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Journal of Bacteriology May 2024() 's initial rise to fame derived from its alluring production of blue-green light. Subsequent studies to probe the mechanisms underlying this bioluminescence helped... (Review)
Review
() 's initial rise to fame derived from its alluring production of blue-green light. Subsequent studies to probe the mechanisms underlying this bioluminescence helped the field discover the phenomenon now known as quorum sensing. Orthologs of quorum-sensing regulators (i.e., LuxR and LuxI) originally identified in were subsequently uncovered in a plethora of bacterial species, and analogous pathways were found in yet others. Over the past three decades, the study of this microbe has greatly expanded to probe the unique role of as the exclusive symbiont of the light organ of the Hawaiian bobtail squid, . Buoyed by this optically amenable host and by persistent and insightful researchers who have applied novel and cross-disciplinary approaches, has developed into a robust model for microbe-host associations. It has contributed to our understanding of how bacteria experience and respond to specific, often fluxing environmental conditions and the mechanisms by which bacteria impact the development of their host. It has also deepened our understanding of numerous microbial processes such as motility and chemotaxis, biofilm formation and dispersal, and bacterial competition, and of the relevance of specific bacterial genes in the context of colonizing an animal host. Parallels in these processes between this symbiont and bacteria studied as pathogens are readily apparent, demonstrating functional conservation across diverse associations and permitting a reinterpretation of "pathogenesis." Collectively, these advances built a foundation for microbiome studies and have positioned to continue to expand the frontiers of our understanding of the microbial world inside animals.
Topics: Aliivibrio fischeri; Animals; Decapodiformes; Quorum Sensing; Symbiosis; Gene Expression Regulation, Bacterial; Bacterial Proteins; Host Microbial Interactions
PubMed: 38695522
DOI: 10.1128/jb.00035-24 -
Scientific Reports Apr 2024Although the 16S rRNA gene is frequently used as a phylogenetic marker in analysis of environmental DNA, this marker often fails to distinguish closely related species,...
Although the 16S rRNA gene is frequently used as a phylogenetic marker in analysis of environmental DNA, this marker often fails to distinguish closely related species, including those in the genus Vibrio. Here, we investigate whether inclusion and analysis of 23S rRNA sequence can help overcome the intrinsic weaknesses of 16S rRNA analyses for the differentiation of Vibrio species. We construct a maximum likelihood 16S rRNA gene tree to assess the use of this gene to identify clades of Vibrio species. Within the 16S rRNA tree, we identify the putative informative bases responsible for polyphyly, and demonstrate the association of these positions with tree topology. We demonstrate that concatenation of 16S and 23S rRNA genes increases the number of informative nucleotide positions, thereby overcoming ambiguities in 16S rRNA-based phylogenetic reconstructions. Finally, we experimentally demonstrate that this approach considerably improves the differentiation and identification of Vibrio species in environmental samples.
Topics: Vibrio; Phylogeny; RNA, Ribosomal, 16S; rRNA Operon; RNA, Ribosomal, 23S; Genetic Variation
PubMed: 38688963
DOI: 10.1038/s41598-024-60505-9 -
The Science of the Total Environment Jul 2024A recently synthesized aminated 3,4-dioxygenated xanthone (Xantifoul2) was found to have promising antifouling (AF) effects against the settlement of the macrofouler...
A recently synthesized aminated 3,4-dioxygenated xanthone (Xantifoul2) was found to have promising antifouling (AF) effects against the settlement of the macrofouler Mytilus galloprovincialis larvae. Preliminary assessment indicated that Xantifoul2 has reduced ecotoxicological impacts: e.g., being non-toxic to the marine crustacea Artemia salina (<10 % mortality at 50 μM) and showing low bioconcentration factor in marine organisms. In order to meet the EU Biocidal Product Regulation, a preliminary hazard assessment of this new nature-inspired antifouling (NIAF) agent was conducted in this work. Xantifoul2 did not affect the swimming ability of the planktonic crustacean Daphnia magna, the growth of the diatom Phaeodactylum tricornutum, and the cellular respiration of luminescent Gram-negative bacteria Vibrio fischeri, supporting the low toxicity towards several non-target marine species. Regarding human cytotoxicity, Xantifoul2 did not affect the cell viability of retinal human cells (hTERT-RPE-1) and lipidomic studies revealed depletion of lipids involved in cell death, membrane modeling, lipid storage, and oxidative stress only at a high concentration (10 μM). Accelerated degradation studies in water were conducted under simulated sunlight to allow the understanding of putative transformation products (TPs) that could be generated in the aquatic ecosystems. Both Xantifoul2 and photolytic-treated Xantifoul2 in the aqueous matrix were therefore evaluated on several nuclear receptors (NRs). The results of this preliminary hazard assessment of Xantifoul2, combined with the high degradation rates in water, provide strong evidence of the safety of this AF agent under the evaluated conditions, and provide the support for future validation studies before this compound can be introduced in the market.
