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.

Microorganisms in high-salt environments (including halophilic and halotolerant bacteria) are widely distributed in extreme habitats such as salt lakes, oceans, and saline soils. Due to their unique metabolic adaptation mechanisms, they have become an important source of structurally novel natural products. This article outlines their taxonomic status and ecological distribution, with a focus on summarizing the chemical structures of compatible solutes such as ectoine and glycine betaine among primary metabolites, and their core roles in osmotic pressure regulation and biomacromolecule protection. The structural types of secondary metabolites, including alkaloids, terpenoids, steroids, and polyketides, are systematically reviewed. Furthermore, this article summarizes the biological activities such as antibacterial, antitumor, antioxidant, enzyme inhibitory, and photoprotective effects and discusses the structure-activity relationships of secondary metabolites. Considering the unique properties of these metabolites, this article analyzes their application prospects in fields such as medicine and health, biomaterials, and environmental remediation. This review aims to provide a theoretical reference for the in-depth development of microbial resources in high-salt environments and the discovery of novel bioactive molecules.

Microorganisms, as the oldest and most diverse life forms on Earth, possess significant development value due to their differentiated metabolic potential and biosynthetic capabilities, serving as core resources for the development of novel drugs and natural active products. Currently, the deep integration of artificial intelligence (AI) with microbial strain development is driving a paradigm shift in life sciences from “empirical screening” to “rational design”. This shift is driven both by the limitations of conventional research methods in addressing the complexity of microbial resources and by the unique advantages of AI in multi-omics data analysis, model prediction, and experimental process optimization. This article systematically reviews the roles of AI in the development and application of microbial strains, covering four aspects: strain breeding, metabolite development, disease diagnosis and treatment, and xenobiotic synthesis. Additionally, it discusses the core advantages and existing limitations of AI in the strain development process. In summary, through automated modeling and scientific prediction, AI not only accelerates the efficiency of microbial strain development but also provides multi-dimensional optimization strategies, serving as a core driver for technological innovation. The integration of AI is expected to break through traditional industrial bottlenecks and promote the sustainable development of the microbial industry.

Objective To identify high-quality yeast strains in the Xinjiang traditional milk wine fermentation system and screen specialized strains suitable for the milk wine fermentation, thereby providing a theoretical basis and strain reserves for the development of dedicated fermentation agents. Methods With alcohol production, ester production, lactose utilization ability, as well as acid (pH), glucose, and ethanol tolerance as screening criteria, the gradient dilution separation method combined with selective media was employed to isolate yeast strains. Morphological observation and molecular biological identification were conducted to determine the taxonomic status of the strains. The growth characteristics, carbon source utilization ability, and biosafety of the strains were investigated. The fermentation flavor contributions of the strains were evaluated through sensory assessment and electronic nose technology. Results Forty yeast strains were isolated and purified from Xinjiang traditional milk wine starter and traditional fermented dairy products. After multiple rounds of screening, two strains (J17 and J23) with excellent functions were obtained, tolerating pH 2.5, 350 g/L glucose, and 47.34 g/L ethanol. They were identified as Kluyveromyces marxianus and Pichia kudriavzevii,respectively. The growth curves of the two strains showed that the logarithmic phase began at the time point of 4 h and the stationary phase started at 12 h and 18 h, respectively. The co-culture test confirmed no antagonistic effects and demonstrated symbiotic relationships between the two strains. Carbon source utilization tests indicated that both strains efficiently utilized seven carbon sources, including glucose, lactose, and sucrose, demonstrating strong metabolic adaptability. Biosafety testing revealed that neither strain exhibited hemolytic activity and was sensitive to antifungal drugs such as ketoconazole, meeting the safety standards for food fermentation strains. Electronic nose analysis revealed that the 1:1 mixed strain (HJ) fermentation of milk wine substrate exhibited significantly higher response values for flavor compounds such as alkanes, sulfides, alcohols, and aldehydes/ketones than the single-strain fermentation groups and controls. Both the cumulative contribution rate of PCA and the cumulative discriminant rate of LDA reached 99.97%. Sensory assessment demonstrated that the HJ fermented milk wine scored higher than that of other strain combinations in four dimensions: appearance, aroma, taste, and style. Conclusion K. marxianus J17 and P. kudriavzevii J23 demonstrate high tolerance, broad-spectrum carbon source utilization ability, excellent biosafety, and synergistic aroma enhancement, showing the potential as specialized fermentation agents for milk wine production and providing high-quality microbial resources for the fermentation of traditional milk wine.

