The human microbiome plays a crucial role in maintaining health, and its dysregulation is strongly associated with various diseases, including intestinal inflammation, metabolic disorders, and neurological conditions. As microbiome datasets grow in size and complexity, conventional statistical methods often fail to capture the intricate patterns within these high-dimensional, sparse, and structured data. This review systematically examines the integration of artificial intelligence (AI), particularly machine learning (ML) and deep learning (DL) techniques, in probiotic research and microecological personalized nutrition. We evaluate how AI accelerates the discovery of novel probiotic candidates from metagenomic data, improves prediction of probiotic efficacy and mechanism of action, deciphers complex host-microbe interactions through multi-omics integration, and enables the design of personalized intervention strategies. This review highlights a paradigm shift from empirical, one-size-fits-all approaches toward data-driven, personalized strategies in microbiome-based health management, offering new opportunities for precision nutrition and disease prevention.

[Objective] To improve the flavour quality of redried tobacco leaves and explore new microbial resources for fermentation. [Methods] A yeast strain PT-1 with pronounced fruit-aroma-producing ability was isolated and screened from commercially available Kyoho grapes. It was identified as Debaryomyces hansenii through rDNA-ITS sequence analysis. This strain was applied to the fermentation of redried tobacco leaves. By treating the tobacco leaves with a yeast suspension at an application rate equivalent to 4% of the tobacco leaf mass, we systematically evaluated the effects on the chemical composition, sensory quality, and microbial community structure of the tobacco leaves. [Results] After inoculation with D. hansenii, the total sugar and reducing sugar contents in tobacco leaves increased by 0.85% and 0.46%, respectively, while the total alkaloids and total nitrogen decreased by 0.07% and 0.05%, respectively. Sensory evaluation results indicated that the treatment group was superior to the control group in terms of aroma quality, sweetness, and aftertaste. High-throughput sequencing results showed that the bacterial diversity on the surface of tobacco leaves remained relatively stable after inoculation, while the fungal diversity significantly decreased. The microbial community structure was markedly simplified, with Debaryomyces becoming the overwhelmingly dominant genus (99.66%). Correlation analysis showed that D. hansenii was significantly positively correlated with total sugar, reducing sugar, aroma quality, and sweetness, and was negatively correlated with total nitrogen, total alkaloids, and strength, suggesting a potential association with improved tobacco leaf quality. [Conclusion] This study expands the pool of aroma-producing yeast resources and verifies the application potential of D. hansenii in tobacco leaf fermentation. The process is simple and low-cost, with a clear flavour-modulating effect. These findings provide a theoretical basis and a practical foundation for constructing an efficient and controllable functional microbial fermentation system.

