacterial transformation.

Environment international, 185:108499 pii:S0160-4120(24)00085-0 [Epub ahead of print].

The transportation of antibiotic resistance genes (ARGs) in manure-soil-plant continuums poses risks to human health. Horizontal gene transfer, particularly for bacterial transformation, is an important way for ARG dissemination. As crucial components in soils, iron oxides impacted the fates of various abiotic and biotic contaminants due to their active properties. However, whether they can influence the transformation of ARGs is unknown, which waits to be figured out to boost the assessment and control of ARG spread risks. In this study, we have investigated the effects of goethite, hematite, and magnetite (0-250 mg/L, with sizes < 100 nm and > 100 nm) on the transfer of ampicillin resistance genes to Escherichia coli cells. At lower iron oxide concentrations, the transformation of ARGs was first facilitated (transformation frequency reached up to 3.38-fold higher), but the facilitating effects gradually weakened and eventually disappeared as concentrations further increased. Particle size and iron oxide type were not the universal determinants controlling the transformation. At lower concentrations, iron oxides interacted with proteins and phospholipids in E. coli envelope structures, and induced the overgeneration of intracellular reactive oxygen species. Consequently, they led to pore formation and permeability enhancement on the cell membrane, thus promoting the transformation. The facilitation was also associated with the carrier-like effect of iron oxides for antibiotic resistance plasmids. At higher concentrations, the weakened facilitations were attributed to the aggregation of iron oxides. In this study, we highlight the crucial roles of the concentrations (contents) of iron oxides on the dissemination of ARGs in soils; this study may serve as a reference for ARG pollution control in future agricultural production.

RevDate: 2024-02-18

Zheng W, Teng X, Jiang T, et al (2024)

Genome analysis of a novel avian atadenovirus reveals a possible horizontal gene transfer.

Virology, 593:109999 pii:S0042-6822(24)00020-5 [Epub ahead of print].

We report the discovery and characterization of a novel adenovirus, Zoothera dauma adenovirus (ZdAdV), from a wild bird species, Zoothera dauma (Scaly thrush). This new atadenovirus was discovered by metagenomic sequencing without virus cultivation. Analyses of the full genome sequence revealed that this new virus is a distinct member of the genus Atadenovirus and represents a novel species. ZdAdV has a genome of 34,760 bp with 28 predicted genes and 39% GC content. ZdAdV is the first atadenovirus to contain ORF19, a gene previously found only in aviadenoviruses. Phylogenetic analysis of ORF19 suggests that it was acquired by ZdAdV through horizontal gene transfer from an aviadenovirus. By analyzing all orthologous genes of aviadenovirus, mastadenovirus, atadenovirus, and siadenovirus, we also found potential horizontal gene transfer for the E4 gene in Pigeon aviadenovirus B. Our study widens our knowledge concerning the genetic diversity and evolutionary history of atadenoviruses and their potential for cross-species transmission.

RevDate: 2024-02-17

Liu Q, Jia J, Hu H, et al (2024)

Nitrogen and phosphorus limitations promoted bacterial nitrate metabolism and propagation of antibiotic resistome in the phycosphere of Auxenochlorella pyrenoidosa.

Journal of hazardous materials, 468:133786 pii:S0304-3894(24)00365-0 [Epub ahead of print].

Despite that nitrogen (N) and phosphorus (P) play critical roles in the lifecycle of microalgae, how N and P further affect the distribution of bacteria and antibiotic resistance genes (ARGs) in the phycosphere is still poorly understood. In this study, the effects of N and P on the distribution of ARGs in the phycosphere of Auxenochlorella pyrenoidosa were investigated. Results showed that the growth and chlorophyll synthesis of microalgae were inhibited when N or P was limited, regardless of the N/P ratios, but the extracellular polymeric substances content and nitrate assimilation efficiency were enhanced in contrast. Metagenomic sequencing revealed that N or P limitation resulted in the recruitment of specific bacteria that highly contribute to the nitrate metabolism in the phycosphere. Besides, N or P limitation promoted the propagation of phycosphere ARGs, primarily through horizontal gene transfer mediated by mobile genetic elements. The enrichment of specific bacteria induced by changes in the algal physiology also contributed to the ARGs proliferation under nutrient limitation. Our results demonstrated that the reduction of algal cells caused by nutrient limitation could promote the propagation of ARGs, which provides new insights into the occurrence and spread of ARGs in the phycosphere.

RevDate: 2024-02-17

Ko I, Kranse OP, Senatori B, et al (2024)

A critical appraisal of DNA transfer from plants to parasitic cyst nematodes.

Molecular biology and evolution pii:7608856 [Epub ahead of print].

Plant-parasitic nematodes are one of the most economically important pests of crops. It is widely accepted that Horizontal Gene Transfer (HGT) - the natural acquisition of foreign genes in parasitic nematodes - contributes to parasitism. However, an apparent paradox has emerged from HGT analyses: On one hand, distantly related organisms with very dissimilar genetic structures (i.e. bacteria), and only transient interactions with nematodes as far as we know, dominate the list of putative donors; while on the other hand, considerably more closely related organism (i.e. the host plant), with similar genetic structure (i.e. introns) and documented long-term associations with nematodes, are rare among the list of putative donors. Given that these nematodes ingest cytoplasm from a living plant cell for several weeks, there seems to be a conspicuous absence of plant-derived cases. Here we used comparative genomic approaches to evaluate possible plant-derived HGT events in plant parasitic nematodes. Our evidence supports a cautionary message for plant-derived HGT cases in the sugar beet cyst nematode, Heterodera schachtii. We propose a four step model for HGT from plant to parasite in order to evaluate why the absence of plant-derived HGT cases is observed. We find that the plant genome is mobilised by the nematode during infection, but that uptake of said "mobilome" is the first major barrier to HGT from host to nematode. These results provide new insight into our understanding of the prevalence/role of nucleic acids exchange in the arms race between plants and plant parasites.