Soil nutrient deficiency is a major limiting factor affecting crop yields. Excessive use of chemical fertilizers can lead to soil compaction, environmental pollution, and decreased crop yields and quality. Microalgae-based fertilizer, functioning as a novel green bio-fertilizer, not only effectively promotes crop growth but also enhances soil fertility under various adverse soil conditions. Objectives This study investigated the effects of different fertilizer treatments on the growth of foxtail millet (Setaria italica L.) and the physicochemical properties, enzymes activities, and microbial communities of infertile soil, aiming to provide theoretical support for the application of microalgae-based fertilizer in chemical fertilizer reduction and green sustainable agricultural production. Methods The foxtail millet cultivar ‘Jingu 21’ was cultivated in this study under five fertilizer treatments: full chemical fertilizer (T1), chemical-microalgae integrated fertilizer (T2: 80% chemical fertilizer+20% microalgae-based fertilizer; T3: 60% chemical fertilizer+40% microalgae-based fertilizer; T4: 40% chemical fertilizer+60% microalgae-based fertilizer), and full microalgae-based fertilizer (T5). The growth indexes, biomass, and pigment content of foxtail millet in each treatment were determined, and the physicochemical properties, enzyme activities, and bacterial community characteristics of the infertile soil were measured, after 90 days of cultivation. Results Among the five fertilizer treatments, T4 had the most significant effect of promoting the seedling growth of foxtail millet in the infertile soil. Compared with T1, T4 increased the seedling height, the aboveground dry weight, and the content of chlorophyll a, chlorophyll b, and carotenoids by 26.41%, 126.47%, 17.1%, 24.5%, and 28.0%, respectively. In addition, T5, T2, T3, and T4 increased the content of total nitrogen, available phosphorus, and organic matter and the activities of sucrase, nitrate reductase, peroxidase, and phosphatase in the soil, compared with T1, and T4 had the most significant soil improvement effect. The 16S rRNA gene amplicon sequencing results showed that compared with T1 and T5, T4 increased the diversity of soil microorganisms, in which the relative abundance of Acidobacteriota and Chloroflexi was significantly increased. The correlation analysis showed that the composition of soil microbial diversity was significantly and positively correlated with urease, and the soil microbial community composition had significantly positive correlations with available phosphorus, sucrase, peroxidase, and urease. Redundancy analysis showed that urease and available phosphorus were the main environmental factors affecting the soil bacterial community structure. The relative abundance of Chloroflexi had significantly positive correlations with the urease activity and the available phosphorus content. Conclusion The combined application of microalgae-based fertilizer with reduced chemical fertilizer not only effectively improves the nutrient content and enzyme activities but also enhances the microbial diversity and community structure in the soil, thereby promoting the growth of foxtail millet seedlings in infertile soil.

As a pioneer species in desert areas and the main host of Cistanche deserticola, Atriplex canescens is widely planted in the Ulan Buh Desert in Inner Mongolia. Rhizosphere and endophytic microorganisms play a significant role in the growth and stress resistance of plants. However, few studies have been conducted on the growth-promoting functions of rhizosphere and endophytic bacteria on A. canescens in the Ulan Buh Desert. Objective We screened plant growth-promoting strains from the rhizosphere and endophytic bacteria of A. canescens, aiming to provide microbial resources for the sustainable breeding of A. canescens in this region. Methods Rhizosphere soil and plant samples of A. canescens were collected from the Ulan Buh Desert in Dengkou County, Inner Mongolia. Rhizosphere and endophytic bacteria were isolated and purified. The plant growth-promoting effects of these bacteria and the plant growth-promoting bacteria of Astragalus previously obtained by our research group on A. canescens seedlings were investigated. Molecular biological identification and functional analysis were conducted on the strains with significant plant growth-promoting effects. Then, these strains were combined and the growth-promoting effects of the strain combinations on A. canescens were evaluated. Results A total of 60 rhizosphere bacterial strains and 14 endophytic bacterial strains of A. canescens were isolated. Two endophytic bacterial strains significantly promoted the growth of A. canescens seedlings. Among the Astragalus growth-promoting bacteria tested, three strains had significant growth-promoting effects on A. canescens seedlings. The five plant growth-promoting strains were identified as four species belonging to three genera: Pseudomonas, Bacillus, and Acinetobacter. These strains had different levels of nitrogen fixation, inorganic and organic phosphorus solubilization, potassium feldspar and potassium aluminum silicate solubilization, and indole-3-acetic acid (IAA) and biofilm production. Most of the strains had the ability to produce siderophores. Multiple strain combinations promoted the growth of A. canescens. Combinations 2 (IH-2, IH-9, and TYA27), 3 (IH-2, IH-9, and PAS13-2) and 4 (IH-2, TYA39, and TYA27) demonstrated the best comprehensive plant growth-promoting effects, with Pseudomonas bijieensis IH-2 as the core strain. Conclusion The growth-promoting bacteria of A. canescens in the Ulan Buh Desert mainly include Pseudomonas and Bacillus. P. bijieensis plays a core role in the plant growth-promoting bacterial combinations.

