[Objective] The rhizosphere of plants hosts a diverse array of microorganisms that play a crucial role in plant growth and health. This study identified functional bacteria in the rhizosphere soil of an economic bamboo species Indosasa acutiligulata and assessed the effects of synthetic microbial communities (SynComs) on bamboo growth. The results are expected to provide implications for enhancing forest quality and utilizing beneficial microorganisms in bamboo cultivation. [Methods] Rhizosphere soil samples of In. acutiligulata were collected from the Jiuyi Mountain National Nature Reserve. Bacteria were isolated by the dilution culture method, and a phylogenetic tree was established by the maximum-likelihood algorithm based on 16S rRNA gene sequences. Specific media and colorimetric assays were employed to study the functions of strains. The strains with plant growth-promoting effects and no antagonistic effects between each other were combined. The effects of SynComs on the growth of Phyllostachys edulis seedlings were examined by re-inoculation experiments. [Results] Seventy strains of rhizosphere bacteria were isolated, representing 35 genera belonging to 21 families of four phyla. The dominant phylum was Pseudomonadota and the predominant family was Burkholderiaceae. Functional analyses revealed that 30 strains produced indole-3-acetic acid (IAA), while 16 strains produced siderophores. Among those with dual functions, there were four strains capable of solubilizing inorganic phosphorus, four strains capable of mineralizing organic phosphorus, and three strains capable of solubilizing potassium. Strains TR5, TN6, and TN26 exhibited capabilities to produce IAA and siderophores, as well as solubilize inorganic phosphorus and mineralize organic phosphorus. They were identified as Burkholderia pyrrocinia, Burkholderia paludis, and Paraburkholderia kirstenboschensis, respectively, based on physiological and biochemical properties and 16S rRNA gene sequences alignments. Re-inoculation experiments demonstrated that the SynCom FH, comprising strains TR5, TN6, and TN26, significantly enhanced the root, leaf, and rhizoma growth of Ph. edulis seedlings. [Conclusion] The rhizosphere of In. acutiligulata harbors diverse functional microorganisms capable of producing IAA and siderophores, solubilizing phosphorus, and releasing potassium. The re-inoculation experiments confirmed that the SynCom FH promotes the growth of Ph. edulis seedlings.

The toxin-antitoxin (TA) system is ubiquitous in bacteria and archaea. A typical TA system generally consists of a toxin that inhibits bacterial growth and an antitoxin that neutralizes toxin toxicity. At present, TA systems are classified into types I-VIII, of which type II system is the most extensively studied. In addition, researchers have found that there are atypical TA systems such as monocistronic TA systems and three-component TA systems. After the discovery of the first TA system (CcdB/CcdA) in the 1980s, TA systems have been shown to play a key role in the physiological processes of microorganisms. In this paper, we review the research results about the roles of TA systems in resisting bacteriophage infections in recent years and summarize the neutralization mechanisms. In particular, we brief how TA systems specifically sense the invading bacteriophages and the underlying molecular mechanisms, aiming to provide reference for the research on the roles and regulation mechanisms of unknown TA systems in the future.

Shikimic acid (SA) is an important natural compound with many biological activities, including antiviral, antithrombotic, analgesic, antimicrobial, and anti-cancer properties. Due to its diverse applications in medicine, cosmetics, food, and agriculture, SA is considered a highly promising biomolecule. As a precursor of aromatic compounds, SA plays a crucial role in various metabolic pathways within organisms. Traditional methods for producing SA mainly rely on plant extraction (such as star anise) or chemical synthesis. However, these approaches face challenges such a high costs, low efficiency, and environmental concerns. With the ongoing advancements in synthetic biology and metabolic engineering, the production of SA through metabolic engineering has emerged as a focal point of research, offering a more sustainable and cost-effective alternative. This paper reviews the applications and production methods of SA, with a particular emphasis on recent progress and optimization strategies in its biosynthesis.

