Search Results (150)

A large majority of cone snails (a species in the genus Conus) are vermivorous (worm-hunting), but the diversity and bioactivity of their venom peptides remain largely unexplored. In this study, we report the first venom gland transcriptomes from two species in the Rhizoconus clade, Conus capitaneus and Conus mustelinus, and a new Conus miles transcriptome from a specimen collected in the Philippines. From the set of assembled sequences, a total of 225 C. capitaneus, 121 C. miles, and 168 C. mustelinus putative peptide toxin transcripts were identified, which were assigned to 27 canonical gene superfamilies in C. capitaneus and 24 in C. miles and in C. mustelinus. Most of these venom peptides are novel, and some exhibit new cysteine patterns. Clustering also revealed 12 putative novel gene superfamilies, highlighting the diversity of uncharacterized venom peptides in this group. The O1-, M-, O2-, and con-ikot-ikot superfamilies were the most abundant, while gene superfamilies such as D and G2 were highly expressed. Several hormone-like conopeptides were also identified in this study, revealing the vast diversity of conopeptides from the Rhizoconus species. Full article

Vomitoxin is a member of the monotrichous mycotoxin family with a complex chemical structure and significant biological activity. This toxin has strong immunosuppressive toxic effects and can cause serious damage to human and animal health. In this study, an on-site immune detection method based on an immune SiO₂@QD fluorescent probe was developed, which realized the rapid and quantitative detection of emetic toxins in grains. Polyethyleneimine (PEI) is a polymer containing a large number of amino groups, and the binding of PEI to the surface of quantum dots can serve to regulate growth and provide functionalized groups. A SiO₂@QD nanotag with good dispersibility and a high fluorescence intensity was synthesized by combining a PEI interlayer on the surface of SiO₂ nanospheres. Utilizing the electrostatic adsorption of the amino group in PEI, CdSe/ZnS QDs were self-assembled on the surface of SiO₂ nanospheres. In the stability test, the SiO₂@QDs could maintain basically the same fluorescence intensity for 90 consecutive days in the dark at 4 °C, showing a high fluorescence stability. The fluorescence-enhanced QD immune probe was formed by coupling with anti-DON monoclonal antibodies through carbodiimide chemical synthesis. For the detection of spiked wheat flour samples, the immuno-SiO₂@QD fluorescent probe showed excellent sensitivity and stability, the detection limit reached 0.25 ng/mL, and the average recovery rate was 92.2–101.6%. At the same time, the immuno-SiO₂@QD fluorescent probe is simple to operate, is capable of rapid responses, and has great potential in the rapid detection of vomitoxins in grains. Full article

In the process of long-term co-evolution, endophytes and host plants benefit from and interact with each other, resulting in positive effects such as promoting plant growth, enhancing resistance, producing beneficial secondary metabolites, and negative effects such as carrying pathogens and producing toxins. In addition to the vegetative organs, plant seeds are also colonized by diverse endophytes and serve as vectors for the transmission of endophytes across plant generations. Seed endophytes, termed seed-borne endophytes (SBEs), have attracted much attention because these endophytes are involved in the assembly of the plant association microbiome and exert effects on progeny plants through vertical transfer. However, the importance of SBEs may still be underestimated. The present paper reviews the diversity, origin, and vertical transmission of seed endophytes, as well as their interaction and function with hosts, so as to provide a reference for future research and application of seed endophytes. Full article