Para-ethoxyaniline (ETH), a widely used industrial raw material and intermediate, persists in the environment, posing potential risks to ecosystems and human health. Objective To isolate an efficient ETH-degrading strain from activated sludge, optimize its degradation conditions, and elucidate the gene regulatory mechanisms and metabolic pathways under ETH stress by transcriptomic and mass spectrometric analyses. Methods A strain capable of utilizing ETH as the sole carbon source was isolated from activated sludge and identified through morphological observation, physiological and biochemical tests, and phylogenetic tree construction based on 16S rRNA gene sequences. The effects of temperature, pH, and initial ETH concentration on bacterial growth and degradation efficiency were examined. Transcriptome sequencing was employed to identify differentially expressed genes (DEGs), with selected up-regulated DEGs validated by real-time reverse transcription quantitative (RT-qPCR). Furthermore, mass spectrometry was employed to investigate the metabolic pathways. Results A highly efficient ETH-degrading strain, designated DQ78 and identified as Pseudomonas sp., was isolated. Under optimal conditions (28 ℃, pH 8.0, 4 mmol/L ETH, and 1% inoculum), it completely degraded ETH within 40 h. Three metabolic intermediates were identified, allowing the proposal of a preliminary degradation pathway. Transcriptomic analysis revealed 3 380 DEGs under ETH stress, including 1 609 up-regulated and 1 771 down-regulated genes. GO enrichment indicated up-regulated genes were primarily involved in 57 GO terms such as amino acid metabolism, cell motility, iron binding, and transport, which might activate the synthesis of ETF-degrading enzymes and enhance substrate uptake and transmembrane metabolism of intermediates. The down-regulated genes were enriched in 58 GO terms such as peptide metabolism and synthesis, ribosomal structure, and cellular components, suggesting a metabolic reallocation toward stress adaptation. KEGG analysis predicted 183 up-regulated pathways and 184 down-regulated pathways such as flagellar assembly, sulfur metabolism, and extracellular biosynthesis under ETH stress, indicating enhanced chemotaxis, enzyme secretion, and stress-resistant substance synthesis. Conclusion Strain DQ78 achieved complete degradation of ETH within 40 h, being a promising candidate for the bioremediation of ETH-contaminated environments. Transcriptomic analysis reveals the molecular regulatory mechanism of this strain in response to ETH, which lays a theoretical foundation for further exploring the genetic foundation of microbial degradation of organic pollutants.

Objective To investigate the growth-promoting properties and mechanisms of Bacillus amyloliquefaciens DGL1 isolated from arid sandy soils of the Qinghai-Xizang Plateau on oat plants under drought stress, thus providing a high-quality microbial resource and a theoretical basis for developing microbial fertilizers suitable for arid regions. Methods The growth-promoting effects of strain DGL1 on oat root length, plant height, and fresh weight under drought stress were determined. The degree of cell membrane lipid peroxidation and the activities of antioxidant enzymes in oat plants under drought stress were measured. The genome and transcriptome of strain DGL1 were sequenced via high-throughput technology. Results Strain DGL1 significantly increased the root length, plant height, and fresh weight of oat plants under drought stress. It markedly elevated the activities of antioxidant enzymes [(superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT)] while reducing the content of malondialdehyde and H₂O₂. Genomic analysis revealed that DGL1 carried the genes related to oxidative stress (gpx encoding glutathione peroxidase, opuD encoding glycine-betaine transporter, and ahpF encoding alkyl hydroperoxide reductase), synthesis of the IAA precursor l-tryptophan (trpA, trpB, and trpC), and flagellar biosynthesis (FliP, FliQ, and FliR). Transcriptome sequencing further revealed that genes associated with biofilm formation, nitrogen and phosphorus uptake, material and energy metabolism, and auxin precursor synthesis—all crucial for root colonization—presented upregulated expression under drought stress. The strain might enhance plant drought tolerance via these pathways. Conclusion Strain DGL1 can enhance the drought tolerance of oat plants and has great potential for application in developing bio-inoculants for arid land agriculture.