[Objective] To elucidate the enzymatic-producing properties and environmental tolerance of culturable microorganisms from medium-high temperature Daqu, as well as their regulatory effects on the solid-state fermentation system of Baijiu, to investigate the differences of functional microorganism distribution across different Daqu grades, and to provide a theoretical basis for the development of fortified microbial starters and the optimization of brewing processes. [Methods] The isolation of functional microorganisms, along with the evaluation of enzyme-producing characteristics, growth properties, and environmental tolerance, was conducted on post-fermentation medium-high temperature Daqu of superior-grade and premium-grade used in the production of Nongjiangjianxiangxing Baijiu (strong-sauce aroma-type Baijiu). Moreover, solid-state simulated fermentation experiments were conducted to investigate the regulatory effects of four dominant strains on the physicochemical properties and volatile flavor compounds of the fermented grains. [Results] In this study, a total of 44 strains were isolated from Daqu of premium-grade and superior-grade used in the production of Nongjiangjianxiangxing Baijiu (29 from premium-grade Daqu and 15 from superior-grade Daqu), belonging to 5 phyla and 8 genera, with Bacillus being the dominant genus (accounting for 43.2%). A total of 28 amylase-producing strains (20 from premium-grade, 8 from superior-grade) and 4 cellulase-producing strains (3 from premium-grade, 1 from superior-grade) were primarily screened. Although the premium-grade Daqu contained a higher number of enzyme-producing strains, the strains from the superior-grade Daqu exhibited greater average enzyme production capacity. After secondary screening, strains T41, Y46, and T47 were identified as high-yield amylase-producing functional microorganisms, and strain Y22 as a high-yield cellulose-producing functional microorganism. The tolerance assays revealed that Y46 exhibited the strongest adaptability to high temperature, ethanol stress, and lactic acid stress, and Y22 exhibited the strongest acid tolerance whereas T41 showed the best performance under glucose stress. The results from the solid-state simulated fermentation indicated that all four tested strains contributed to maintaining fermentation ecosystem stability. The strains significantly enhanced starch degradation, achieving reduction rates (from 7.0% to 9.5%), with Y22 exhibiting the most pronounced degradation efficiency. The differential regulatory effects were observed on reducing sugar utilization and volatile flavor compound synthesis, particularly esters. Notably, T41 showed the most pronounced enhancement in flavor compound accumulation. [Conclusion] Post-fermentation medium-high temperature Daqu harbors abundant enzyme-producing functional microorganisms. Significant differences were observed in the quantity and enzyme-producing performance of functional strains across Daqu of different grades, with amylase-producing strains exhibiting a higher isolation rate than cellulase-producing strains. The four screened functional strains possess excellent enzymatic properties and environmental adaptability. In the simulated Baijiu fermentation system, these strains maintained acidity stability, enhanced starch utilization efficiency, and promoted the formation of flavor compounds. Among them, strains T41 and T47 exhibited superior overall fermentation performance and demonstrated considerable potential for practical application. These findings provide valuable microbial resources and a scientific basis for the development of functional microbial starters and the operation of Baijiu brewing processes.

[Objective] To elucidate the signal sensing logic of the three-component EsrISR system, which is composed of the accessory protein EsrI, the histidine kinase EsrS, and the response regulator EsrR, in Corynebacterium glutamicum under hyperosmotic stress and its molecular mechanism for maintaining cell wall homeostasis. [Methods] The core stress-responsive gene cluster was identified through RNA-seq. A series of deletion mutants and overexpression strains were constructed through homologous recombination technology. The transcriptional fusion reporter system, field emission scanning electron microscopy/transmission electron microscopy (FESEM/TEM), electrophoretic mobility shift assay (EMSA), and real-time quantitative reverse transcription PCR, (RT-qPCR) were employed to systematically investigate the sensing threshold, stress response patterns, and global target gene networks of this system. [Results] RNA-seq showed that the esrISR gene cluster was significantly upregulated under 1.7 mol/L NaCl stress. Under the same stress conditions, the deletion of the regulator EsrR led to a significant decrease in biomass, with the maximum OD₆₀₀ dropping to 47.8% of that of the wild type. Moreover, severe damage and collapse of the cell wall were observed via electron microscopy. The construction and analysis of reporter plasmids showed that this system was driven by an internal promoter, peaking at 1.7 mol/L NaCl, with a maximum fluorescence intensity of 880 RFU/OD₆₀₀. The proposed regulatory model indicated that in the absence of external stress, EsrS mainly exerted phosphatase activity to repress the transcription of esrI, thereby maintaining the repressed state of the system (deletion of esrS led to an approximately 15.0-fold upregulation of esrI). Upon sensing hyperosmotic signals, EsrS changed its activity, promoting the phosphorylation of the regulator EsrR. Subsequently, the phosphorylated EsrR specifically bound to the core regulatory region, thereby activating the positive feedback regulatory loop. Transcriptomic analysis revealed significant alterations in the expression of key genes associated with cell wall homeostasis in the esrR deletion mutant (ΔesrR). RT-qPCR analysis confirmed that EsrR functioned as a crucial regulator of cell wall biosynthesis primarily by positively activating key pathway genes. Specifically, the peptidoglycan synthesis genes murB and CGL_RS01830 were downregulated by 95.0% in ΔesrR and upregulated by 2.0-6.5 fold in esrR-OE; the trehalose biosynthesis genes treS, treY, and treZ were downregulated by 75.0%-83.0% in ΔesrR and upregulated by 2.5-4.2 fold in esrR-OE; cmrA and gatC were significantly repressed in ΔesrR and upregulated by 3.5-folds in esrR-OE, thereby effectively maintaining the physical homeostasis of the cell wall. [Conclusion] This study provides new insights into the regulation of cell wall homeostasis by the three-component EsrISR system in Corynebacterium, providing critical genetic targets for the robustness engineering of industrial chassis strains.

