Objective To investigate the changes in gut microbiota, serum metabolites, and differentially expressed genes (DEGs) in the lung tissue of the mouse model of pulmonary fibrosis and explore the potential associations via multi-omics analysis. Methods A mouse model of pulmonary fibrosis was established by the dynamic inhalation exposure method and evaluated. Metagenomic sequencing was performed to analyze the microecological changes in cecal contents. Untargeted metabolomics was employed to detect serum metabolite alterations, and transcriptomic sequencing was conducted to profile DEGs in the lung tissue. Bioinformatics methods were comprehensively used to explore correlations and potential functional modules among differential microbial taxa, metabolites, and genes. Results Pathological changes of pulmonary fibrosis were successfully induced in the model mice, accompanied by the upregulated expression of transforming growth factor-beta (TGF-β), tumor necrosis factor-alpha (TNF-α), and fibrosis-related genes in the lung tissue. Omics results indicated the presence of gut microbiota dysbiosis, serum amino acid metabolic disorder, and lung transcriptome remodeling in the model mice. Correlation analysis demonstrated that the four differential bacterial species were strongly correlated with multiple serum metabolites, among which Akkermansia muciniphila and Ligilactobacillus murinus were jointly associated with 22 differential metabolites. A cross-omics network was constructed with these 22 differential metabolites and DEGs. Topological analysis identified five key subnetworks: (1) Inosine triphosphate serves as a phosphate donor and is converted to inosine diphosphate via multiple pathways; (2) Uridine triphosphate (UTP) undergoes an amination reaction to form cytidine triphosphate (CTP); (3) Serine/threonine-protein kinase 11, Fas-activated serine/threonine kinase, and cyclic GMP-dependent protein kinase act as core kinase nodes; (4) The reaction between serine and homocysteine bridges the metabolic pathways of methionine and cysteine; (5) Prostaglandin H₂ is catalytically converted into thromboxane A₂. Conclusion There are significant statistical correlations among gut microbiota, serum metabolites, and DEGs in the lung tissue in the mouse model of pulmonary fibrosis. We identify the core association network and potential functional modules, which provide references for the subsequent mechanism exploration of pulmonary fibrosis.

Objective To explore plant growth promoting rhizobacteria (PGPR) resources from the rhizosphere soil of maize in a maize-soybean rotation system and elucidate their roles in promoting the growth of maize and soybean, thus providing a theoretical basis and practical support at the microbial level for the sustainable development of agriculture. Methods Actinomycetes strains were isolated from the rhizosphere soil of maize via the dilution plating method with Gauze’s Synthetic Medium No. 1. The strains capable of secreting protease, producing siderophores, and fixing nitrogen were selected out. The isolated strains were identified by means of morphological observation and 16S rRNA gene sequence analysis. After optimization of the fermentation conditions and tests of stress tolerance, a synthetic microbial consortium (SMC) was prepared. Its growth-promoting effects on maize and soybean were evaluated through seed germination tests and pot experiments. Results A total of 105 Actinomycetes strains were isolated, five of which simultaneously exhibited the abilities of siderophore production, protease secretion, and nitrogen fixation. These strains were identified as Arthrobacter pokkalii (JM-18, JM-21), A. oryzae (JM-24), A. ginsengisoli (JM-47), and A. pascens (JM-48). They were mixed in equal proportions to form a SMC. Growth promotion assays showed that the SMC significantly improved maize seed germination and maize plant growth in pots. Specifically, the SMC increased the root length and shoot length in the seed germination assay by 120.22% and 20.94%, respectively, and it also significantly increased the plant height, root length, fresh weight, and dry weight of maize plants in pots. Moreover, the SMC markedly promoted soybean development, increasing soybean shoot length by 42.08% during seed germination. For potted soybean plants, the SMC increased the plant height, root length, fresh weight, and dry weight by 39.40%, 93.31%, 161.14%, and 163.57%, respectively. Conclusion We successfully identified five Actinomycetes strains capable of secreting protease, producing siderophores, and fixing nitrogen. The SMC constructed from these strains significantly enhances the growth of both maize and soybean. This study offers promising microbial resources for the development of efficient and environmentally friendly biofertilizers.