RevDate: 2024-02-17

Zhao D, Zhang S, Chen J, et al (2024)

Members of the class Candidatus Ordosarchaeia imply an alternative evolutionary scenario from methanogens to haloarchaea.

The ISME journal pii:7513321 [Epub ahead of print].

The origin of methanogenesis can be traced to the common ancestor of non-DPANN archaea, whereas haloarchaea (or Halobacteria) are believed to have evolved from a methanogenic ancestor through multiple evolutionary events, including the loss of genes associated with methanogenesis. However, due to the accelerated evolution and compositional bias of proteins adapting to hypersaline habitats, Halobacteria exhibit substantial evolutionary divergence from methanogens, and the identification of the closest methanogen (either Methanonatronarchaeia or other related taxa) to Halobacteria remains a subject of debate. Here, we obtained five metagenome-assembled genomes with high completeness from soda-saline lakes on the Ordos Plateau in Inner Mongolia, China, and we proposed the name Candidatus Ordosarchaeia for this novel class. Phylogenetic analyses revealed that Ca. Ordosarchaeia is firmly positioned near the median position between the Methanonatronarchaeia and Halobacteria-Hikarchaeia lineages. Functional predictions supported the transitional status of Ca. Ordosarchaeia with the metabolic potential of nonmethanogenic and aerobic chemoheterotrophy, as did remnants of the gene sequences of methylamine/dimethylamine/trimethylamine metabolism and coenzyme M biosynthesis. Based on the similarity of the methyl-coenzyme M reductase genes mcrBGADC in Methanonatronarchaeia with the phylogenetically distant methanogens, an alternative evolutionary scenario is proposed, in which Methanonatronarchaeia, Ca. Ordosarchaeia, Ca. Hikarchaeia and Halobacteria share a common ancestor that initially lost mcr genes. However, certain members of Methanonatronarchaeia subsequently acquired mcr genes through horizontal gene transfer from distantly related methanogens. This hypothesis is supported by amalgamated likelihood estimation, phylogenetic analysis, and gene arrangement patterns. Altogether, Ca. Ordosarchaeia genomes clarify the sisterhood of Methanonatronarchaeia with Halobacteria and provide new insights into the evolution from methanogens to haloarchaea.

RevDate: 2024-02-17

Wang X, Zhang H, Yu S, et al (2024)

Inter-plasmid transfer of antibiotic resistance genes accelerates antibiotic resistance in bacterial pathogens.

The ISME journal pii:7513094 [Epub ahead of print].

Antimicrobial resistance (AMR) is a major threat for public health. Plasmids play a critical role in the spread of AMR via horizontal gene transfer between bacterial species. However, it remains unclear how plasmids originally recruit and assemble various antibiotic resistance genes (ARGs). Here, we track ARG recruitment and assembly in clinically relevant plasmids by combining a systematic analysis of 2420 complete plasmid genomes and experimental validation. Results showed that ARG transfer across plasmids is prevalent, 87% ARGs were observed to potentially transfer among various plasmids among 8229 plasmid-borne ARGs. Interestingly, recruitment and assembly of ARGs occurs mostly among compatible plasmids within the same bacterial cell, with over 88% of ARG transfers occurring between compatible plasmids. Integron and insertion sequences drive the ongoing ARG acquisition by plasmids, especially in which IS26 facilitates 63.1% of ARG transfer events among plasmids. In vitro experiment validated the important role of IS26 involved in transferring gentamicin resistance gene aacC1 between compatible plasmids. Multilevel network analysis showed four beta-lactam genes (blaTEM-1, blaNDM-4, blaKPC-2, and blaSHV-1) shuffling among 1029 plasmids and 45 clinical pathogens, suggesting that clinically alarming ARGs transferred accelerate the propagation of antibiotic resistance in clinical pathogens. ARGs in plasmids are also able to transmit across clinical and environmental boundaries, in terms of the high sequence similarities of plasmid-borne ARGs between clinical and environmental plasmids. This study demonstrated that inter-plasmid ARG transfer is a universal mechanism for plasmid to recruit various ARGs, thus advancing our understanding of the emergence of multi-drug resistant plasmids.

RevDate: 2024-02-17

Takeuchi N, Fullmer MS, Maddock DJ, et al (2024)

The constructive black queen hypothesis: new functions can evolve under conditions favouring gene loss.

The ISME journal pii:7585950 [Epub ahead of print].

Duplication is a major route for emergence of new gene functions. However, emergence of new gene function via this route may be reduced in prokaryotes, as redundant genes are often rapidly purged. In lineages with compact, streamlined genomes, it thus appears challenging for novel function to emerge via duplication and divergence. A further pressure contributing to gene loss occurs under Black Queen dynamics, as cheaters that lose the capacity to produce a public good can instead acquire it from neighbouring producers. We propose that Black Queen dynamics can favour the emergence of new function because under an emerging Black Queen dynamic there is high gene redundancy, spread across a community of interacting cells. Using computational modelling, we demonstrate that new gene functions can emerge under Black Queen dynamics. This result holds even if there is deletion bias due to low duplication rates and selection against redundant gene copies resulting from the high cost associated with carrying a locus. However, when the public good production costs are high, Black Queen dynamics impede fixation of new function. Our results expand the mechanisms by which new gene function can emerge in prokaryotic systems.

RevDate: 2024-02-16

Maddamsetti R, Yao Y, Wang T, et al (2024)

Duplicated antibiotic resistance genes reveal ongoing selection and horizontal gene transfer in bacteria.

Nature communications, 15(1):1449.

