The spread of antibiotic resistance has made bacterial infections a global public health crisis, posing serious challenges to conventional antibiotic therapy and creating an urgent need to develop novel antibacterial strategies. As viruses are capable of specifically lysing bacteria, phages represent a promising alternative therapeutic strategy due to their unique killing mechanisms and high host specificity. Nevertheless, they face limitations in monotherapy due to their narrow host ranges and the emergence of phage-resistant bacteria. In recent years, phage-antibiotic combination therapy has garnered significant attention. It demonstrates unique advantages in enhancing bactericidal effects, synergistically inhibiting dual-resistance mechanisms, broadening the host range, disrupting biofilms, and treating complex infections. This therapy not only overcomes the limitations of single phage therapy but also paves new avenues for treating multidrug-resistant bacterial infections. This review systematically summarizes the synergistic mechanisms, key influencing factors, current challenges, and optimization strategies of phage-antibiotic combination therapy, aiming to provide a theoretical foundation and practical guidance for further research and clinical translation in this field.

Objective As a zoonotic pathogen, Proteus mirabilis poses a serious challenge to public health due to its multi-antibiotic resistance and the synergistic effect of virulence genes. To characterize the antibiotic resistance transmission of bacteria in the food chain in Zhejiang Province, this study systematically monitored the antibiotic resistance phenotypes and genes of isolates from cattle slaughterhouses and farmers’ markets, and analyzed the distribution differences of antibiotic resistance genes (ARGs), virulence genes (VGs), and mobile genetic elements (MGEs). Methods A total of 384 samples (feces, carcasses, environment, etc.) were collected from cattle slaughterhouses and farmers’ markets, and the strains were identified by 16S rRNA gene sequencing. Twenty ARGs and 10 VGs were detected by the K-B disc diffusion method and PCR, and the ARGs and VGs carried by P. mirabilis were analyzed. The ARG clusters were analyzed by sequencing of integron gene cassettes, and the co-occurrence network of ARGs, VGs, and MGEs was constructed. Subsequently, conjugative transfer experiments were carried out to explore the horizontal transmission potential of ARGs. Results A total of 101 strains of P. mirabilis were isolated, with the total isolation rate of 26.30%. The isolation rate of strains from slaughterhouses (33.85%) was significantly higher than that from farmers’ markets (18.75%). The resistance rates to ceftriaxone sodium, amoxicillin, and erythromycin were all over 90.00%. Among the ARGs, bla_TEM (89.09%), sul1 (77.71%), and tetA (63.29%) had the highest detection rates, and the distribution of ARGs in slaughterhouses was more complex. The VGs fliL (92.08%) and zapA (80.20%) were highly expressed in the isolates, which suggested potential pathogenicity. The detection rate of integrons in slaughterhouses was significantly higher than that in farmers’ markets, and PCR amplification results showed that there were a variety of ARGs, including aminoglycoside and trimethoprim resistance genes. Co-occurrence network analysis showed that ARGs, VGs, and MGEs had significantly positive correlations, and type I integron (intI1) was the hub gene. Conjugative transfer experiments confirmed that bla_TEM could be transmitted across species via horizontal transmission. Conclusion Compared with farmers’ markets, slaughterhouses are key nodes in the spread of antibiotic resistance due to the antibiotic exposure pressure, high organism density, and rich mobile components. The findings emphasize the importance of strengthening antibiotic management and monitoring the transmission chain of ARGs, providing a scientific basis for the prevention and control of antibiotic resistance under the framework of “One Health”.