Objective The effects of the helper strain (Priestia endophytica)1-112 on the growth of Ketogulonicigenium vulgare and the biotransformation of 2-keto-L-glonic acid (2-KLG) remain unclear. In this study, we cultured the helper strain in different media to study the mechanisms of the growth- and 2-KLG biotransformation-promoting effects of the helper strain on K. vulgare. Methods We used different media (minimal, mixed, and fementation media) to culture the helper strain and investigated the effects of the strain on the growth and 2-KLG biotransformation of K. vulgare. The differently expressed genes (DEGs) and associated metabolic pathways in the helper strain cultured in different media were analyzed by transcriptomics to screen the key factors in the co-culture system. The effects of key factors on the growth and 2-KLG biotransformation of K. vulgare were evaluated to explore their roles in the co-culture system. Results Strain 1-112 cultured in the minimal medium lost or reduced the ability to promote 2-KLG production, while it retained the ability to promote the growth of K. vulgare. This result indicated that the helper strain promoted 2-KLG biotransformation through two distinct mechanisms. There were 1 859 DEGs in strain 1-112 cultured in fermentation medium in comparison with the minimal medium, and the DEGs were significantly enriched in the pathways such as nicotinate and nicotinamide metabolism, carbon metabolism, arginine and proline metabolism, and amino acid biosynthesis. In addition, the helper strain cultured in the minimal medium containing some key factors could restore the ability to promote 2-KLG production. Glycine, proline, biotin, and nicotinic acid were found to be essential for promoting K. vulgare growth, whereas glycine, threonine, biotin, and nicotinic acid played critical roles in enhancing 2-KLG biotransformation. Conclusion The helper strain promoted the growth and 2-KLG biotransformation of K. vulgare through different mechanisms.

Microorganisms represent the largest untapped resource reservoir on the Earth, and breakthroughs in their isolation and cultivation are prerequisites for fundamental advances in the life sciences. This review focuses on recent progress in the isolation and screening technologies for bacteria, fungi, and archaea. It systematically elucidates how the development and application of cutting-edge isolation and screening technologies have enhanced the efficiency of isolating previously uncultivable and rare microbial taxa. By summarizing lineage-specific strategies—such as multi-omics targeting and single-cell precision localization for bacteria, metabolomics-guided screening and microfluidic technology for fungi, and co-culture systems coupled with extreme-condition cultivation for archaea—this review highlights the core value of interdisciplinary technology integration in bridging genomic data with in situ functional validation. Finally, the article prospectively addresses challenges in data integration and the construction of automated workflows, thereby outlining a strategic pathway for the systematic exploration of microbial resources.

Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a class of secondary metabolites synthesized by the ribosomes of microorganisms and formed through a series of post-translational modifications. They have diverse structures, high stability, and antimicrobial, antiviral, anti-inflammatory or anti-tumor activities. Moreover, they are not prone to generating drug resistance, thus showcasing great potential to be applied in the fields of medicine, food, and agriculture. The genomes of microorganisms harbor a large number of biosynthetic gene clusters for RiPPs, while many of them require the producing strains to be cultivated in specific conditions or to interact with other environmental microorganisms, being the “dark matter” in the genome. Heterologous biosynthesis is an effective means to obtain novel RiPPs and make use of them. This article reviews the recent research progress in the diversity, bioactivity, genomic mining, and heterologous biosynthesis of RiPPs from microorganisms, with the expectation of providing a theoretical basis for a deeper understanding of the molecular structures and functions of RiPPs, as well as for the development and application of novel microbial active metabolites and their producers.

Respiratory viral infections pose a severe threat to global public health security, and exploring effective strategies to prevent them is of clinical significance. The gut microbiota plays a crucial role in regulating anti-infective immunity by remodeling the immune microenvironment, maintaining the immune homeostasis and boosting antiviral defenses of the host. Conversely, dysbiosis of the gut microbiota can disrupt immune homeostasis, resulting in impaired innate immune responses and abnormal activation of adaptive immunity, thereby raising the risk of respiratory viral infections in the host. This study elaborates on the essential role of the gut microbiota in the antiviral immune response of the host across multiple aspects. (1) It thoroughly explains how the gut microbiota contributes to forming an immune defense barrier by performing physiological functions such as secreting antimicrobial peptides, metabolizing nutrients, preserving mucosal barrier integrity, and modulating immune homeostasis of the host. (2) It analyzes the antiviral immune regulatory network that involves the regulation of type I interferon responses and immune cell differentiation, all within the context of gut microbiota balance and dysbiosis. (3) It explores how probiotics exert antiviral effects through mechanisms such as inhibiting viral proliferation, improving the host’s immune response, reducing secondary infections, and restoring gut microbiota balance. Although breakthroughs have been made in understanding the ternary interaction network of the microbiota, the immune system, and viral infection, the molecular mechanisms behind its dynamic balance and precise regulation still urgently need detailed investigation. Specifically, the mechanisms of interactions between gut microbiota metabolites and host epigenetic regulation, along with the long-term protective strategies of microbiota-induced immune homeostasis against viral infection, remain to be systematically revealed through multi-omics technologies.