Topics: Biofouling; Animals; Water Pollutants, Chemical; Aliivibrio fischeri; Xanthones; Mytilus; Diatoms; Humans; Daphnia; Artemia
PubMed: 38688370
DOI: 10.1016/j.scitotenv.2024.172824 -
Emerging Microbes & Infections Dec 2024, an emergent species of genus, exists in aquatic and marine environments. It has undergone genetic diversification, but its detailed genomic diversity is still...
, an emergent species of genus, exists in aquatic and marine environments. It has undergone genetic diversification, but its detailed genomic diversity is still unclear. Here, we performed a multi-dimensional comparative genomic analysis to explore the population phylogeny, virulence-related genes and potential drug resistance genes of 184 isolates. Although genetic diversity is complex, we analysed the population structure using three sub-datasets, including the subdivision for three lineages into sublineages and the distribution of strains in the marine ecological niche. Accessory genes, most of which reclassified genomes as different but with relatively close affinities, were nonuniformly distributed among these isolates. We demonstrated that the spread of some post-evolutionary isolates (mainly L3 strains isolated from Chinese territorial seas) was likely to be closely related to human activities, whereas other more ancestral strains (strains in the L1 and L2) tended to be locally endemic and formed clonal complex groups. In terms of pathogenicity, the potential virulence factors were mainly associated with toxin, adherence, motility, chemotaxis, and the type III secretion system (T3SS). We also found five types of antibacterial drug resistance genes. The prevalence of β-lactam resistance genes was 100%, which indicated that there may be a potential risk of natural resistance to β-lactam drugs. Our study reveals insights into genomic characteristics, evolution and potential virulence-associated gene profiles of .
Topics: Vibrio alginolyticus; Genome, Bacterial; Phylogeny; Virulence Factors; Evolution, Molecular; Virulence; Vibrio Infections; Genetic Variation; Humans; Anti-Bacterial Agents; Drug Resistance, Bacterial; Animals
PubMed: 38687697
DOI: 10.1080/22221751.2024.2350164 -
Proceedings of the National Academy of... May 2024Several microbial genomes lack textbook-defined essential genes. If an essential gene is absent from a genome, then an evolutionarily independent gene of unknown...
Several microbial genomes lack textbook-defined essential genes. If an essential gene is absent from a genome, then an evolutionarily independent gene of unknown function complements its function. Here, we identified frequent nonhomologous replacement of an essential component of DNA replication initiation, a replicative helicase loader gene, in . Our analysis of genomes revealed two genes with unknown function, named and , that were substantially enriched in genomes without the known helicase-loader genes. These genes showed no sequence similarities to genes with known function but encoded proteins structurally similar with a viral helicase loader. Analyses of genomic syntenies and coevolution with helicase genes suggested that encodes a helicase loader. The in vitro assay showed that VdhL1 and VdhL2 promote the helicase activity of DnaB. Furthermore, molecular phylogenetics suggested that / were derived from phages and replaced an intrinsic helicase loader gene of over 20 times. This high replacement frequency implies the host's advantage in acquiring a viral helicase loader gene.
Topics: Vibrionaceae; DNA Helicases; DNA Replication; Phylogeny; Bacterial Proteins; Viral Proteins; Bacteriophages; Evolution, Molecular; Genome, Bacterial; DnaB Helicases; Vibrio
PubMed: 38683976
DOI: 10.1073/pnas.2317954121 -
Foods (Basel, Switzerland) Apr 2024A novel storage technique that combines the low-frequency electric field (LFEF) and ice temperature was used to extend the shelf life of Pacific white shrimp (). The...