Objective The mesophilic salt-tolerant xylanase XynRBM26, a member of the GH10 family, holds significant application value in industrial fields such as animal feed. This study improved the thermostability of this enzyme by protein modification via rational design, aiming to lay a foundation for the industrial application of XynRBM26 preparations. Methods The bioinformatics software FoldX was used to conduct positionscan of the 3D structure predicted by AlphaFold 2.0 for XynRBM26. The mutants with free energy changes less than -0.5 kcal/mol were selected to construct an initial electronic library. According to the Pro effect and screening principles for potential mutants, an electronic library composed of Pro mutations was subsequently established. Finally, site-directed mutagenesis was employed to construct mutant genes, and positive mutants were screened after heterologous expression, purification, and experimental verification. Results After screening of the initial potential mutants, a small and precise mutant library consisting of 21 Pro effect mutants was constructed. All the mutants were experimentally validated, and positive single-point mutants D222P, V182P, D344P, and A352P with significantly increased T_m values were screened out. Through subsequent stacking screening, a three-point stacked Pro effect mutant with superior properties was obtained. The combination of this mutant with the experimentally screened positive mutant G115D produced the most stable mutant M4 (G115D-D222P-D344P-A352P). Compared with wild-type XynRBM26, M4 showed increases of 6.5 °C and 5 °C in T_m and optimal temperature, respectively. Moreover, M4 presented the half-life (t_1/2) at 55 °C 7.5-fold longer than the wild type, and its relative activity at the optimal temperature was 3.44 folds that of the wild type. Conclusion Screening thermostable mutants of the salt-tolerant xylanase XynRBM26 of the GH10 family based on the Pro effect and two different effect superimposing strategies is an effective approach.

In multicellular organisms, cell death is perpetually in a dynamic process. Apoptosis as a pivotal form of regulated cell death, mainly encompasses two pathways: the intrinsic pathway and the extrinsic pathway. During the pathogen infection, host cells are capable of eliminating the infected cells through apoptosis. On the other hand, pathogens have evolved a multitude of strategies to regulate host cell apoptosis. These strategies involve the use of effector proteins to modulate cellular signaling pathways, the regulation of the expression of apoptosis-related genes, the control of key proteins within the apoptosis pathway, and the modulation of the activity of proteases in the Caspase family. This article provides a comprehensive review of the molecular mechanisms and strategies by which intracellular pathogens, such as viruses, bacteria, parasitic fungi, and parasites, regulate host cell apoptosis. The aim is to offer valuable references for further exploration of the intricate interaction mechanisms between pathogens and hosts.

Objective To breed Bifidobacterium adolescentis strains that can adapt to the gastrointestinal environment of felines and have strong intestinal colonization capabilities. Methods B. adolescentis was isolated from the feces of felines with long and regular life spans. The original strain QC-Y (with the life span extension rate reaching 33.85%) was selected through biomass assessments and mouse life span experiments and it was identified as B. adolescentis. After radiation-induced mutation, QC-Y-09 was screened out by the biomass assessment, gastrointestinal tolerance domestication, and evaluation. Results QC-Y-09 showed the biomass 55.667 times and the tolerance score 5.66 times that of QC-Y. Moreover, the tolerance of the strain to the feline gastrointestinal environment showed good genetic stability. The survival rates of the 10th generation of QC-Y-09 in the artificial gastric juice, intestinal juice, anaerobic, and micro-aerobic environments were 18.80%, 41.60%, 93.26%, and 48.39%, respectively, which were 62.67%, 108.53%, 97.92%, and 94.40% of those of the original generation. The intestinal colonization test showed that the colonization ability of QC-Y-09 in felines was significantly stronger than that of QC-Y and human-derived B. adolescentis. Seven days after the feeding of the microbial inoculum was stopped, the viable count of B. adolescentis in the feline feces of the QC-Y-09 group still reached 4.37 lg CFU/g, which was 1.74 lg CFU/g and 3.02 lg CFU/g, respectively, higher than those of the QC-Y group and the human-derived B. adolescentis group. In addition, QC-Y-09 had a good relieving effect on the feline food change stress, reducing the feline food change stress rate by 85.71%. The results of SNP analysis showed that QC-Y-09 was significantly different from QC-Y at the gene level, and the differentially expressed genes were mainly enriched in the ribosome structure and aminoacyl-tRNA biosynthesis pathway. Conclusion Feline-derived B. adolescentis QC-Y-09 bred in this study can effectively adapt to the gastrointestinal environment and colonize the intestines of felines. This study provides both theoretical and practical bases for the application of B. adolescentis in functional food for felines.

