Using genomic analysis and in vitro assays, this study examined the properties of L. chiayiensis AACE3, which was isolated from fermented blueberries. The genetic study of the genome displayed genes for biofilm development (luxS, ccpA, brpA), resistance against oxidative stressors (tpx, trxA, trxB, hslO), tolerance to acidic environments (dltA, dltC), adaptation to fluctuating osmotic conditions (opuBB, gbuA, gbuB, gbuC), and mechanisms for adherence (luxS, dltA, dltC). Compared to the other three L. chiayiensis strains, 112 unique genes were identified in the AACE3 strain. The presence of genes like clpP, pepO, and feoA in AACE3 potentially grants it a superior capacity for environmental adaptation compared to other L. chiayiensis strains. An in vitro study of AACE3's properties uncovered significant antibacterial activity against a spectrum of eight common pathogens: Streptococcus agalactiae, Staphylococcus aureus, Escherichia coli, Salmonella enteritidis, Salmonella choleraesuis, Shigella flexneri, Pseudomonas aeruginosa, and Klebsiella pneumoniae. Moreover, AACE3 displayed a survival rate exceeding 80% in all simulations of gastrointestinal fluid, showcasing considerable antioxidant capacity. It is noteworthy that the cell culture supernatant demonstrated a stronger antioxidant capacity than both intact cells and ultrasonically processed bacterial extracts in all the experiments performed. The antioxidant capacity, according to these results, might stem from particular metabolites and extracellular enzymes secreted by AACE3. Subsequently, the self-agglomeration of AACE3 contributed to its moderate biofilm production. The L. chiayiensis AACE3 strain, upon thorough consideration, presents itself as a promising candidate for fighting the rising incidence of pathogen infections and antioxidant production.Stutzerimonas balearica, or Pseudomonas balearica, is predominantly located in environments contaminated by oil. S. balearica's ability to flourish amidst the breakdown of pollutant compounds positions it as a species of significant interest for potential bioremediation applications. Although, the reported diversity of S. balearica is relatively scarce. Genome sequences of S. balearica strains originating from various sources were analyzed in this study, demonstrating the species' remarkable diversity and an open pan-genome. This indicates that continued sequencing efforts will further reveal new genetic and functional attributes. A reevaluation of the 16S rRNA gene nucleotide signatures and intra- and interspecies variations in S. balearica was undertaken. Examining 16S rRNA gene sequences from public databases yielded 158 extra bacterial strains, with 23% of them categorized as S. balearica. Environmental diversity encompassing a wide array of habitats exhibited detections of the species, though the highest incidence occurred in aquatic and polluted locations, often correlating with petroleum. Analysis of S. balearica's genome and phenotype underscored its varied inherent capabilities in the degradation of aromatic compounds. Knowledge of S. balearica's biology and diversity is enhanced by this study, laying the groundwork for future endeavors with this species.RNA modifications occurring after transcription, often referred to as the epitranscriptome, are essential in regulating gene expression throughout the developmental process. Recently, deep learning (DL) has been successfully used to predict RNA modification sites, yielding promising outcomes. Nonetheless, a scarcity of pertinent research leaves the optimal deep learning architecture for certain pyrimidine modifications, including 5-methyluridine (m5U), uncertain. To overcome this knowledge shortfall, we initially carried out a comparative evaluation of widely used deep learning models for epigenetic research, leveraging the functionalities of autoBioSeqpy. For the task of m5U site classification, we found the best architectural variations, which were achieved by meticulously refining the layer depth and neuron width parameters. Further, the acquisition of this knowledge spurred the creation of Deepm5U, a superior convolutional-recurrent neural network, accurately identifying m5U sites from RNA. The successful application of Deepm5U enabled transcriptome-wide m5U profiling across various sequencing technologies and diverse cell types. We further validated that deep neural network interpretation methods, specifically LayerUMAP and DeepSHAP, can unveil crucial insights into the inner workings and operational characteristics of the models. For the design of new algorithms in the field of RNA modifications, our practical approach involved the meticulous development, benchmarking, and in-depth analysis of deep learning models.The growing concern surrounding carbapenemase genes, along with colistin resistance genes (mcr-1) and tigecycline resistance genes (tet(X)), highlights a significant risk to both clinical treatment and public health. A study was conducted to determine the prevalence of carbapenemase genes, mcr-1, and tet(X) in a sample of 298 Escherichia coli strains originating from a Chinese teaching hospital. The following carriage patterns were observed across a total of eight, six, and