Background: Escherichia coli is one of the most studied bacteria worldwide due to its genetic plasticity. Recently, in addition to characterizing its pathogenic potential, research has focused on understanding its resistance profile to inhibitory agents, whether these be antibiotics or sanitizers. Objectives: The present study aimed to investigate six of the main serogroups of foodborne infection (O26, O45, O103, O111, O121, and O157) and to understand the dynamics of heterogeneity in resistance to sanitizers derived from quaternary ammonium compounds (QACs) and peracetic acid (PAA) using whole-genome sequencing (WGS). Methods: Twenty-four E. coli strains with varied resistance profiles to QACs and PAA were analyzed by WGS using NovaSeq6000 (150 bp Paired End reads). Bioinformatic analyses included genome assembly (Shovill), annotation via Prokka, antimicrobial resistance gene identification using Abricate, and core-genome analysis using Roary. A multifactorial multiple correspondence analysis (MCA) was conducted to explore gene–sanitizer relationships. In addition, a large-scale analysis utilizing the NCBI Pathogen Detection database involved a 2 × 2 chi-square test to examine associations between the presence of qac and stx genes. Results: The isolates exhibited varying antimicrobial resistance profiles, with O45 and O157 being the most resistant serogroups. In addition, the qac gene was identified in only one strain (S22), while four other strains carried the stx gene. Through multifactorial multiple correspondence analysis, the results obtained indicated that strains harboring genes encoding Shiga toxin (stx) presented profiles that were more likely to be sensitive to QACs. To further confirm these results, we analyzed 393,216 E. coli genomes from the NCBI Pathogen Detection database. Our results revealed a significant association (p < 0.001) between the presence of qac genes and the absence of stx1, stx2, or both toxin genes. Conclusion: Our findings highlight the complexity of bacterial resistance mechanisms and suggest that non-pathogenic strains may exhibit greater tolerance to QAC sanitizer than those carrying pathogenicity genes, particularly Shiga toxin genes. Full article

Bacillus cereus sensu lato (B. cereus s.l.) are significant spoilage and pathogenic microorganisms found in various foodstuffs. They are responsible for defects like sweet curdling in milk, which impacts dairy product storage and distribution. Nevertheless, the genetic mechanisms underlying B. cereus-induced sweet curdling remain poorly characterized. In this study, we investigated the genetic and functional basis underlying this phenomenon through whole genome sequencing of the newly isolated B. cereus strain BC46 and transcriptome sequencing at two phases of its growth in milk. Hybrid assembly of Illumina and Nanopore reads resulted in a 5.6 Mb genome with 35.1% GC content, classifying BC46 as B. cereus sensu stricto (B. cereus s.s.) within the panC group IV. Several virulence factors, antimicrobial resistance genes, and cold shock proteins were identified in the genome. A distinct functional profile of BC46 was observed before and after the development of sweet curdling in milk. Genes associated with sporulation, toxin production, hydrolysis, and proteolysis were upregulated in sweet-curdled samples. Our findings highlight potential gene targets that may play an important role in the BC46-induced sweet curdling in milk, enhancing our understanding of its molecular basis and supporting the development of new genetic approaches for early spoilage detection. Full article

The insecticidal Cry proteins from Bacillus thuringiensis are used in biopesticides or transgenic crops for pest control. The Cry1I protein family has unique characteristics of being produced during the vegetative rather than sporulation phase, its protoxins forming dimers in solution, and exhibiting dual toxicity against lepidopteran and coleopteran pests. The Cry1Ia protoxin undergoes sequential proteolysis from the N- and C-terminal ends, producing intermediate forms with insecticidal activity, while in some cases, the fully processed toxin is inactive. We investigated the oligomerization and toxicity of Cry1Ia intermediate forms generated through trypsinization (T-Int) and larval gut fluid (GF-Int) treatments, as well as the fully trypsinized protein (toxin). Heterologously expressed intermediate forms assembled into oligomers and showed similar toxicity to Cry1Ia protoxin against Ostrinia nubilalis (European corn borer) larvae, while the toxin form was ~30 times less toxic. In contrast, bioassays with Leptinotarsa decemlineata (Colorado potato beetle) larvae did not show significant differences in toxicity among Cry1Ia protoxin, T-Int, GF-Int, and fully processed toxin. These results suggest that the Cry1I mode of action differs by insect order, with N-terminal cleavage affecting toxicity against lepidopteran but not coleopteran larvae. This knowledge is essential for designing pest control strategies using Cry1I insecticidal proteins. Full article