CsgD, a core regulatory protein for the biofilm formation of Salmonella, exerts its function by regulating the expression of key components (curli and cellulose) of the biofilm. In recent years, significant progress has been achieved in analyzing the regulatory network of Salmonella CsgD protein and its complex influencing factors. Focusing on the regulatory function of CsgD in the biofilm formation of Salmonella, this paper systematically introduces how environmental factors affect the CsgD expression and comprehensively analyzes the multi-level regulatory effects of various regulatory factors on CsgD, aiming to enrich our understanding about the mechanism and regulatory network of the biofilm formation of Salmonella and provide possible research directions.

[Objective] To elucidate the phylogenetic position and mine the gene resources for synthesis of secondary metabolites from Streptomyces sp. YH02, a Gram-positive actinomycete strain isolated from the soil sediment of Yuncheng Salt Lake in Shanxi. [Methods] Illumina and PacBio platforms were used for whole genome sequencing of YH02, which was followed by gene prediction, functional annotation, prediction of secondary metabolite synthetic gene clusters (BGCs), comparative genomic analysis, and morphological, physiological, and biochemical characterization. [Results] The YH02 genome was a linear chromosome spanning 8 285 116 bp, with the G+C content of 71.77% and 7 237 open reading frames. Gene annotations in the GO, COG, KEGG, and CAZy identified 2 829, 5 478, 4 805, and 279 genes, respectively. The subcellular localization analysis predicted various secretion system-related proteins and 1 030 transporters. Additionally, 32 secondary metabolite BGCs were predicted in strain YH02, involving the synthesis of various natural products such as terpenoids, non-ribosomal peptides, polyketides, and ribosomally synthesized and post-translationally modified peptides. The comparative genomic analysis revealed 15 739 pan-genome orthologous gene clusters and 4 267 core genome orthologous gene clusters. The phylogenetic analysis based on the 16S rRNA gene sequence revealed a proximate phylogenetic affiliation between strain YH02 and Streptomycesvenezuelae ATCC 10712 as well as Streptomyceszaomyceticus NBC 00278. However, the average nucleotide identity (ANI) value was below the threshold of 95.00%, and the digital DNA-DNA hybridization (dDDH) value was less than 70.00%. YH02 exhibited light pink aerial mycelia on the ISP 2 medium. It showed significant differences in tolerance to pH, sodium chloride, and growth temperature compared with its closely related strains. Additionally, this strain demonstrated weak starch hydrolysis activity, positive gelatin liquefaction, positive nitrate reduction, and slow milk coagulation. [Conclusion] Based on the findings from genomic, physiological, and biochemical analyses, strain YH02 is confirmed as a potential new species of Streptomyces. This study not only enriches the microbial resource pool but also provides a theoretical basis and potential genetic resources for mining the natural products with unique mechanisms of action.

[Objective] To study the effect of Alistipesfinegoldii (AF) on inflammatory bowel disease (IBD) and the underlying mechanism. [Methods] Six-week-old male C57BL/6J mice were administrated with streptomycin for three days and then randomly assigned into the control, phosphate buffered saline (PBS), and AF groups. Mice were administrated with AF suspension (1×10⁹ CFU, 200 μL per mouse) or PBS by gavage for two weeks, followed by drinking of the water containing 2.5% dextran sulfate sodium (DSS) for one week for the modeling of colitis. The weight loss fraction percentage, fecal characteristics, blood fecesstools, and colon length were determined. The colon tissue was stained with hematoxylin-eosin for the scoring of histopathological changes, and feces samples were collected at the beginning and end of the experiment for sequencing of 16S rRNA gene amplicons at the beginning and end of the experiment. The mRNA levels of colon tissue-associated intestinal barrier proteins and inflammatory mediators were determined by qPCR. [Results] The mice in the AF group had severer disease conditions than those in the PBS group regarding the weight loss percentage, disease activity index, colon shortening, and histopathological score. Compared with the PBS group, the AF group showed down-regulated mRNA levels of occludin and claudin 5 and up-regulated mRNA level of interleukin (IL)-17A. The AF group had lower alpha diversity of intestinal flora than the PBS group, and the beta diversity showed significant differences between AF and PBS groups. The linear discriminant analysis effect size (LEfSe) results revealed that the significantly differential bacteria between AF and PBS groups were Bacilli, Erysipelotrichales, Erysipelotichaceae, Odoribacter, Marinifilaceae, Dubosiella, and Dubosiellanewyorkensis. [Conclusion] AF promotes the secretion of inflammatory mediators, impairs the permeability of the intestinal mucosa, and alters the structure and diversity of the intestinal flora, thereby promoting the development of IBD.