[Objective] L-histidine is a high-value, imidazole-containing amino acid with broad applications in the pharmaceutical, food, and additive industries. The fermentative production of L-histidine remains constrained by the low carbon flux through the core biosynthetic route, limited precursor availability, and by-product accumulation. [Methods] With Escherichia coli as the chassis, L-histidine biosynthesis was systematically improved through rational metabolic engineering. [Results] The flux toward L-histidine was enhanced by elimination of transcriptional attenuation of the histidine operon, introduction of an efficient adenosine triphosphate (ATP) phosphoribosyltransferase mutant, and plasmid-based overexpression of key pathway genes. The pentose phosphate pathway was reconstructed to increase the precursor 5-phosphoribosyl pyrophosphate (PRPP) supply. In parallel, carbon loss was reduced by blocking formate- and acetate-forming pathways. Nitrogen sources were subsequently evaluated, and fermentation parameters, including temperature, pH, and dissolved oxygen, were systematically optimized. Under the optimized conditions, the L-histidine titer, yield, and productivity reached 34.84 g/L, 0.13 g/g, and 0.73 g/(L·h), respectively. In addition, the analysis of key gene expression and intracellular metabolites suggested that process optimization was conducive to enhancing the expression of the main synthetic pathway, improving energy and redox states, and increasing the ammonia donor supply. [Conclusion] The results establish an effective metabolic engineering strategy and a process basis for efficient microbial production of L-histidine.

[Objective] To obtain the strains with strong saline-alkali tolerance and plant growth-promoting traits from the severe saline-alkali soil in Xinjiang, thereby providing excellent strain resources for the development of microbial fertilizers and soil improvement agents. [Methods] Bacteria with strong saline-alkali tolerance were screened using modified LB medium. Subsequently, the strain was taxonomically identified based on morphology, physiological-biochemical tests and 16S rRNA sequencing, and its plant growth-promoting properties were characterized systematically. In addition, the strain was whole-genome sequenced via the Illumina NovaSeq X Plus platform. [Results] A strain with strong saline-alkali tolerance and multiple plant growth-promoting functions was isolated and designated as Bacillus zhangzhouensis A015 (CCTCC M20242724). It could tolerate 250 g/L NaCl and grow within a range of pH 2.0-12.0. Results of multifunctional growth-promoting tests revealed that strain A015 could produce ACC deaminase, and exhibited nitrogen fixation, potassium solubilization, organic phosphorus and inorganic phosphorus solubilization abilities. The nitrogenase activity of strain A015 was (185.36±4.16) ng/L. Its organic phosphorus solubilization index was 1.35±0.15, with lecithin conversion amount of (3.77±0.07) mg/L. The inorganic phosphorus solubilization index was 1.42±0.04, and the transformation amount of calcium phosphate reached up to (24.79±0.59) mg/L. Besides, the potassium solubilization index was 1.30±0.08, and the transformation capacity of feldspar powder was (5.16±0.18) mg/L. Wheat seed germination and growth promotion assays demonstrated that, compared with the control group (CK), inoculation with strain A015 significantly promoted the growth of wheat plumules and radicles on water agar media with 0-20 g/L NaCl. Specifically, under 5 g/L NaCl stress, remarkable growth promotion effects on plumule and radicle length were observed, with the growth increments of 43.86% and 20.14%, respectively. Notably, this strain could still effectively facilitate root growth under high salt stress of 15-20 g/L NaCl. The whole-genome sequence of A015 was deposited in NCBI, with the accession number JBSPZB000000000. Genome analysis revealed 25 saline-alkali tolerance-related genes, which were mainly involving mrp, mle, and nha gene clusters; meanwhile, 65 plant growth-promoting genes were identified, including nif, gdh, and kef gene clusters. [Conclusion] A strain of Bacillus A015 with strong salt-alkali tolerance and excellent plant growth-promoting ability was obtained from severe saline-alkali soil in Xinjiang. Genomic analysis further revealed genes linked to its salt-alkali tolerance and plant growth promotion capabilities. The findings provide theoretical basis and practical support for the development of saline-alkali soil microbial fertilizers in Xinjiang and the exploration of the strain’s stress tolerance mechanisms.