Campylobacter is one of the leading bacterial causes of gastroenteritis worldwide. It frequently contaminates poultry and other raw meat products, which are the primary sources of Campylobacter infections in humans. Plasmids, known as important mobile genetic elements, often carry genes for antibiotic resistance, virulence, and self-mobilization. They serve as the main vectors for transferring genetic material and spreading resistance and virulence among bacteria. In this study, we identified 34 new plasmids from 43 C. jejuni and C. coli strains isolated from retail meat using long-read and short-read genome sequencing. Pangenomic analysis of the plasmid assemblies and reference plasmids from GenBank revealed five distinct groups, namely, pTet, pVir, mega plasmids (>80 kb), mid plasmids (~30 kb), and small plasmids (<6 kb). Pangenomic analysis identified the core and accessory genes in each group, indicating a high degree of genetic similarity within groups and substantial diversity between the groups. The pTet plasmids were linked to tetracycline resistance phenotypes in host strains. The mega plasmids carry multiple genes (e.g., aph(3’)-III, type IV and VI secretion systems, and type II toxin–antitoxin systems) important for plasmid mobilization, virulence, antibiotic resistance, and the persistence of Campylobacter. Together, the identification and comprehensive genetic characterization of new plasmids from Campylobacter food isolates contributes to understanding the mechanisms of gene transfer, particularly the spread of genetic determinants of virulence and antibiotic resistance in this important pathogen. Full article

Vibrio ordalii is the causative agent of atypical vibriosis in salmonids cultured in Chile. While extensive research provides insights into V. ordalii through phenotypic, antigenic, and genetic typing, as well as various virulence mechanisms, proteomic characterization remains largely unexplored. This study aimed to advance the proteomic knowledge of Chilean V. ordalii Vo-LM-18 and its OMVs, which have known virulence. Using Nano-UHPLC-LC-MS/MS, we identified 2242 proteins and 1755 proteins in its OMVs. Of these, 644 unique proteins were detected in V. ordalii Vo-LM-18, namely 156 unique proteins in its OMVs and 1596 shared proteins. The major categories for the OMVs were like those in the bacteria (i.e., cytoplasmic and cytoplasmic membrane proteins). Functional annotation identified 37 biological pathways in V. ordalii Vo-LM-18 and 28 in its OMVs. Proteins associated with transport, transcription, and virulence were predominant in both. Evident differences in protein expression were found. OMVs expressed a higher number of virulence-associated proteins, including those related to iron- and heme-uptake mechanisms. Notable pathways in the bacteria included flagellum assembly, heme group-associated proteins, and protein biosynthesis. This proteomic analysis is the first to detect the RTX toxin in a V. ordalii strain (Vo-LM-18) and its vesicles. Our results highlight the crucial role of OMVs in the pathogenesis and adaptation of V. ordalii, suggesting use as potential diagnostic biomarkers and therapeutic targets for bacterial infections. Full article

The dispersal of plant pathogens is a threat to the global economy and food industry which necessitates the need to discover efficient biocontrol agents such as bacteria, fungi, etc., inhibiting them. Here, we describe the Bacillus mycoides strain b12.3 isolated from the soil of Olkhon Island in Lake Baikal, Russia. By applying the co-cultivation technique, we found that the strain inhibits the growth of plant pathogens, such as the bacteria Xanthomonas campestris, Clavibacter michiganensis, and Pectobacterium atrospecticum, as well as the fungus Alternaria solani. To elucidate the genomic fundament explaining these activities, we leveraged next-generation whole-genome sequencing and obtained a high-quality assembly based on short reads. The isolate bore seven known BGCs (biosynthetic gene clusters), including those responsible for producing bacillibactin, fengycin, and petrobactin. Moreover, the genome contained insecticidal genes encoding for App4Aa1, Tpp78Ba1, and Spp1Aa1 toxins, thus implicating possible pesticidal potential. We compared the genome with the 50 closest assemblies and found that b12.3 is enriched with BGCs. The genomic analysis also revealed that genomic architecture corresponds to the experimentally observed activity spectrum implying that the combination of produced secondary metabolites delineates the range of inhibited phytopathogens Therefore, this study deepens our knowledge of the biology and ecology of B. mycoides residing in the Lake Baikal region. Full article