Horizontal gene transfer (HGT) and gene duplication are often considered as separate mechanisms driving the evolution of new functions. However, the mobile genetic elements (MGEs) implicated in HGT can copy themselves, so positive selection on MGEs could drive gene duplications. Here, we use a combination of modeling and experimental evolution to examine this hypothesis and use long-read genome sequences of tens of thousands of bacterial isolates to examine its generality in nature. Modeling and experiments show that antibiotic selection can drive the evolution of duplicated antibiotic resistance genes (ARGs) through MGE transposition. A key implication is that duplicated ARGs should be enriched in environments associated with antibiotic use. To test this, we examined the distribution of duplicated ARGs in 18,938 complete bacterial genomes with ecological metadata. Duplicated ARGs are highly enriched in bacteria isolated from humans and livestock. Duplicated ARGs are further enriched in an independent set of 321 antibiotic-resistant clinical isolates. Our findings indicate that duplicated genes often encode functions undergoing positive selection and horizontal gene transfer in microbial communities.

RevDate: 2024-02-16

Holert J, Borker A, Nübel LL, et al (2024)

Bacteria use a catabolic patchwork pathway of apparently recent origin for degradation of the synthetic buffer compound TRIS.

The ISME journal, 18(1):.

The synthetic buffer compound TRIS (2-amino-2-(hydroxymethyl)propane-1,3-diol) is used in countless applications, and no detailed information on its degradation has been published so far. Herein, we describe the discovery of a complete bacterial degradation pathway for TRIS. By serendipity, a Pseudomonas strain was isolated from sewage sludge that was able to grow with TRIS as only carbon and nitrogen source. Genome and transcriptome analyses revealed two adjacent gene clusters embedded in a mobile genetic element on a conjugative plasmid to be involved in TRIS degradation. Heterologous gene expression revealed cluster I to encode a TRIS uptake protein, a TRIS alcohol dehydrogenase, and a TRIS aldehyde dehydrogenase, catalyzing the oxidation of TRIS into 2-hydroxymethylserine. Gene cluster II encodes a methylserine hydroxymethyltransferase (mSHMT) and a d-serine dehydratase that plausibly catalyze the conversion of 2-hydroxymethylserine into pyruvate. Conjugational plasmid transfer into Pseudomonas putida KT2440 enabled this strain to grow with TRIS and with 2-hydromethylserine, demonstrating that the complete TRIS degradation pathway can be transmitted by horizontal gene transfer. Subsequent enrichments from wastewater purification systems led to the isolation of further TRIS-degrading bacteria from the Pseudomonas and Shinella genera carrying highly similar TRIS degradation gene clusters. Our data indicate that TRIS degradation evolved recently via gene recruitment and enzyme adaptation from multiple independent metabolic pathways, and database searches suggest that the TRIS degradation pathway is now globally distributed. Overall, our study illustrates how engineered environments can enhance the emergence of new microbial metabolic pathways in short evolutionary time scales.

RevDate: 2024-02-16

Zheng Y, Wang B, Gao P, et al (2024)

Novel order-level lineage of ammonia-oxidizing archaea widespread in marine and terrestrial environments.

The ISME journal, 18(1):.

Ammonia-oxidizing archaea (AOA) are among the most ubiquitous and abundant archaea on Earth, widely distributed in marine, terrestrial, and geothermal ecosystems. However, the genomic diversity, biogeography, and evolutionary process of AOA populations in subsurface environments are vastly understudied compared to those in marine and soil systems. Here, we report a novel AOA order Candidatus (Ca.) Nitrosomirales which forms a sister lineage to the thermophilic Ca. Nitrosocaldales. Metagenomic and 16S rRNA gene-read mapping demonstrates the abundant presence of Nitrosomirales AOA in various groundwater environments and their widespread distribution across a range of geothermal, terrestrial, and marine habitats. Terrestrial Nitrosomirales AOA show the genetic capacity of using formate as a source of reductant and using nitrate as an alternative electron acceptor. Nitrosomirales AOA appear to have acquired key metabolic genes and operons from other mesophilic populations via horizontal gene transfer, including genes encoding urease, nitrite reductase, and V-type ATPase. The additional metabolic versatility conferred by acquired functions may have facilitated their radiation into a variety of subsurface, marine, and soil environments. We also provide evidence that each of the four AOA orders spans both marine and terrestrial habitats, which suggests a more complex evolutionary history for major AOA lineages than previously proposed. Together, these findings establish a robust phylogenomic framework of AOA and provide new insights into the ecology and adaptation of this globally abundant functional guild.

RevDate: 2024-02-16

Kolan D, Cattan-Tsaushu E, Enav H, et al (2024)

Tradeoffs between phage resistance and nitrogen fixation drive the evolution of genes essential for cyanobacterial heterocyst functionality.

The ISME journal, 18(1):.

Harmful blooms caused by diazotrophic (nitrogen-fixing) Cyanobacteria are becoming increasingly frequent and negatively impact aquatic environments worldwide. Cyanophages (viruses infecting Cyanobacteria) can potentially regulate cyanobacterial blooms, yet Cyanobacteria can rapidly acquire mutations that provide protection against phage infection. Here, we provide novel insights into cyanophage:Cyanobacteria interactions by characterizing the resistance to phages in two species of diazotrophic Cyanobacteria: Nostoc sp. and Cylindrospermopsis raciborskii. Our results demonstrate that phage resistance is associated with a fitness tradeoff by which resistant Cyanobacteria have reduced ability to fix nitrogen and/or to survive nitrogen starvation. Furthermore, we use whole-genome sequence analysis of 58 Nostoc-resistant strains to identify several mutations associated with phage resistance, including in cell surface-related genes and regulatory genes involved in the development and function of heterocysts (cells specialized in nitrogen fixation). Finally, we employ phylogenetic analyses to show that most of these resistance genes are accessory genes whose evolution is impacted by lateral gene transfer events. Together, these results further our understanding of the interplay between diazotrophic Cyanobacteria and their phages and suggest that a tradeoff between phage resistance and nitrogen fixation affects the evolution of cell surface-related genes and of genes involved in heterocyst differentiation and nitrogen fixation.

RevDate: 2024-02-17

Zhang S, Yang C, Qiu Y, et al (2024)

Conserved untranslated regions of multipartite viruses: Natural markers of novel viral genomic components and tags of viral evolution.