Objective To explore the functions of type XI histidine kinase genes in Botrytis cinerea, thereby establishing a foundation for further elucidation of the molecular mechanisms involving histidine kinase-related genes in the growth, development, and pathogenic processes of plant pathogenic fungi. Methods Through knockout vector construction, ATMT transformation, and PCR/qPCR validation, we obtained the mutant ΔBcHK91. The colony growth, sclerotium formation, conidial production and morphology, conidial germination rate, appressorium and infection cushion formation rates, pathogenicity, cell wall/membrane integrity assays and transcriptome profiling were conducted to evaluate the effect of BcHK91 knockout on B. cinerea strain B05.10, thereby elucidating the biological function of this gene. Results Two BcHK91 knockout mutants were successfully obtained and designated as ΔBcHK91-A and ΔBcHK91-B. The phenotypic analysis revealed that the knockout of BcHK91 reduced the conidial length, conidial production, conidial germination rate, appressorium formation rate, infection cushion formation rate, and pathogenicity. Moreover, the mutant formed no sclerotium and showed increased sensitivityto Congo red and SDS compared with the wild-type strain B05.10 and the ectopic insertion strain ET. To reveal the transcription mechanisms of BcHK91, we compared the transcriptomes of B05.10 and ΔBcHK91 by RNA-seq. A total of 1 533 differentially expressed genes (DEGs) were predicted in ΔBcHK91, including 1 017 genes with up-regulated expression and 516 genes with down-regulated expression. Gene ontology (GO) and clusters of orthologous groups (COG) annotation showed that the DEGs were mainly involved in cell process and metabolic process of biological processes, cellular anatomical entity and intracellular of cellular components, and catalytic activity, binding, and transporter activity of molecular functions. The Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis showed that the DEGs were mainly involved in carbohydrate transport and metabolism, starch and sucrose metabolism, and mitogen-activated protein kinase (MAPK) cascade response and other physiological metabolic pathways related tothe phenotype and pathogenicity of ΔBcHK91. In silico analysis of the DEGs suggested that 17 DEGs were related to the growth and development, oxidative stress, cell wall biosynthesis, cell membrane integrity, sclerotial initials, and pathogenicity. The results of qPCR demonstrated that the expression levels of 13 genes matched the trends observed in RNA-seq data, confirming the high reliability of the transcriptome analysis. Conclusion In B. cinerea, BcHK91 plays critical roles in asexual development, environmental stress responses, and pathogenicity.

Objective To study the protective effect of baicalin on mice infected by porcine extraintestinal pathogenic Escherichia coli (ExPEC) PCN033 strain and explore the underlying mechanism. Methods The mouse infection model and Western blotting were employed to determine the clinical features, survival rate, bacterial loads in different tissue samples, pathological changes, and expression levels of P65, IκBα, NLRP3, ASC, and Caspase-1 of mice in the infection group and the baicalin treatment group. Results After baicalin treatment, the mental state of mice in the baicalin treatment group was obviously better than that in the infection group. The survival rate of mice in the baicalin treatment group was higher than that in the infection group, and the colonization ability of PCN033 in the blood, brain, and lung of mice in the baicalin treatment group was lower than that in the infection group. Further studies showed that baicalin inhibited the PCN033 infection-induced activation of phosphorylation of P65 and IκBα and down-regulated the expression levels of NLRP3, ASC, and Caspase-1 in mice. Conclusion Baicalin alleviated the inflammatory response caused by porcine ExPEC infection by inhibiting NF-κB signaling pathway and blocking the activation of NLRP3 inflammasome, thereby reducing the clinical symptoms and tissue damage in mice. It is suggested that baicalin may be a potential drug to prevent and treat porcine ExPEC infection by regulating the inflammatory response.