A novel storage technique that combines the low-frequency electric field (LFEF) and ice temperature was used to extend the shelf life of Pacific white shrimp (). The study investigated the effect of LFEF treatment on the quality and microbial composition of during storage at ice temperature. The results showed that the LFEF treatment significantly extended the shelf life of shrimp during storage at ice temperature. The total volatile base nitrogen (TVB-N) and pH of samples increased over time, while the total viable count (TVC) showed a trend of first decreasing and then increasing. Obviously, shrimp samples treated with LFEF had a lower pH, TVB-N and TVC values than the untreated samples ( < 0.05) at the middle and late stages of storage. LFEF treatment increased the diversity and altered the composition of the microbial communities in . Additionally, the treatment led to a decrease in the relative abundance of dominant spoilage bacteria, including , and , in stored at ice temperature for 11 days. Furthermore, correlation analysis indicated that TVB-N and pH had a significant and positive correlation with , suggesting that had a greater impact on shrimp quality. This study supports the practical application of accelerated low-frequency electric field-assisted shrimp preservation as an effective means of maintaining shrimp meat quality.
PubMed: 38672816
DOI: 10.3390/foods13081143 -
BMC Microbiology Apr 2024Vibrio parahaemolyticus is the predominant etiological agent of seafood-associated foodborne illnesses on a global scale. It is essential to elucidate the mechanisms by...
BACKGROUND
Vibrio parahaemolyticus is the predominant etiological agent of seafood-associated foodborne illnesses on a global scale. It is essential to elucidate the mechanisms by which this pathogen disseminates. Given the existing research predominantly concentrates on localized outbreaks, there is a pressing necessity for a comprehensive investigation to capture strains of V. parahaemolyticus cross borders.
RESULTS
This study examined the frequency and genetic attributes of imported V. parahaemolyticus strains among travelers entering Shanghai Port, China, between 2017 and 2019.Through the collection of 21 strains from diverse countries and regions, Southeast Asia was pinpointed as a significant source for the emergence of V. parahaemolyticus. Phylogenetic analysis revealed clear delineation between strains originating from human and environmental sources, emphasizing that underlying genome data of foodborne pathogens is essential for environmental monitoring, food safety and early diagnosis of diseases. Furthermore, our study identified the presence of virulence genes (tdh and tlh) and approximately 120 antibiotic resistance-related genes in the majority of isolates, highlighting their crucial involvement in the pathogenesis of V. parahaemolyticus.
CONCLUSIONS
This research enhanced our comprehension of the worldwide transmission of V. parahaemolyticus and its antimicrobial resistance patterns. The findings have important implications for public health interventions and antimicrobial stewardship strategies, underscoring the necessity for epidemiological surveillance of pathogen at international travel hubs.
Topics: Vibrio parahaemolyticus; Humans; China; Vibrio Infections; Phylogeny; Foodborne Diseases; Genome, Bacterial; Travel; Virulence Factors; Genomics; Drug Resistance, Bacterial; Anti-Bacterial Agents; Seafood
PubMed: 38671363
DOI: 10.1186/s12866-024-03303-7 -
Microbiology Spectrum Jun 2024The fastest replicating bacterium is a rising workhorse for molecular and biotechnological research with established tools for efficient genetic manipulation. Here, we...
UNLABELLED
The fastest replicating bacterium is a rising workhorse for molecular and biotechnological research with established tools for efficient genetic manipulation. Here, we expand on the capabilities of multiplex genome editing by natural transformation (MuGENT) by identifying a neutral insertion site and showing how two selectable markers can be swapped at this site for sequential rounds of natural transformation. Second, we demonstrated that MuGENT can be used for complementation by gene insertion at an ectopic chromosomal locus. Additionally, we developed a robust method to cure the competence plasmid required to induce natural transformation. Finally, we demonstrated the ability of MuGENT to create massive deletions; the 280 kb deletion created in this study is one of the largest artificial deletions constructed in a single round of targeted mutagenesis of a bacterium. These methods each advance the genetic potential of and collectively expand upon its utility as an emerging model organism for synthetic biology.
IMPORTANCE
is an emerging model organism for molecular and biotechnological applications. Its fast growth, metabolic versatility, and ease of genetic manipulation provide an ideal platform for synthetic biology. Here, we develop and apply novel methods that expand the genetic capabilities of the model system. Prior studies developed a method to manipulate multiple regions of the chromosome in a single step. Here, we provide new resources that diversify the utility of this method. We also provide a technique to remove the required genetic tools from the cell once the manipulation is performed, thus establishing "clean" derivative cells. Finally, we show the full extent of this technique's capability by generating one of the largest chromosomal deletions reported in the literature. Collectively, these new tools will be beneficial broadly to the community and specifically to the advancement of as a model system.