Objective Sebum metabolism disorders are a key contributing factor to various dermatological conditions. As an emerging class of microbial agents, postbiotics show potential in regulating metabolic processes. This study aimed to investigate the efficacy and mechanisms of Lacticaseibacillus paracasei CCFM1224 postbiotics in alleviating sebum metabolism disorders and explore the active components responsible for the effects. Methods Using a mouse model of oleic acid-induced sebum metabolism disorders, we comprehensively evaluated the efficacy of CCFM1224 postbiotics in ameliorating sebum imbalance. This evaluation encompassed phenotypic measurements, hormonal parameters, and skin lipid content. Changes in the expression of genes related to skin lipid metabolism were measured via real-time quantitative PCR. Subsequently, a free fatty acid-induced lipid accumulation model in HepG2 cells was utilized to screen the active components of postbiotics. Results CCFM1224 postbiotics significantly ameliorated sebum metabolism disorders in mice. This was evidenced by mitigated abnormal weight gain, a reduced testicle index, alleviated histopathological skin damage, and decreased levels of inflammatory cytokines (IL-6, IL-1β, and TNF-α) as well as triglyceride (TG) and non-esterified fatty acid (NEFA) in the skin tissue. CCFM1224 postbiotics modulated sebum metabolism by downregulating the expression of lipogenesis-related genes (FASN, PPAR-γ, and SREBP-1c) and upregulating the expression of lipolysis-related genes (PPAR-α, HSL, and ATGL). Further cellular validation identified the inactivated bacterial cell component as the key functional fraction, which effectively alleviated intracellular lipid accumulation and associated damage, thereby clarifying the material basis for the effects of CCFM1224 postbiotics. Conclusion L. paracasei CCFM1224 ameliorate sebum metabolism disorders by modulating hormone secretion and lipid metabolic pathways. The key bioactive components were identified as the inactivated bacterial cells, rather than the fermentation supernatant. This finding provides a theoretical foundation for the application of postbiotics in regulating lipid metabolism disorders and establishes a basis for developing related functional microbial preparations.

Fusarium proliferatum is a critical pathogenic fungus causing soybean root rot. A halotolerant biocontrol strain Bacillus sp. YH7-4 was isolated from the Yuncheng Salt Lake. Objective To investigate strain YH7-4 in terms of the effect on soybean growth and the control efficacy against soybean root rot. Additionally, we sought to elucidate the antifungal mechanisms of this strain and identify antimicrobial genes through whole genome sequencing. Methods The plate dual-culture method was adopted to assess the antifungal activity of strain YH7-4. Pot experiments were conducted to evaluate the safety of the strain to soybean seedlings and the control efficacy against root rot. Illumina and PacBio platforms were used for whole genome sequencing of YH7-4. Subsequent analyses included metabolic system assessment, virulence factor prediction, transporter analysis, identification of genes related to biocontrol functions, comparative genomics, and biochemical assays. Results Strain YH7-4 demonstrated the inhibition rates exceeding 75.00% against several plant pathogens, including F. proliferatum, Phytophthora sojae, Colletotrichum truncatum, and Phomopsis longicolla. Pot experiments showed that at the OD₆₀₀ value of 0.8, YH7-4 suspension significantly increased the root length and dry weight of soybean seedlings, while excessively high concentrations abolished this effect. The control efficacy of YH7-4 against F. proliferatum-induced soybean root rot reached 56.02%. Whole genome sequencing revealed a genome of 3 945 352 bp with the G+C content of 46.51% and 3 756 predicted coding genes. These genes were annotated against databases including NR, Swiss-Prot, Pfam, COG, GO, and KEGG, with 3 753, 3 537, 3 358, 3 082, 1 756, and 2 845 sequences successfully annotated, respectively. Among the proteins encoded by these genes, 130 proteins belonged to the CAZy family. Twelve secondary metabolite biosynthetic gene clusters were identified, including eight known biosynthetic gene clusters for antibiotics (surfactin, macrolactin H, bacillaene, fengycin, difficidin, bacillibactin, bacilysin, and butirosin A/butirosin B) and four gene clusters with unknown functions. Additionally, two siderophore-related genes, one gene encoding 2,3-butanediol (associated with induced systemic resistance), and 15 genes involved in biofilm formation were identified. Comparative genomics analysis indicated that YH7-4 was a strain of Bacillus velezensis and shared 2 898 orthologous core gene clusters. Biochemical characterization showed that YH7-4 had the ability to produce amylase, protease, pectinase, and cellulase. Conclusion The halotolerant strain B. velezensis YH7-4 isolated from the Yuncheng Salt Lake shows excellent control efficacy against soybean root rot. Its genome harbors genes linked to biocontrol traits and antimicrobial substance production, which makes this strain a promising candidate for managing soybean root rot and other plant fungal diseases. This study applies salt lake-derived bacteria to plant roots, demonstrating their influence on soybean growth while providing a theoretical basis for further elucidating the antifungal mechanisms of B. velezensis YH7-4.