Virus evolution, 10(1):veae004.

Viruses with split genomes are classified as being either segmented or multipartite based on whether their genomic segments occur within a single virion or across different virions. Despite variations in number and sequence during evolution, the genomic segments of many viruses are conserved within the untranslated regions (UTRs). In this study, we present a methodology that combines RNA sequencing with iterative BLASTn of UTRs (https://github.com/qq371260/Iterative-blast-v.1.0) to identify new viral genomic segments. Some novel multipartite-like viruses related to the phylum Kitrinoviricota were annotated using sequencing data from field plant samples and public databases. We identified potentially plant-infecting jingmen-related viruses (order Amarillovirales) and jivi-related viruses (order Martellivirales) with at least six genomic components. The number of RNA molecules associated with a genome of the novel viruses in the families Closteroviridae, Kitaviridae, and Virgaviridae within the order Martellivirales reached five. Several of these viruses seem to represent new taxa at the subgenus, genus, and family levels. The diversity of novel genomic components and the multiple duplication of proteins or protein domains within single or multiple genomic components emphasize the evolutionary roles of genetic recombination (horizontal gene transfer), reassortment, and deletion. The relatively conserved UTRs at the genome level might explain the relationships between monopartite and multipartite viruses, as well as how subviral agents such as defective RNAs and satellite viruses can coexist with their helper viruses.

RevDate: 2024-02-14

Curry KD, Yu FB, Vance SE, et al (2024)

Reference-free Structural Variant Detection in Microbiomes via Long-read Coassembly Graphs.

bioRxiv : the preprint server for biology pii:2024.01.25.577285.

Bacterial genome dynamics are vital for understanding the mechanisms underlying microbial adaptation, growth, and their broader impact on host phenotype. Structural variants (SVs), genomic alterations of 10 base pairs or more, play a pivotal role in driving evolutionary processes and maintaining genomic heterogeneity within bacterial populations. While SV detection in isolate genomes is relatively straightforward, metagenomes present broader challenges due to absence of clear reference genomes and presence of mixed strains. In response, our proposed method rhea, forgoes reference genomes and metagenome-assembled genomes (MAGs) by encompassing a single metagenome coassembly graph constructed from all samples in a series. The log fold change in graph coverage between subsequent samples is then calculated to call SVs that are thriving or declining throughout the series. We show rhea to outperform existing methods for SV and horizontal gene transfer (HGT) detection in two simulated mock metagenomes, which is particularly noticeable as the simulated reads diverge from reference genomes and an increase in strain diversity is incorporated. We additionally demonstrate use cases for rhea on series metagenomic data of environmental and fermented food microbiomes to detect specific sequence alterations between subsequent time and temperature samples, suggesting host advantage. Our innovative approach leverages raw read patterns rather than references or MAGs to include all sequencing reads in analysis, and thus provide versatility in studying SVs across diverse and poorly characterized microbial communities for more comprehensive insights into microbial genome dynamics.

RevDate: 2024-02-16
CmpDate: 2024-02-15

Arbulu S, M Kjos (2024)

Revisiting the Multifaceted Roles of Bacteriocins : The Multifaceted Roles of Bacteriocins.

Microbial ecology, 87(1):41.

Bacteriocins are gene-encoded antimicrobial peptides produced by bacteria. These peptides are heterogeneous in terms of structure, antimicrobial activities, biosynthetic clusters, and regulatory mechanisms. Bacteriocins are widespread in nature and may contribute to microbial diversity due to their capacity to target specific bacteria. Primarily studied as food preservatives and therapeutic agents, their function in natural settings is however less known. This review emphasizes the ecological significance of bacteriocins as multifunctional peptides by exploring bacteriocin distribution, mobility, and their impact on bacterial population dynamics and biofilms.

RevDate: 2024-02-14
CmpDate: 2024-02-14

Neil B, Cheney GL, Rosenzweig JA, et al (2024)

Antimicrobial resistance in aeromonads and new therapies targeting quorum sensing.

Applied microbiology and biotechnology, 108(1):205.

Aeromonas species (spp.) are well-known fish pathogens, several of which have been recognized as emerging human pathogens. The organism is capable of causing a wide spectrum of diseases in humans, ranging from gastroenteritis, wound infections, and septicemia to devastating necrotizing fasciitis. The systemic form of infection is often fatal, particularly in patients with underlying chronic diseases. Indeed, recent trends demonstrate rising numbers of hospital-acquired Aeromonas infections, especially in immuno-compromised individuals. Additionally, Aeromonas-associated antibiotic resistance is an increasing challenge in combating both fish and human infections. The acquisition of antibiotic resistance is related to Aeromonas' innate transformative properties including its ability to share plasmids and integron-related gene cassettes between species and with the environment. As a result, alternatives to antibiotic treatments are desperately needed. In that vein, many treatments have been proposed and studied extensively in the fish-farming industry, including treatments that target Aeromonas quorum sensing. In this review, we discuss current strategies targeting quorum sensing inhibition and propose that such studies empower the development of novel chemotherapeutic approaches to combat drug-resistant Aeromonas spp. infections in humans. KEY POINTS: • Aeromonas notoriously acquires and maintains antimicrobial resistance, making treatment options limited. • Quorum sensing is an essential virulence mechanism in Aeromonas infections. • Inhibiting quorum sensing can be an effective strategy in combating Aeromonas infections in animals and humans.

RevDate: 2024-02-14
CmpDate: 2024-02-14

Bernabeu M, Cabello-Yeves E, Flores E, et al (2024)

Role of vertical and horizontal microbial transmission of antimicrobial resistance genes in early life: insights from maternal-infant dyads.

Current opinion in microbiology, 77:102424.

