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International Journal of Food... Jun 2024The Protected Designation of Origin (PDO) indication for foods intends to guarantee the conditions of production and the geographical origin of regional products within...
The Protected Designation of Origin (PDO) indication for foods intends to guarantee the conditions of production and the geographical origin of regional products within the European Union. Honey products are widely consumed due to their health-promoting properties and there is a general interest in tracing their authenticity. In this regard, metagenomics sequencing and machine learning (ML) have been proposed as complementary technologies to improve the traceability methods of foods. Therefore, the aim of this study was to analyze the metagenomic profiles of Spanish honeys from three different PDOs (Granada, Tenerife and Villuercas-Ibores), and compare them with non-PDO honeys using ML models (PLS, RF, LOGITBOOST, and NNET). According to the results obtained, non-PDO honeys and Granada PDO showed higher beta diversity values than Tenerife and Villuercas-Ibores PDOs. ML classification of honey products allowed the identification of different microbial biomarkers of the geographical origin of honeys: Lactobacillus kunkeei, Parasaccharibacter apium and Lactobacillus helsingborgensis for PDO honeys and Paenibacillus larvae, Lactobacillus apinorum and Klebsiella pneumoniae for non-PDO honeys. In addition, potential microbial biomarkers of some honey varieties including L. kunkeei for Albaida and Retama del Teide varieties, and P. apium for Tajinaste variety, were identified. ML models were validated on an independent set of samples leading to high accuracy rates (above 90 %). This work demonstrates the potential of ML to differentiate different types of honey using metagenome-based methods, leading to high performance metrics. In addition, ML models discriminate both the geographical origin and variety of products corresponding to different PDOs and non-PDO products. Results here presented may contribute to develop enhanced traceability and authenticity methods that could be applied to a wide range of foods.
PubMed: 38879955
DOI: 10.1016/j.ijfoodmicro.2024.110789 -
Proceedings of the National Academy of... Jun 2024
PubMed: 38870063
DOI: 10.1073/pnas.2410191121 -
International Journal of Systematic and... Jun 2024A Gram-stain-positive, aerobic bacterium, designated as YPD9-1, was isolated from the gut contents of a spotty belly greenling, , collected near Dokdo island, South...
A Gram-stain-positive, aerobic bacterium, designated as YPD9-1, was isolated from the gut contents of a spotty belly greenling, , collected near Dokdo island, South Korea. The rod-shaped cells were oxidase-positive, and catalase-negative. The major cellular fatty acids were anteiso-C, iso-C, C, iso-C and iso-C. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and two unidentified lipids. The DNA G+C content was 47.6 mol% and the predominant respiratory quinone was menaquinone MK-7. The 16S rRNA gene sequence of YPD9-1 showed low sequence similarities to species of the genus , Gsoil 1138 (97.21 % of sequence similarity), CJ25 (97.12 %) and JJ-42 (96.89 %). The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that YPD9-1 formed a distinct branch among other species of the genus . The digital DNA-DNA hybridisation, average nucleotide identity, and average amino acid identity values between YPD9-1 and the related species were in the ranges of 15.3-16.2 %, 74.1-78.4 %, and 71.1-71.9 %, respectively, which are below the species cutoff values. On the basis of the results of the polyphasic analysis, we conclude that strain YPD9-1 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain of is YPD9-1 (=KCTC 43424 =LMG 32988).
Topics: RNA, Ribosomal, 16S; Base Composition; Phylogeny; DNA, Bacterial; Republic of Korea; Fatty Acids; Paenibacillus; Bacterial Typing Techniques; Sequence Analysis, DNA; Vitamin K 2; Animals; Nucleic Acid Hybridization; Phospholipids
PubMed: 38869487
DOI: 10.1099/ijsem.0.006419 -
Microbial Cell Factories Jun 2024The gram-positive bacterium Bacillus subtilis is widely used for industrial enzyme production. Its ability to secrete a wide range of enzymes into the extracellular...
BACKGROUND
The gram-positive bacterium Bacillus subtilis is widely used for industrial enzyme production. Its ability to secrete a wide range of enzymes into the extracellular medium especially facilitates downstream processing since cell disruption is avoided. Although various heterologous enzymes have been successfully secreted with B. subtilis, the secretion of cytoplasmic enzymes with high molecular weight is challenging. Only a few studies report on the secretion of cytoplasmic enzymes with a molecular weight > 100 kDa.
RESULTS
In this study, the cytoplasmic and 120 kDa β-galactosidase of Paenibacillus wynnii (β-gal-Pw) was expressed and secreted with B. subtilis SCK6. Different strategies were focused on to identify the best secretion conditions. Tailormade codon-optimization of the β-gal-Pw gene led to an increase in extracellular β-gal-Pw production. Consequently, the optimized gene was used to test four signal peptides and two promoters in different combinations. Differences in extracellular β-gal-Pw activity between the recombinant B. subtilis strains were observed with the successful secretion being highly dependent on the specific combination of promoter and signal peptide used. Interestingly, signal peptides of both the general secretory- and the twin-arginine translocation pathway mediated secretion. The highest extracellular activity of 55.2 ± 6 µkat/L was reached when secretion was mediated by the PhoD signal peptide and expression was controlled by the P promoter. Production of extracellular β-gal-Pw was further enhanced 1.4-fold in a bioreactor cultivation to 77.5 ± 10 µkat/L with secretion efficiencies of more than 80%.
CONCLUSION
For the first time, the β-gal-Pw was efficiently secreted with B. subtilis SCK6, demonstrating the potential of this strain for secretory production of cytoplasmic, high molecular weight enzymes.