Topics: Vibrio; Plasmids; Gene Editing; Genetic Engineering; Synthetic Biology; Genome, Bacterial
PubMed: 38667341
DOI: 10.1128/spectrum.03964-23 -
Ecotoxicology and Environmental Safety Jun 2024In this study, the impact of calcination of zeolites on the ecotoxicity of carbamazepine solutions in two matrices, water and synthetic sewage, was assessed. Two types...
In this study, the impact of calcination of zeolites on the ecotoxicity of carbamazepine solutions in two matrices, water and synthetic sewage, was assessed. Two types of zeolites were tested: natural zeolite, in the form of a zeolite rock consisting mainly of clinoptilolite, and a synthetic zeolite type 5 A. Additionally, zeolites were calcined at a temperature of 200 °C. The kinetics of carbamazepine adsorption in aqueous solutions and in synthetic sewage matrix was determined. Higher adsorption capacity was obtained for carbamazepine aqueous solutions as well as zeolites after the calcination process. Considering type of zeolite, the highest and fastest uptake of carbamazepine was observed for natural zeolite after calcination. In the case of ecotoxicity, carbamazepine solutions before adsorption was the most toxic towards Raphidocelis subcapitata, next Aliivibrio fischeri and Daphnia magna, regardless to the matrix type. The differentiation in toxicity regarding the type of matrix was observed, in the case of algae and bacteria, higher toxicity was demonstrated by carbamazepine solutions in the water matrix, while in the case of crustaceans-the sewage matrix. After the adsorption process, the toxicity of carbamazepine solutions on zeolites decreased by 34.5-60.9 % for R. subcapitata, 33-39 % for A. fischeri and 55-60 % for D. magna, thus confirming the effectiveness of the proposed method of carbamazepine immobilization.
Topics: Carbamazepine; Zeolites; Water Pollutants, Chemical; Daphnia; Adsorption; Animals; Sewage; Aliivibrio fischeri; Kinetics
PubMed: 38653020
DOI: 10.1016/j.ecoenv.2024.116320 -
ACS Applied Materials & Interfaces Jun 2024Enzyme-linked immunosorbent assay (ELISA) is the gold standard technique for measuring protein biomarkers due to its high sensitivity, specificity, and throughput....
Enzyme-linked immunosorbent assay (ELISA) is the gold standard technique for measuring protein biomarkers due to its high sensitivity, specificity, and throughput. Despite its success, continuous advancements in ELISA and immunoassay formats are crucial to meet evolving global challenges and to address new analytical needs in diverse applications. To expand the capabilities and applications of immunoassays, we introduce a novel ELISA-like assay that we call Bioluminescent-bacteria-linked immunosorbent assay (BBLISA). BBLISA is an enzyme-free assay that utilizes the inner filter effect between the bioluminescent bacteriaand metallic nanoparticles (gold nanoparticles and gold iridium oxide nanoflowers) as molecular absorbers. Functionalizing these nanoparticles with antibodies induces their accumulation in wells upon binding to molecular targets, forming the classical immune-sandwich complex. Thanks to their ability to adsorb the light emitted by the bacteria, the nanoparticles can suppress the bioluminescence signal, allowing the rapid quantification of the target. To demonstrate the bioanalytical properties of the novel immunoassay platform, as a proof of principle, we detected two clinically relevant biomarkers (human immunoglobulin G and SARS-CoV-2 nucleoprotein) in human serum, achieving the same sensitivity and precision as the classic ELISA. We believe that BBLISA can be a promising alternative to the standard ELISA techniques, offering potential advancements in biomarker detection and analysis by combining nanomaterials with a low-cost, portable bioluminescent platform.
Topics: Humans; Enzyme-Linked Immunosorbent Assay; Gold; Biomarkers; Luminescent Measurements; Metal Nanoparticles; SARS-CoV-2; Immunoglobulin G; Aliivibrio fischeri; COVID-19; Iridium
PubMed: 38651970
DOI: 10.1021/acsami.4c01744