Objective As biocatalysts, halohydrin dehalogenases can catalyze both cyclization and ring-opening reactions and are widely used in the synthesis of chiral epoxides and other compounds. The eco-friendly and efficient preparation of halohydrin dehalogenases is thus of great significance. In this study, we optimized the N-terminus of the coding sequence of the halohydrin dehalogenase HheC based on the mRNA secondary structure to achieve the efficient expression of this enzyme and then applied this enzyme in the synthesis of chiral epichlorohydrin. Methods The mRNA prediction tools was used to predict the secondary structure and thermodynamic properties of 5′mRNA. To reduce the stability of the mRNA secondary structure and increase folding free energy (ΔG), we designed the 5′mRNA sequence without changing the amino acid sequence. Furthermore, we characterized the expression efficiency and catalytic performance of this enzyme. Results The HheC mutant was obtained via the design of the 5′mRNA sequence, with the protein level increasing from 16.71% to 33.39% and the relative activity towards 1,3-dichloro-2-propanol increasing by three folds. Conclusion The optimization based on the secondary structure of 5′mRNA improves the expression level of HheC and enhances the synthesis efficiency of the target product, laying a foundation for constructing the route of enzymatic catalytic synthesis of chiral epichlorohydrin.

Sulfate-reducing bacteria (SRB) with unique reductive capabilities enable simultaneous sulfate reduction and heavy metal removal, demonstrating potential in heavy metal pollution remediation. Objective To isolate efficient SRB strains from marine sediments and investigate their reductive characteristics and application prospects in Cr(VI) contamination remediation. Methods We enriched and screened out an efficient SRB strain and systematically analyzed its sulfate reduction efficiency, Cr(VI) removal efficiency, and metabolic responses under environmental stressors (such as pH, sulfate concentration, and heavy metal concentration). This strain was then used to synthesize biological iron sulfide composite, the physicochemical characteristics of which were then investigated by scanning electron microscopy (SEM), X-ray diffraction (XRD), and Fourier-transform infrared spectroscopy (FTIR). Furthermore, the feasibility of applying the biological iron sulfide composite in the remediation of Cr(VI)-contaminated environments was explored. Results Strain S5 was identified as Desulfovibrio sp. with GenBank accession number OR140726. Its protein concentration and sulfate reduction followed an S-shaped curve. This strain exhibited a certain degree of acid tolerance, with the OD₆₀₀ and sulfate reduction rate reaching 0.16±0.01 and (83.71±1.49)% at pH 5.0, respectively. The strain exhibited sulfate reduction capability in the presence of 0.5-1.3 g/L sulfate, achieving a maximum reduction rate of (92.27±1.20)%. In the presence of 10-30 mg/L Cr(VI), strain S5 demonstrated efficient Cr(VI) removal. However, when the Cr(VI) concentration was higher than 30 mg/L, the Cr(VI) removal rate of this strain decreased significantly. The biological iron sulfide composite prepared based on strain S5 was porous, amorphous, and rich in functional groups such as C=O, N-H, and Fe-S, and its Cr(VI) removal rates were above 85% and did not differ significantly when exposed to Cr(VI) at high concentrations. Conclusion Desulfovibrio sp. S5 is a strain with high efficiency of sulfate reduction and Cr(VI) removal, and the biological iron sulfide composite prepared with it can overcome the limitation of higher Cr(VI) concentration and maintain high Cr(VI) removal rate, which has obvious advantages in the remediation of Cr(VI) pollution. The results of this study can provide a scientific basis for the application of SRB in the bioremediation of Cr(VI)-polluted environments.

Mobile genetic elements drive bacterial evolution, while exposing bacteria to the risk of invasion by “selfish genes”. In the arms race with mobile genetic elements, bacteria have evolved a range of immune systems that can protect hosts from invading nucleic acids. These immune systems are capable of preventing the invasion of mobile genetic elements, degrading invading nucleic acids, inhibiting the replication or transcription of invading nucleic acids, or inducing abortive infections to protect the population. Although much is known about the working mechanisms of these host immune systems, it remains unclear how bacteria orchestrate different defense strategies in response to different stages of nucleic acid invasion. Based on our research and different immune strategies of bacteria to limit mobile genetic elements in different spatiotemporal dimensions, this review summarizes and classifies the host immune systems. The elucidation of these multilayered immune mechanisms not only reveals the arms race between host and mobile gene elements in the evolutionary process but also underpins the development of new biotechnologies.