Pesticide-free agriculture is a fundamental pillar of environmentally friendly agriculture. To this end, there is an active search for new bacterial strains capable of synthesizing secondary metabolites and toxins that protect crops from pathogens and pests. In this study, we isolated a novel strain d21.2 of Peribacillus frigoritolerans from a soil sample collected in the Republic of Dagestan, Russia. Leveraging several bioinformatic approaches on Illumina-based whole-genome assembly, we revealed that the strain harbors certain insecticidal loci (coding for putative homologs of Bmp and Vpa) and also contains multiple BGCs (biosynthetic gene clusters), including paeninodin, koranimine, schizokinen, and fengycin. In total, 21 BGCs were predicted as synthesizing metabolites with bactericidal and/or fungicidal effects. Importantly, by applying a re-scaffolding pipeline, we managed to robustly predict MGEs (mobile genetic elements) associated with BGCs, implying high genetic plasticity. In addition, the d21.2’s genome was free from genes encoding for enteric toxins, implying its safety in use. A comparison with available genomes of the Peribacillus frigoritolerans strain revealed that the strain described here contains more functionally important loci than other members of the species. Therefore, strain d21.2 holds potential for use in agriculture due to the probable manifestation of bactericidal, fungicidal, growth-stimulating, and other useful properties. The assembled genome is available in the NCBI GeneBank under ASM4106054v1. Full article

Competition between bacterial species is a major factor shaping microbial communities. It is possible but remains largely unexplored that competition between bacterial pathogens can be mediated through antagonistic effects of bacterial effector proteins on host systems, particularly the actin cytoskeleton. Using Salmonella Typhimurium invasion into cells as a model, we demonstrate that invasion is inhibited if the host actin cytoskeleton is disturbed by actin-specific toxins, namely, Vibrio cholerae MARTX actin crosslinking (ACD) and Rho GTPase inactivation (RID) domains, Photorhabdus luminescens TccC3, and Salmonella’s own SpvB. We noticed that ACD, being an effective inhibitor of tandem G-actin-binding assembly factors, is likely to inhibit the activity of another Vibrio effector, VopF. In reconstituted actin polymerization assays and by live-cell microscopy, we confirmed that ACD potently halted the actin nucleation and pointed-end elongation activities of VopF, revealing competition between these two V. cholerae effectors. These results suggest that bacterial effectors from different species that target the same host machinery or proteins may represent an effective but largely overlooked mechanism of indirect bacterial competition in host-associated microbial communities. Whether the proposed inhibition mechanism involves the actin cytoskeleton or other host cell compartments, such inhibition deserves investigation and may contribute to a documented scarcity of human enteric co-infections by different pathogenic bacteria. Full article

Leafy greens are a significant source of produce-related Shiga toxin-producing Escherichia coli (STEC) outbreaks in the United States, with agricultural water often implicated as a potential source. Current FDA outbreak detection protocols are time-consuming and rely on sequencing methods performed in costly equipment. This study evaluated the potential of Oxford Nanopore Technologies (ONT) with Q20+ chemistry as a cost-effective, rapid, and accurate method for identifying and clustering foodborne pathogens. The study focuses on assessing whether ONT Q20+ technology could facilitate near real-time pathogen identification, including SNP differences, serotypes, and antimicrobial resistance genes. This pilot study evaluated different combinations of two DNA extraction methods (Maxwell RSC Cultured Cell DNA kit and Monarch high molecular weight extraction kits) and two ONT library preparation protocols (ligation and the rapid barcoding sequencing kit) using five well-characterized strains representing diverse foodborne pathogens. High-quality, closed bacterial genomes were obtained from all combinations of extraction and sequencing kits. However, variations in assembly length and genome completeness were observed, indicating the need for further optimization. In silico analyses demonstrated that Q20+ nanopore sequencing chemistry accurately identified species, genotype, and virulence factors, with comparable results to Illumina sequencing. Phylogenomic clustering showed that ONT assemblies clustered with reference genomes, though some indels and SNP differences were observed, likely due to sequencing and analysis methodologies rather than inherent genetic variation. Additionally, the study evaluated the impact of a change in the sampling rates from 4 kHz (260 bases pair second) to 5 kHz (400 bases pair second), finding no significant difference in sequencing accuracy. This evaluation workflow offers a framework for evaluating novel technologies for use in surveillance and foodborne outbreak investigations. Overall, the evaluation demonstrated the potential of ONT Q20+ nanopore sequencing chemistry to assist in identifying the correct strain during outbreak investigations. However, further research, validation studies, and optimization efforts are needed to address the observed limitations and fully realize the technology’s potential for improving public health outcomes and enabling more efficient responses to foodborne disease threats. Full article