Topics: Bacillus subtilis; beta-Galactosidase; Paenibacillus; Molecular Weight; Cytoplasm; Promoter Regions, Genetic; Bacterial Proteins; Recombinant Proteins; Protein Sorting Signals
PubMed: 38867249
DOI: 10.1186/s12934-024-02445-7 -
Microbiology Resource Announcements Jun 2024In this study, we have identified and characterized three genomes from bacteria isolated from the rhizosphere of CMAA1738 and CMAA1739 were obtained from the wheat...
In this study, we have identified and characterized three genomes from bacteria isolated from the rhizosphere of CMAA1738 and CMAA1739 were obtained from the wheat landrace Iran 1-29-11334, and CMAA1741 was isolated from the wheat landrace Karakilcik.
PubMed: 38860798
DOI: 10.1128/mra.00036-24 -
International Journal of Systematic and... Jun 2024
Topics: Bees; Animals; Paenibacillus; RNA, Ribosomal, 16S; DNA, Bacterial; Phylogeny; Sequence Analysis, DNA; Bacterial Typing Techniques; Fatty Acids; Base Composition
PubMed: 38848114
DOI: 10.1099/ijsem.0.006408 -
Microbiology Resource Announcements Jun 2024sp. RC80 was isolated from temperate deciduous forest soil in New England. The assembled genome is a single contig with 5,977,337 bp and 97.15% estimated completion....
sp. RC80 was isolated from temperate deciduous forest soil in New England. The assembled genome is a single contig with 5,977,337 bp and 97.15% estimated completion. RC80 contains features for 2,3-butanediol dehydrogenase production and pathways involved in ethanol production.
PubMed: 38847544
DOI: 10.1128/mra.01067-23 -
Heliyon Jun 2024Endophytic bacteria, living inside plants, are competent plant colonizers, capable of enhancing immune responses in plants and establishing a symbiotic relationship with... (Review)
Review
Endophytic bacteria, living inside plants, are competent plant colonizers, capable of enhancing immune responses in plants and establishing a symbiotic relationship with them. Endophytic bacteria are able to control phytopathogenic fungi while exhibiting plant growth-promoting activity. Here, we discussed the mechanisms of phytopathogenic fungi control and plant growth-promoting actions discovered in some major groups of beneficial endophytic bacteria such as , and . Most of the studied strains in these genera were isolated from the rhizosphere and soils, and a more extensive study of these endophytic bacteria is needed. It is essential to understand the underlying biocontrol and plant growth-promoting mechanisms and to develop an effective screening approach for selecting potential endophytic bacteria for various applications. We have suggested a screening strategy to identify potentially useful endophytic bacteria based on mechanistic phenomena. The discovery of endophytic bacteria with useful biocontrol and plant growth-promoting characteristics is essential for developing sustainable agriculture.
PubMed: 38841467
DOI: 10.1016/j.heliyon.2024.e31573 -
BioRxiv : the Preprint Server For... May 2024The paenilamicins are a group of hybrid non-ribosomal peptide-polyketide compounds produced by the honey bee pathogen that display activity against Gram-positive...
The paenilamicins are a group of hybrid non-ribosomal peptide-polyketide compounds produced by the honey bee pathogen that display activity against Gram-positive pathogens, such as . While paenilamicins have been shown to inhibit protein synthesis, their mechanism of action has remained unclear. Here, we have determined structures of the paenilamicin PamB2 stalled ribosomes, revealing a unique binding site on the small 30S subunit located between the A- and P-site tRNAs. In addition to providing a precise description of interactions of PamB2 with the ribosome, the structures also rationalize the resistance mechanisms utilized by . We could further demonstrate that PamB2 interferes with the translocation of mRNA and tRNAs through the ribosome during translation elongation, and that this inhibitory activity is influenced by the presence of modifications at position 37 of the A-site tRNA. Collectively, our study defines the paenilamicins as a new class of context-specific translocation inhibitors.
PubMed: 38826346
DOI: 10.1101/2024.05.21.595107 -
PeerJ 2024American foulbrood (AFB), caused by the highly virulent, spore-forming bacterium , poses a significant threat to honey bee brood. The widespread use of antibiotics not...
BACKGROUND & OBJECTIVES
American foulbrood (AFB), caused by the highly virulent, spore-forming bacterium , poses a significant threat to honey bee brood. The widespread use of antibiotics not only fails to effectively combat the disease but also raises concerns regarding honey safety. The current computational study was attempted to identify a novel therapeutic drug target against , a causative agent of American foulbrood disease in honey bee.
METHODS
We investigated effective novel drug targets through a comprehensive pan-proteome and hierarchal subtractive sequence analysis. In total, 14 strains of genomes were used to identify core genes. Subsequently, the core proteome was systematically narrowed down to a single protein predicted as the potential drug target. Alphafold software was then employed to predict the 3D structure of the potential drug target. Structural docking was carried out between a library of phytochemicals derived from traditional Chinese flora ( > 36,000) and the potential receptor using Autodock tool 1.5.6. Finally, molecular dynamics (MD) simulation study was conducted using GROMACS to assess the stability of the best-docked ligand.
RESULTS
Proteome mining led to the identification of Ketoacyl-ACP synthase III as a highly promising therapeutic target, making it a prime candidate for inhibitor screening. The subsequent virtual screening and MD simulation analyses further affirmed the selection of ZINC95910054 as a potent inhibitor, with the lowest binding energy. This finding presents significant promise in the battle against
CONCLUSIONS
Computer aided drug design provides a novel approach for managing American foulbrood in honey bee populations, potentially mitigating its detrimental effects on both bee colonies and the honey industry.
Topics: Animals; Bees; Paenibacillus larvae; Proteome; Anti-Bacterial Agents; Molecular Docking Simulation; Molecular Dynamics Simulation; Bacterial Proteins
PubMed: 38818453
DOI: 10.7717/peerj.17292