one E. coli isolates, respectively: blaNDM (268%), mcr-1 (201%), and tet(X4) (034%). The blaNDM gene demonstrated high similarity to multiple plasmids of the same incompatibility type in the Enterobacteriaceae, being located on IncX3 (n=4), F2A-B- (n=3), and F2A1B1 (n=1) plasmids. ssr signal Six strains harboring MCR genes had mcr-1 integrated within IncI2 plasmids, an arrangement mirroring that of mcr-1-bearing IncI2 plasmids observed in Chinese animal sources. A 5-bp direct repeat formation was observed in four mcr-1-positive plasmids due to the insertion of the blaCTX-M-55/64/132/199 gene, located within the transposition unit ISEcp1-blaCTX-M-orf477, near the dnaJ gene. The IncX1 plasmid contained tet(X) and four other resistance genes, aadA2, tet(A), floR, and lnu(F), in a clustered arrangement. This plasmid showed striking similarity to other tet(X4)-containing IncX1 plasmids from animal or food-derived Escherichia and Klebsiella samples, save for the absence of the conjugative transfer region present on the IncX1 plasmids. Although a low prevalence of blaNDM, mcr-1, and tet(X) was found in E. coli from patients in this study, their spread coupled with successful pandemic plasmids demands further investigation and action. The monitoring of these crucial resistance genes in patients, who exhibit these specific traits, should be given more attention and resources.Low-acid canned foods can experience flat sour spoilage due to the presence of Geobacillus stearothermophilus, a highly thermophilic, spore-forming Gram-positive bacterium. Addressing this concern entailed isolating phage GR1, which infects G. stearothermophilus, from the soil and subsequently analyzing its constituent endolysin LysGR1. Within the Siphoviridae family, phage GR1 harbors a DNA genome of 79,387 base pairs, with 108 predicted open reading frames. GR1 exhibited a remarkably low degree of homology with previously documented phages, signifying its unique nature. LysGR1, the endolysin from GR1, comprises an N-terminal amidase domain serving as the enzymatic active domain (EAD) and two C-terminal LysM domains acting as the cell wall binding domain (CBD). Specific G. stearothermophilus strains are targeted by GR1, but LysGR1 demonstrated a markedly broader killing effect, eliminating every tested G. stearothermophilus strain and several foodborne pathogens like Clostridium perfringens, Listeria monocytogenes, and Escherichia coli O157H7. LysGR1 EAD, in a solitary capacity, displays lytic activity against numerous bacteria, including Bacillus cereus, which is not stopped by the presence of a complete endolysin. The eradication of *G. stearothermophilus* biofilms is effectively achieved by both LysGR1 and its engineered domain, demonstrating substantial thermal stability. Following a 15-minute incubation period at 70°C, about 70% of their lytic activity remains. In view of the superior thermal stability, substantial lytic activity, and outstanding biofilm reduction displayed by LysGR1 and its EAD, we hypothesize their potential as effective biocontrol agents against *G. stearothermophilus* and foodborne pathogens.Substantial economic damage results from viral infections that affect orchids, important ornamental plants. Among orchid viruses, Cymbidium mosaic virus (CymMV), Odontoglossum ringspot virus (ORSV), and Cymbidium ringspot virus (CymRSV) are prominently notable for their prevalence and significance. This study proposes a triplex TaqMan quantitative real-time PCR system for simultaneous detection of CymMV, ORSV, and CymRSV. For the amplification of CymMV, ORSV, and CymRSV, we devised specific primers and probes, yielding amplified sequences of 156, 148, and 145 base pairs, respectively. For CymMV and CymRSV, the triplex qRT-PCR assay had a minimum detection limit of 1 copy per assay; the assay's minimum detection limit for ORSV was 10 copies per assay. The detection limits, at a stable level, for CymMV, ORSV, and CymRSV are 10, 102, and 102 copies per assay, respectively. Accordingly, the system demonstrated a substantial increase in sensitivity, approximately 10-fold to 104-fold higher than RT-PCR's. The triplex assay exhibits exceptional reliability and accuracy, as evidenced by its intra-assay and inter-assay coefficients of variation (CVs) for Cq values being less than 0.55% and 0.95%, respectively. In addition, a total of 66 samples from five distinct orchid genera were screened using the established assay and gene chip. The superior sensitivity of the triplex probe qRT-PCR, compared to the gene chip according to detection results, validates the triplex real-time PCR assay's applicability to the detection of field samples. The triplex real-time RT-PCR assay, as our investigation shows, provides a swift, uncomplicated, and accurate procedure for detecting the presence of CymMV, ORSV, and CymRSV in orchids.The surface proteins of Gram-positive pathogens represent critical virulence factors, meaningfully influencing host-microbe relationships. Protein-mediated host invasion and pathogen transmission, alongside heme-iron acquisition from hemoproteins, along with subversion of innate and adaptive immunity, drive the bacterial survival and pathogenesis in a hostile environment.