Early life represents a critical window for metabolic, cognitive and immune system development, which is influenced by the maternal microbiome as well as the infant gut microbiome. Antibiotic exposure, mode of delivery and breastfeeding practices modulate the gut microbiome and the reservoir of antibiotic resistance genes (ARGs). Vertical and horizontal microbial gene transfer during early life and the mechanisms behind these transfers are being uncovered. In this review, we aim to provide an overview of the current knowledge on the transfer of antibiotic resistance in the mother-infant dyad through vertical and horizontal transmission and to highlight the main gaps and challenges in this area.

RevDate: 2024-02-14

Charubin K, Hill JD, ET Papoutsakis (2024)

DNA transfer between two different species mediated by heterologous cell fusion in Clostridium coculture.

mBio, 15(2):e0313323.

Prokaryotic evolution is driven by random mutations and horizontal gene transfer (HGT). HGT occurs via transformation, transduction, or conjugation. We have previously shown that in syntrophic cocultures of Clostridium acetobutylicum and Clostridium ljungdahlii, heterologous cell fusion leads to a large-scale exchange of proteins and RNA between the two organisms. Here, we present evidence that heterologous cell fusion facilitates the exchange of DNA between the two organisms. Using selective subculturing, we isolated C. acetobutylicum cells which acquired and integrated into their genome portions of plasmid DNA from a plasmid-carrying C. ljungdahlii strain. Limiting-dilution plating and DNA methylation data based on PacBio Single-Molecule Real Time (SMRT) sequencing support the existence of hybrid C. acetobutylicum/C. ljungdahlii cells. These findings expand our understanding of multi-species microbiomes, their survival strategies, and evolution.IMPORTANCEInvestigations of natural multispecies microbiomes and synthetic microbial cocultures are attracting renewed interest for their potential application in biotechnology, ecology, and medical fields. Previously, we have shown the syntrophic coculture of C. acetobutylicum and C. ljungdahlii undergoes heterologous cell-to-cell fusion, which facilitates the exchange of cytoplasmic protein and RNA between the two organisms. We now show that heterologous cell fusion between the two Clostridium organisms can facilitate the exchange of DNA. By applying selective pressures to this coculture system, we isolated clones of wild-type C. acetobutylicum which acquired the erythromycin resistance (erm) gene from the C. ljungdahlii strain carrying a plasmid with the erm gene. Single-molecule real-time sequencing revealed that the erm gene was integrated into the genome in a mosaic fashion. Our data also support the persistence of hybrid C. acetobutylicum/C. ljungdahlii cells displaying hybrid DNA-methylation patterns.

RevDate: 2024-02-14

Hofstaedter CE, Chandler CE, Met CM, et al (2024)

Divergent Pseudomonas aeruginosa LpxO enzymes perform site-specific lipid A 2-hydroxylation.

mBio, 15(2):e0282323.

Pseudomonas aeruginosa can survive in a myriad of environments, partially due to modifications of its lipid A, the membrane anchor of lipopolysaccharide. We previously demonstrated that divergent late acyltransferase paralogs, HtrB1 and HtrB2, add acyloxyacyl laurate to lipid A 2- and 2'-acyl chains, respectively. The genome of P. aeruginosa also has genes which encode two dioxygenase enzymes, LpxO1 and LpxO2, that individually hydroxylate a specific secondary laurate. LpxO1 acts on the 2'-acyloxyacyl laurate (added by HtrB2), whereas LpxO2 acts on the 2-acyloxyacyl laurate (added by HtrB1) in a site-specific manner. Furthermore, while both enzyme pairs are evolutionarily linked, phylogenomic analysis suggests the LpxO1/HtrB2 enzyme pair as being of ancestral origin, present throughout the Pseudomonas lineage, whereas the LpxO2/HtrB1 enzyme pair likely arose via horizontal gene transfer and has been retained in P. aeruginosa over time. Using a murine pulmonary infection model, we showed that both LpxO1 and LpxO2 enzymes are functional in vivo, as direct analysis of in vivo lipid A structure from bronchoalveolar lavage fluid revealed 2-hydroxylated lipid A. Gene expression analysis reveals increased lpxO2 but unchanged lpxO1 expression in vivo, suggesting differential regulation of these enzymes during infection. We also demonstrate that loss-of-function mutations arise in lpxO1 and lpxO2 during chronic lung infection in people with cystic fibrosis (CF), indicating a potential role for pathogenesis and airway adaptation. Collectively, our study characterizes lipid A 2-hydroxylation during P. aeruginosa airway infection that is regulated by two distinct lipid A dioxygenase enzymes.IMPORTANCEPseudomonas aeruginosa is an opportunistic pathogen that causes severe infection in hospitalized and chronically ill individuals. During infection, P. aeruginosa undergoes adaptive changes to evade host defenses and therapeutic interventions, increasing mortality and morbidity. Lipid A structural alteration is one such change that P. aeruginosa isolates undergo during chronic lung infection in CF. Investigating genetic drivers of this lipid A structural variation is crucial in understanding P. aeruginosa adaptation during infection. Here, we describe two lipid A dioxygenases with acyl-chain site specificity, each with different evolutionary origins. Further, we show that loss of function in these enzymes occurs in CF clinical isolates, suggesting a potential pathoadaptive phenotype. Studying these bacterial adaptations provides insight into selection pressures of the CF airway on P. aeruginosa phenotypes that persist during chronic infection. Understanding these adaptive changes may ultimately provide clinicians better control over bacterial populations during chronic infection.

RevDate: 2024-02-13

Vargas-Gastélum L, Romer AS, Ghotbi M, et al (2024)

Herptile gut microbiomes: a natural system to study multi-kingdom interactions between filamentous fungi and bacteria.

mSphere [Epub ahead of print].