[Objective] To develop a safe, effective, and identifiable new vaccine. [Methods] The gene deletion strain S2Δbp26 was constructed by homologous recombination with S2 as the parental strain. The stability, safety, and efficacy of S2Δbp26 were then evaluated. [Results] The phenotype and genotype of S2Δbp26 did not change after 20 successive passages invitro. The experiments in mice and guinea pigs showed that there was no difference in biosafety between S2Δbp26 and S2. The bacterial load was less than 2×10⁵ CFU per gram of spleen in guinea pigs inoculated with S2Δbp26 at different passages and S2, which suggested that the virulence of the mutant strain was attenuated. The mice inoculated with S2ΔBP26 had a shorter 50% recovery time than those inoculated with S2. Meanwhile, the mice immunized with S2Δbp26 could successfully resist the challenge with M28 wild-type strain at a dose of 2×10⁵ CFU/mouse. [Conclusion] S2Δbp26 was successfully constructed, with excellent safety and immunoprotective capacity, which provided technical reserves for the development of identifiable vaccines for brucellosis.

[Objective] To explore the effects of freeze-thaw on oat silage during the aerobic exposure stage. [Methods] Oat silage was stored at a constant temperature (20 ℃, group 20, control) and freeze-thaw conditions (20 ℃ and -5 ℃ alternating every 12 h, group S) for 60 days and then subjected to aerobic exposure. Samples were collected on day 60 of ensiling and after aerobic exposure for 1, 3, and 5 days, respectively, for the determination of fermentation quality and nutritional quality as well as for 16S rRNA gene and ITS sequencing. [Results] The pH rose as the aerobic exposure was prolonged. The samples subjected to aerobic exposure at room temperature showed more rapid increases in ammonia nitrogen content and pH and more rapid decreases in lactic acid and acetic acid content than those subjected to aerobic exposure at freeze-thaw temperatures. Propionic acid and butyric acid were produced more rapidly in the S group, especially in the case of aerobic exposure at room temperature. Enterobacteria and yeast increased while lactic acid bacteria decreased as the aerobic exposure was prolonged (P<0.05). Shannon and Simpson indices of bacteria increased during aerobic exposure, and the relative abundance of lactic acid bacteria kept decreasing. The bacterial community structure presented a significant difference on days 3 of aerobic exposure, and microbial succession was accelerated by aerobic exposure at room temperature compared with that at the freeze-thaw temperature, with more species and higher counts of yeast and molds indicative of spoilage in the S group. [Conclusion] Freeze-thaw accelerated aerobic deterioration, especially aerobic exposure at room temperature. This study provides theoretical guidance for high-quality modulation and storage of oat silage in alpine areas.