Water quality and aquatic ecosystems along lakeshores are vital for ecological balance and human well-being. However, research has primarily focused on plankton, with benthic niches being largely overlooked. To enhance understanding of benthic microbial communities, we utilized 16S and 18S rRNA sequencing alongside multivariate statistical methods to analyze samples from the shoreline of Lake Taihu in Huzhou City, Zhejiang Province. Our results reveal a marked difference in species composition between benthic and planktonic microorganisms, with benthic cyanobacteria predominantly comprising filamentous genera like Tychonema, while 95% of planktonic cyanobacteria were Cyanobium. The β-diversity of benthic microorganisms was notably higher than that of planktonic counterparts. The neutral community model indicated that stochastic processes dominated planktonic microbial assembly, while deterministic processes prevailed in benthic communities. Null models showed that homogeneous selection influenced benthic community assembly, whereas planktonic communities were affected by undominated processes and dispersal limitation. Network analysis indicated that planktonic networks were more stable than benthic networks. Importantly, dominant benthic cyanobacterial genera posed potential toxin risks, highlighting the need for enhanced monitoring and ecological risk assessment. Overall, these findings enhance our understanding of benthic and planktonic microbial communities in lakeshores and offer valuable insights for aquatic assessment and management in eutrophicated environments. Full article

ABC toxin complexes are a class of protein toxin translocases comprised of a multimeric assembly of protein subunits. Each subunit displays a unique composition, contributing to the formation of a syringe-like nano-machine with natural cargo carrying, targeting, and translocation capabilities. Many of these toxins are insecticidal, drawing increasing interest in agriculture for use as biological pesticides. The A subunit (TcA) is the largest subunit of the complex and contains domains associated with membrane permeation and targeting. The B and C subunits, TcB and TcC, respectively, package into a cocoon-like structure that contains a toxic peptide and are coupled to TcA to form a continuous channel upon final assembly. In this review, we outline the current understanding and gaps in the knowledge pertaining to ABC toxins, highlighting seven published structures of TcAs and how these structures have led to a better understanding of the mechanism of host tropism and toxin translocation. We also highlight similarities and differences between homologues that contribute to variations in host specificity and conformational change. Lastly, we review the biotechnological potential of ABC toxins as both pesticides and cargo-carrying shuttles that enable the transport of peptides into cells. Full article

HxTx-Hv1h, a neurotoxic peptide derived from spider venom, has been developed for use in commercial biopesticide formulations. Cell Penetrating Peptides (CPPs) are short peptides that facilitate the translocation of various biomolecules across cellular membranes. Here, we evaluated the aphidicidal efficacy of a conjugated peptide, HxTx-Hv1h/CPP-1838, created by fusing HxTx-Hv1h with CPP-1838. Additionally, we aimed to establish a robust recombinant expression system for HxTx-Hv1h/CPP-1838. We successfully achieved the secretory production of HxTx-Hv1h, its fusion with Galanthus nivalis agglutinin (GNA) forming HxTx-Hv1h/GNA and HxTx-Hv1h/CPP-1838 in yeast. Purified HxTx-Hv1h exhibited contact toxicity against Megoura crassicauda, with a 48 h median lethal concentration (LC₅₀) of 860.5 μg/mL. Fusion with GNA or CPP-1838 significantly enhanced its aphidicidal potency, reducing the LC₅₀ to 683.5 μg/mL and 465.2 μg/mL, respectively. The aphidicidal efficacy was further improved with the addition of surfactant, decreasing the LC₅₀ of HxTx-Hv1h/CPP-1838 to 66.7 μg/mL—over four times lower compared to HxTx-Hv1h alone. Furthermore, we engineered HxTx-Hv1h/CPP-1838 multi-copy expression vectors utilizing the BglBrick assembly method and achieved high-level recombinant production in laboratory-scale fermentation. This study is the first to document a CPP fusion strategy that enhances the transdermal aphidicidal activity of a natural toxin like HxTx-Hv1h and opens up the possibility of exploring the recombinant production of HxTx-Hv1h/CPP-1838 for potential applications. Full article