Reptiles and amphibians (herptiles) are some of the most endangered and threatened species on the planet and numerous conservation strategies are being implemented with the goal of ensuring species recovery. Little is known, however, about the gut microbiome of wild herptiles and how it relates to the health of these populations. Here, we report results from the gut microbiome characterization of both a broad survey of herptiles, and the correlation between the fungus Basidiobolus, and the bacterial community supported by a deeper, more intensive sampling of Plethodon glutinosus, known as slimy salamanders. We demonstrate that bacterial communities sampled from frogs, lizards, and salamanders are structured by the host taxonomy and that Basidiobolus is a common and natural component of these wild gut microbiomes. Intensive sampling of multiple hosts across the ecoregions of Tennessee revealed that geography and host:geography interactions are strong predictors of distinct Basidiobolus operational taxonomic units present within a given host. Co-occurrence analyses of Basidiobolus and bacterial community diversity support a correlation and interaction between Basidiobolus and bacteria, suggesting that Basidiobolus may play a role in structuring the bacterial community. We further the hypothesis that this interaction is advanced by unique specialized metabolism originating from horizontal gene transfer from bacteria to Basidiobolus and demonstrate that Basidiobolus is capable of producing a diversity of specialized metabolites including small cyclic peptides.IMPORTANCEThis work significantly advances our understanding of biodiversity and microbial interactions in herptile microbiomes, the role that fungi play as a structural and functional members of herptile gut microbiomes, and the chemical functions that structure microbiome phenotypes. We also provide an important observational system of how the gut microbiome represents a unique environment that selects for novel metabolic functions through horizontal gene transfer between fungi and bacteria. Such studies are needed to better understand the complexity of gut microbiomes in nature and will inform conservation strategies for threatened species of herpetofauna.

RevDate: 2024-02-12

Behling AH, Wilson BC, Ho D, et al (2024)

Horizontal gene transfer after faecal microbiota transplantation in adolescents with obesity.

Microbiome, 12(1):26.

BACKGROUND: Horizontal gene transfer (HGT) describes the transmission of DNA outside of direct ancestral lineages. The process is best characterised within the bacterial kingdom and can enable the acquisition of genetic traits that support bacterial adaptation to novel niches. The adaptation of bacteria to novel niches has particular relevance for faecal microbiota transplantation (FMT), a therapeutic procedure which aims to resolve gut-related health conditions of individuals, through transplanted gut microbiota from healthy donors.

RESULTS: Three hundred eighty-one stool metagenomic samples from a placebo-controlled FMT trial for obese adolescents (the Gut Bugs Trial) were analysed for HGT, using two complementary methodologies. First, all putative HGT events, including historical HGT signatures, were quantified using the bioinformatics application WAAFLE. Second, metagenomic assembly and gene clustering were used to assess and quantify donor-specific genes transferred to recipients following the intervention. Both methodologies found no difference between the level of putative HGT events in the gut microbiomes of FMT and placebo recipients, post-intervention. HGT events facilitated by engrafted donor species in the FMT recipient gut at 6 weeks post-intervention were identified and characterised. Bacterial strains contributing to this subset of HGT events predominantly belonged to the phylum Bacteroidetes. Engraftment-dependent horizontally transferred genes were retained within recipient microbiomes at 12 and 26 weeks post-intervention.

CONCLUSION: Our study suggests that novel microorganisms introduced into the recipient gut following FMT have no impact on the basal rate of HGT within the human gut microbiome. Analyses of further FMT studies are required to assess the generalisability of this conclusion across different FMT study designs and for the treatment of different gut-related conditions. Video Abstract.

RevDate: 2024-02-11

Li Z, Guo X, Liu B, et al (2024)

Metagenome sequencing reveals shifts in phage-associated antibiotic resistance genes from influent to effluent in wastewater treatment plants.

Water research, 253:121289 pii:S0043-1354(24)00191-X [Epub ahead of print].

Antibiotic resistance poses a significant threat to global health, and the microbe-rich activated sludge environment may contribute to the dissemination of antibiotic resistance genes (ARGs). ARGs spread across various bacterial populations via multiple dissemination routes, including horizontal gene transfer mediated by bacteriophages (phages). However, the potential role of phages in spreading ARGs in wastewater treatment systems remains unclear. This study characterized the core resistome, mobile genetic elements (MGEs), and virus-associated ARGs (vir_ARGs) in influents (Inf) and effluents (Eff) samples from nine WWTPs in eastern China. The abundance of ARGs in the Inf samples was higher than that in the Eff samples. A total of 21 core ARGs were identified, accounting for 38.70 %-83.70 % of the different samples. There was an increase in MGEs associated with phage-related processes from influents to effluents (from 12.68 % to 21.10 %). These MGEs showed strong correlations in relative abundance and composition with the core ARGs in the Eff samples. Across the Inf and Eff samples, 58 unique vir_ARGs were detected, with the Eff samples exhibiting higher diversity of vir_ARGs than the Inf samples. Statistical analyses indicated a robust relationship between core ARG profile, MGEs associated with phage-related processes, and vir_ARG composition in the Eff samples. Additionally, the co-occurrence of MGEs and ARGs in viral genomes was observed, ranging from 22.73 % to 68.75 %. This co-occurrence may exacerbate the persistence and spread of ARGs within WWTPs. The findings present new information on the changes in core ARGs, MGEs, and phage-associated ARGs from influents to effluents in WWTPs and provide new insights into the role of phage-associated ARGs in these systems.

RevDate: 2024-02-10

Liu Z, Heng S, Dai Q, et al (2024)

Simultaneous removal of antibiotic resistance genes and improved dewatering ability of waste activated sludge by Fe(II)-activated persulfate oxidation.

Water research, 253:121265 pii:S0043-1354(24)00167-2 [Epub ahead of print].