Objective The outer membrane protein CirA serves as a specific transporter for catecholate-type siderophores and is involved in the uptake of siderophores and other nutrients, playing a crucial role in bacterial physiology. However, its impact on bacterial antibiotic resistance remains unclear. This study aimed to investigate the role of ahcirA in the antibiotic resistance of Aeromonas hydrophila ATCC 7966 under antibiotic stress, thereby providing a theoretical basis for elucidating the molecular mechanism by which ahcirA regulates bacterial resistance. Methods With A. hydrophila ATCC 7966 as the model organism, an ahcirA knockout strain (ΔahcirA) was constructed, and its susceptibility to multiple quinolones and aminoglycosides was assessed. Quantitative proteomics was further employed to compare protein expression profiles of ΔahcirA with and without antibiotic stress. Bioinformatic approaches were adopted for the functional analysis of differentially expressed proteins. Results In the media containing enrofloxacin and norfloxacin, the growth of ΔahcirA was significantly impaired compared with that of the wild-type strain. In contrast, ΔahcirA exhibited enhanced growth in the media supplemented with kanamycin and streptomycin. Proteomic and bioinformatic analyses revealed that the deletion of ahcirA may alter bacterial antibiotic resistance by affecting the expression of proteins involved in multiple biological processes, such as small molecule metabolism, and by modulating the expression of antibiotic resistance genes. Conclusion CirA plays a significant role in the antibiotic resistance of A. hydrophila. Its absence influences bacterial susceptibility to different classes of antibiotics by regulating the expression of diverse functional proteins and antibiotic resistance genes.

Listeria monocytogenes, as a major causative agent of foodborne illness outbreaks, poses a serious threat to food safety and public health. In complex foodborne pathogen environments, the specific and effective detection methods for L. monocytogenes are crucial. Objective To develop a novel recombinase-aided amplification-exonuclease (RAA-exo) assay for detecting L. monocytogenes. Methods Multiple RAA primer and probe sets targeting hly were designed, and the optimal primer set was selected based on nucleic acid amplification efficiency. The reaction system was rigorously optimized, focusing on the concentrations of A buffer, B buffer, and RAA primers and probe. Results The optimized RAA-exo assay showed a limit of detection (LOD) of 0.5 copies/μL for recombinant plasmids and 10 CFU/mL for L. monocytogenes suspensions. The assay demonstrated high specificity, selectively detecting L. monocytogenes without cross-reactivity to other common foodborne pathogens, including Salmonella, Escherichia coli, Staphylococcus aureus, Bacillus cereus, or other Listeria species (L. ovinae, L. seeligeri, and L. innocua). In a validation study using 44 pork samples, the RAA-exo assay results were in complete agreement with those of the real-time fluorescence PCR internal standard method outlined in the industry standard SN/T 5224—2019. Conclusion The developed RAA-exo assay exhibits high sensitivity and specificity, requires minimal hands-on time, and achieves detection within 20 min at 37 °C. Therefore, the assay is suitable for rapid, on-site testing, serving as an efficient and convenient tool for L. monocytogenes detection, with promising applications in food safety monitoring.

Objective Four-carbon dicarboxylic acids are a class of important platform chemicals widely used in the food, pharmaceutical, and chemical industries. However, the efficiency of microbial fermentation for producing four-carbon dicarboxylic acids still faces challenges, mainly limited by insufficient central carbon metabolic flux and byproduct accumulation. Methods This study used Escherichia coli as the chassis strain and adopted a strategy combining rational metabolic engineering and non-rational modification to systematically optimize the four-carbon dicarboxylic acid synthesis capacity of E. coli. Results The non-cyclic glyoxylate shunt was reconstructed and the expression of key pathway enzymes was optimized to enhance the metabolic flux toward four-carbon dicarboxylic acids. The synthesis capacity of four-carbon dicarboxylic acids was enhanced by employing atmospheric and room-temperature plasma (ARTP) mutagenesis. The knockout of key genes in the acetate, formate, and lactate synthesis pathways effectively minimized carbon flux diversion, thereby enhancing the availability of oxaloacetate, the central precursor to four-carbon dicarboxylic acids. On this basis, through specific modification of terminal metabolic pathways, the engineering strain E. coli Fum02 for fumaric acid production were constructed. Finally, in a 5 L fermenter, the fumaric acid titer, yield, and productivity of the engineering strain E. coli Fum02 reached 45.2 g/L, 0.45 g/g, and 0.23 g/(L·h), respectively. Furthermore, by blocking the succinate dehydrogenase gene (sdhAB) and implementing fermentation optimization strategies, this platform strain could also be redirected toward efficient succinate production. Conclusion This study provides a reference for the metabolic engineering modification of bacteria to produce organic acids and also lays a foundation for the industrial biomanufacturing of four-carbon dicarboxylic acids.

γ-Aminobutyric acid (GABA), a key inhibitory neurotransmitter in the central nervous system, plays a vital role in physiological functions such as promoting sleep, relieving tremors, and regulating blood pressure. Currently, a variety of microorganisms capable of synthesizing GABA have been identified, offering diverse strategic options for the biosynthesis of GABA through different metabolic pathways. This review provides a detailed summary of the major pathways—the GABA shunt pathway and the putrescine pathway—for GABA synthesis in various microorganisms. It systematically outlines the key synthases and metabolites involved in the two pathways, while comparing their synthesis efficiency and respective advantages. Furthermore, this study delves into the regulatory mechanisms underlying GABA biosynthesis in different microorganisms, along with key regulatory targets for enhancing synthesis efficiency. The work aims to establish a theoretical framework for the regulatory mechanisms of microbial-derived GABA synthesis and to provide a scientific basis for improving the efficiency of GABA biosynthesis.