[Objective] The biological regulatory mechanisms of soil microorganisms in response to single heavy metals or organic pollutants have been extensively studied, while the biological mechanisms of microbial responses to combined pollution remain unclear. This study aims to reveal the biological mechanisms of Enterococcus faecalis HHT-1 in response to single and combined stress of cadmium (Cd) and aniline (AN) by transcriptomics. [Methods] Transcriptomics was employed to explore the transcriptional regulation of HHT-1 under single (Cd: 150 mg/L; AN: 2 g/L) and combined stress (150 mg/L Cd and 2 g/L AN) at half inhibitory concentrations (IC₅₀). [Results] Under single Cd stress, HHT-1 upregulated the expression of genes encoding metal-binding proteins and transporters to promote the sequestration or efflux of Cd²⁺. High concentrations of Cd induced oxidative stress in cells, and HHT-1 upregulated the expression of ribosome-related genes and nucleotide-related genes to repair the protein damage and DNA damage caused by oxidative stress, and cleared intracellular reactive oxygen species (ROS) by producing catalase. Moreover, Cd stress upregulated the expression of genes related to virulence and antibiotic resistance in HHT-1. Under the single stress of AN, HHT-1 activated the expression of AN-degrading enzyme genes to reduce its toxicity and upregulated the expression of genes encoding efflux pumps to excrete AN from the cell. AN also caused intracellular oxidative stress, and HHT-1 cleared the ROS by upregulating the expression of glutathione synthase genes. Under the combined stress of Cd and AN, HHT-1 exhibited a complex array of adaptive mechanisms. Initially, HHT-1 upregulated the expression of genes encoding metal transporters and efflux pumps to transport Cd and AN out of the cell, thereby mitigating their toxic effects on the cell. At the same time, HHT-1 cleared intracellular ROS via the dual pathway of catalase and glutathione. In addition, HHT-1 upregulates the expression of virulence and antibiotic resistance genes under combined stress, which may enhance its pathogenicity and resistance. It is worth noting that HHT-1 did not significantly upregulate the expression of AN-degrading enzyme-related genes under the combined stress. [Conclusion] The transcriptional regulation mechanism of E. faecalis HHT-1 in response to the combined stress of Cd and AN is a combination of the transcriptional regulation mechanisms observed under single Cd stress and single AN stress, and it is more similar to the mechanism observed under single Cd stress. HHT-1 mainly responds to the combined stress of Cd and AN by enhancing cell wall synthesis, Cd²⁺ efflux, DNA repair, and ROS scavenging. Genes associated with efflux pumps and glutathione under AN stress continue to be expressed under the combined stress. Both single Cd stress and combined stress of Cd and AN may increase the potential pathogenicity and drug resistance of HHT-1.

[Objective] To identify the active components in Glycyrrhiza uralensis Fisch. that inhibit methicillin-resistant Staphylococcus epidermidis (MRSE) infections and explore their potential antibacterial mechanisms. [Methods] The half-dilution method was employed to assess the inhibitory activities of pharmacological components from G. uralensis against MRSE. The anti-MRSE phenotype of this medicinal herb was evaluated by microbial adhesion to hydrocarbons, crystal violet staining, scanning electron microscopy, and integrated cell imaging. Additionally, metabolomic analysis was conducted via gas chromatography-mass spectrometry (GC-MS), and the activity of intracellular oxidative dehydrogenase was measured by a commercially available reagent kit. The propidium iodide and laurdan dyes were utilized to assess the membrane damage and fluidity of cells. The challenge test was conducted with the larvae of Galleria mellonella to determine the antibacterial activities of tested pharmacological components in vivo. [Results] Licochalcone A, licochalcone C, and glabridin from G. uralensis demonstrated significantly inhibitory activities against MRSE. Among these compounds, licochalcone A exhibited the strongest inhibitory effect on MRSE, with a minimum inhibitory concentration (MIC) of 6.0 μg/mL and a minimum bactericidal concentration (MBC) of 12.0 μg/mL. The metabolomic analysis indicated that licochalcone A primarily influenced the metabolic pathways, secondary metabolite biosynthesis, and ATP-binding cassette (ABC) transport systems of MRSE. This compound impeded the biosynthesis of ornithine, lysine, and niacin, leading to the accumulation of 1,3-dipalmitin in the cells. Phenotypic experiments corroborated that licochalcone A downregulated the tricarboxylic acid (TCA) cycle flux and reduced the intracellular ATP level in MRSE. Furthermore, it inhibited the biofilm formation and intracellular protein expression, thereby preventing MRSE from adhering to HaCaT cells. Additionally, licochalcone A disrupted the structural integrity of the MRSE cell membrane, resulting in cell collapse, deformation, and even rupture and increased the survival rate of G. mellonella larvae following MRSE infection. [Conclusion] Exposure to licochalcone A alters the metabolism of sugars, lipids, and amino acids in MRSE cells, thereby influencing the biofilm formation, biosynthesis of secondary metabolites such as proteins, and the remodeling of cell membranes. Consequently, this alteration results in an antimicrobial phenotype characterized by decreased ATP production, impaired transporter function, and reduced adhesion and infection of MRSE.