Waste activated sludge properties vary widely with different regions due to the difference in living standards and geographical distribution, making a big challenge to developing a universally effective sludge dewatering technique. The Fe(II)-activated persulfate (S2O8[2-]) oxidation process shows excellent ability to disrupt sludge cells and extracellular polymeric substances (EPS), and release bound water from sludge flocs. In this study, the discrepancies in the physicochemical characteristics of sludge samples from seven representative cities in China (e.g., dewaterability, EPS composition, surface charge, microbial community, relative abundance of antibiotic resistance genes (ARGs), etc.) were investigated, and the role of Fe(II)-S2O8[2-] oxidation in enhancing removal of antibiotic resistance genes and dewatering ability were explored. The results showed significant differences between the EPS distribution and chemical composition of sludge samples due to different treatment processes, effluent sources, and regions. The Fe(II)-S2O8[2-] oxidation pretreatment had a good enhancement of sludge dewatering capacity (up to 76 %). Microbial analysis showed that the microbial community in each sludge varied significantly depending on the types of wastewater, the wastewater treatment processes, and the regions, but Fe(II)-S2O8[2-] oxidation was able to attack and rupture the sludge zoogloea indiscriminately. Genetic analysis further showed that a considerable number of ARGs were detected in all of these sludge samples and that Fe(II)-S2O8[2-] oxidation was effective in removing ARGs by higher than 90 %. The highly active radicals (e.g., SO4[-]·, ·OH) produced in this process caused drastic damage to sludge microbial cells and DNA stability while liberating the EPS/cell-bound water. Co-occurrence network analysis highlighted a positive correlation between population distribution and ARGs abundance, while variations in microbial communities were linked to regional differences in living standards and level of economic development. Despite these variations, the Fe(II)-S2O8[2-] oxidation consistently achieved excellent performance in both ARGs removal and sludge dewatering. The significant modularity of associations between different microbial communities also confirms its ability to reduce horizontal gene transfer (HGT) by scavenging microbes.

RevDate: 2024-02-12

Zhao Z, Li Y, Zhai JW, et al (2024)

Organelle Genomes of Epipogium roseum Provide Insight into the Evolution of Mycoheterotrophic Orchids.

International journal of molecular sciences, 25(3):.

Epipogium roseum, commonly known as one of the ghost orchids due to its rarity and almost transparent color, is a non-photosynthetic and fully mycoheterotrophic plant. Given its special nutritional strategies and evolutionary significance, the mitogenome was first characterized, and three plastomes sampled from Asia were assembled. The plastomes were found to be the smallest among Orchidaceae, with lengths ranging from 18,339 to 19,047 bp, and exhibited high sequence variety. For the mitogenome, a total of 414,552 bp in length, comprising 26 circular chromosomes, were identified. A total of 54 genes, including 38 protein-coding genes, 13 tRNA genes, and 3 rRNA genes, were annotated. Multiple repeat sequences spanning a length of 203,423 bp (45.47%) were discovered. Intriguingly, six plastid regions via intracellular gene transfer and four plastid regions via horizontal gene transfer to the mitogenome were observed. The phylogenomics, incorporating 90 plastomes and 56 mitogenomes, consistently revealed the sister relationship of Epipogium and Gastrodia, with a bootstrap percentage of 100%. These findings shed light on the organelle evolution of Orchidaceae and non-photosynthetic plants.

RevDate: 2024-02-10

Zhang J, Wang J, Zhu C, et al (2024)

Chickpea: Its Origin, Distribution, Nutrition, Benefits, Breeding, and Symbiotic Relationship with Mesorhizobium Species.

Plants (Basel, Switzerland), 13(3): pii:plants13030429.

Chickpea (Cicer arietinum L.), encompassing the desi and kabuli varieties, is a beloved pulse crop globally. Its cultivation spans over fifty countries, from the Indian subcontinent and southern Europe to the Middle East, North Africa, the Americas, Australia, and China. With a rich composition of carbohydrates and protein, constituting 80% of its dry seed mass, chickpea is also touted for its numerous health benefits, earning it the title of a 'functional food'. In the past two decades, research has extensively explored the rhizobial diversity associated with chickpea and its breeding in various countries across Europe, Asia, and Oceania, aiming to understand its impact on the sustainable yield and quality of chickpea crops. To date, four notable species of Mesorhizobium-M. ciceri, M. mediterraneum, M. muleiense, and M. wenxiniae-have been reported, originally isolated from chickpea root nodules. Other species, such as M. amorphae, M. loti, M. tianshanense, M. oportunistum, M. abyssinicae, and M. shonense, have been identified as potential symbionts of chickpea, possibly acquiring symbiotic genes through lateral gene transfer. While M. ciceri and M. mediterraneum are widely distributed and studied across chickpea-growing regions, they remain absent in China, where M. muleiense and M. wenxiniae are the sole rhizobial species associated with chickpea. The geographic distribution of chickpea rhizobia is believed to be influenced by factors such as genetic characteristics, competitiveness, evolutionary adaptation to local soil conditions, and compatibility with native soil microbes. Inoculating chickpea with suitable rhizobial strains is crucial when introducing the crop to new regions lacking indigenous chickpea rhizobia. The introduction of a novel chickpea variety, coupled with the effective use of rhizobia for inoculation, offers the potential not only to boost the yield and seed quality of chickpeas, but also to enhance crop productivity within rotation and intercropped systems involving chickpea and other crops. Consequently, this advancement holds the promise to drive forward the cause of sustainable agriculture on a global scale.

RevDate: 2024-02-09

Qiu X, Wang B, Ren S, et al (2024)

Regulation of quorum sensing for the manipulation of conjugative transfer of antibiotic resistance genes in wastewater treatment system.

Water research, 253:121222 pii:S0043-1354(24)00122-2 [Epub ahead of print].

The emergence and transmission of antibiotic resistance genes (ARGs) through plasmid-mediated conjugation has become a significant worldwide public health threat. Biofilms are widely recognized as the primary reservoirs for ARGs, providing favorable conditions for horizontal gene transfer. Quorum sensing (QS) plays a critical role in bacterial biofilm formation, which further influences the spread of bacterial resistance. In this study, we examined the effects of vanillin, a QS inhibitor (QSI), at subinhibitory concentrations (sub-MICs) ranging from 0 - 0.1 g/L, on the transfer of ARGs between Escherichia coli and Pseudomonas aeruginosa. Our findings indicated that vanillin at sub-MICs inhibited the conjugative transfer frequency of the RP4 plasmid. This inhibition was supported by the downregulation of plasmid transfer genes. The suppression of conjugation can mainly be attributed to the inhibition of biofilm formation, the synthesis of extracellular polymeric substances (EPS), and the secretion of virulence factors, all of which are regulated by the bacterial QS system. On the other hand, the levels of ROS and cell membrane permeability were not primary explanations for this phenomenon. Furthermore, vanillin also reduced the conjugative transfer frequency of ARGs in wastewater effluent, providing a potential approach to alleviate bacterial resistance in water environments. These findings underscore the regulatory role of QSI in controlling ARGs transfer and have significant implications for manipulating the dissemination of bacterial resistance in the environment.

RevDate: 2024-02-08

Li Q, Chan YB, Galtier N, et al (2024)

The Effect of Copy Number Hemiplasy on Gene Family Evolution.

Systematic biology pii:7603541 [Epub ahead of print].

The evolution of gene families is complex, involving gene-level evolutionary events such as gene duplication, horizontal gene transfer, and gene loss (DTL), and other processes such as incomplete lineage sorting (ILS). Because of this, topological differences often exist between gene trees and species trees. A number of models have been recently developed to explain these discrepancies, the most realistic of which attempt to consider both gene-level events and ILS. When unified in a single model, the interaction between ILS and gene-level events can cause polymorphism in gene copy number, which we refer to as copy number hemiplasy (CNH). In this paper we extend the Wright-Fisher process to include duplications and losses over several species, and show that the probability of CNH for this process can be significant. We study how well two unified models - MLMSC (MultiLocus MultiSpecies Coalescent), which models CNH, and DLCoal (Duplication, Loss, and Coalescence), which does not - approximate the Wright-Fisher process with duplication and loss. We then study the effect of CNH on gene family evolution by comparing MLMSC and DLCoal. We generate comparable gene trees under both models, showing significant differences in various summary statistics; most importantly, CNH reduces the number of gene copies greatly. If this is not taken into account, the traditional method of estimating duplication rates (by counting the number of gene copies) becomes inaccurate. The simulated gene trees are also used for species tree inference with the summary methods ASTRAL and ASTRAL-Pro, demonstrating that their accuracy, based on CNH-unaware simulations calibrated on real data, may have been overestimated.

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ESP Quick Facts

ESP Origins

In the early 1990's, Robert Robbins was a faculty member at Johns Hopkins, where he directed the informatics core of GDB — the human gene-mapping database of the international human genome project. To share papers with colleagues around the world, he set up a small paper-sharing section on his personal web page. This small project evolved into The Electronic Scholarly Publishing Project.

ESP Support

In 1995, Robbins became the VP/IT of the Fred Hutchinson Cancer Research Center in Seattle, WA. Soon after arriving in Seattle, Robbins secured funding, through the ELSI component of the US Human Genome Project, to create the original ESP.ORG web site, with the formal goal of providing free, world-wide access to the literature of classical genetics.

ESP Rationale

Although the methods of molecular biology can seem almost magical to the uninitiated, the original techniques of classical genetics are readily appreciated by one and all: cross individuals that differ in some inherited trait, collect all of the progeny, score their attributes, and propose mechanisms to explain the patterns of inheritance observed.

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In reading the early works of classical genetics, one is drawn, almost inexorably, into ever more complex models, until molecular explanations begin to seem both necessary and natural. At that point, the tools for understanding genome research are at hand. Assisting readers reach this point was the original goal of The Electronic Scholarly Publishing Project.

ESP Usage

Usage of the site grew rapidly and has remained high. Faculty began to use the site for their assigned readings. Other on-line publishers, ranging from The New York Times to Nature referenced ESP materials in their own publications. Nobel laureates (e.g., Joshua Lederberg) regularly used the site and even wrote to suggest changes and improvements.

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When the site began, no journals were making their early content available in digital format. As a result, ESP was obliged to digitize classic literature before it could be made available. For many important papers — such as Mendel's original paper or the first genetic map — ESP had to produce entirely new typeset versions of the works, if they were to be available in a high-quality format.

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Early support from the DOE component of the Human Genome Project was critically important for getting the ESP project on a firm foundation. Since that funding ended (nearly 20 years ago), the project has been operated as a purely volunteer effort. Anyone wishing to assist in these efforts should send an email to Robbins.

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With the development of methods for adding typeset side notes to PDF files, the ESP project now plans to add annotated versions of some classical papers to its holdings. We also plan to add new reference and pedagogical material. We have already started providing regularly updated, comprehensive bibliographies to the ESP.ORG site.

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If you thought that the history of life could be organized into a simple tree and that genes only moved from parents to progeny, think again. Recent science has shown that sometimes genes move sideways, skipping the reproductive process, and the tree of life looks more like a tangled bush. David Quammen, a masterful science writer, explains these new findings and more. Read this book and you'll learn about the discovery of the archaea — an entirely different form of life, living right here on this planet, and not noticed until Carl Woese found them, by being among the first to use molecular tools to look at organismal relationships. R. Robbins

Electronic Scholarly Publishing
961 Red Tail Lane
Bellingham, WA 98226

E-mail: RJR8222 @ gmail.com

Papers in Classical Genetics

The ESP began as an effort to share a handful of key papers from the early days of classical genetics. Now the collection has grown to include hundreds of papers, in full-text format.

Digital Books

Along with papers on classical genetics, ESP offers a collection of full-text digital books, including many works by Darwin and even a collection of poetry — Chicago Poems by Carl Sandburg.

Timelines

ESP now offers a large collection of user-selected side-by-side timelines (e.g., all science vs. all other categories, or arts and culture vs. world history), designed to provide a comparative context for appreciating world events.

Biographies

Biographical information about many key scientists (e.g., Walter Sutton).

Selected Bibliographies

Bibliographies on several topics of potential interest to the ESP community are automatically maintained and generated on the ESP site.

ESP Picks from Around the Web (updated 07 JUL 2018 )