[Objective] To conduct site-directed mutagenesis on the Ca²⁺-binding sites, Leu²⁵³, and protein surface oxidation-sensitive Met residues of TSS, a collagenolytic protease derived from thermophiles, thereby screening out the variants with improved antioxidant activity, thermostability, and catalytic activity and revealing the intrinsic connection among them. [Methods] Site-directed mutagenesis was conducted on the Ca²⁺-binding sites (Ca1, Ca2, and Ca3) and Leu²⁵³ of TSS and the oxidation-sensitive Met residues on the protein surface. The derived variants were further evaluated for H₂O₂ tolerance, relative activity, and residual activity. Changes in antioxidant activity, catalytic activity, and thermostability after mutations were also studied. [Results] Mutations in amino acid residues at the three Ca²⁺-binding sites led to decreases in catalytic activity and/or thermostability of TSS. The Leu²⁵³ series variants constructed by simulating KP-43 did not enhance the antioxidant activity of TSS. Among the variants of oxidation-sensitive residues, M302L showed increases of 13% and 61% in the catalytic and antioxidant activities, respectively, while remaining unchanged thermostability. Ca²⁺ increased the catalytic activity and thermostability of TSS at high temperatures in a concentration-dependent manner. A high salinity environment with more than 2 mol/L NaCl prolonged the half-life of TSS at 75 ℃ and inhibited the maturation process of TSS proform. [Conclusion] The antioxidant and catalytic activities are positively correlated in the Leu²⁵³ and Met variants of TSS, which conforms to the “Trade-off” mechanism.

[Objective] To explore the structural characteristics of microbial communities in the rhizosphere soil of Meconopsis baileyi along different altitude gradients. [Methods] This study employed high-throughput sequencing to investigate the microbial community composition and diversity in the rhizosphere soil of M. baileyi and conducted a correlation analysis on the microbial community characteristics with environmental factors. [Results] At different altitudinal gradients, there are significant differences in the common genera of bacteria and fungi in the rhizosphere soil of M. baileyi. The common genera at low altitudes are all greater than those at high altitudes, and show a downward trend with increasing altitude. Their diversity initially increased and then decreased with increasing elevation. Fungal species richness generally increased with elevation, whereas bacterial species richness also increased but declined sharply at 4 100 m. Pseudomonadota was the most dominant phylum among soil bacteria, and Ascomycota was the most dominant phylum among soil fungi. Their relative abundance generally showed a downward trend with the rise in altitude. Altitude exerted a more significant shaping effect on the fungal community structure. Although bacterial communities were also affected by altitude, the altitude specificity of taxonomic group distribution was weak, and diversity tended to be more stable.The co-occurrence networks of microorganisms at high altitude gradients were more compact, with core groups being more prominent, which indicated collaborative coexistence of microorganisms in extreme environments. In contrast, the networks at low altitude gradients were looser, with microorganisms surviving independently in suitable environments. Soil pH, electrical conductivity (EC), available phosphorus (AP), soil temperature (ST), and soil moisture content (SMC) were identified as the major drivers shaping microbial community structure across altitudinal gradients. [Conclusion] Altitude significantly affects the species composition and community distribution of rhizosphere microorganisms in M. baileyi. Diversity generally increased initially and then decreased with increasing elevation, whereas species richness showed an overall increasing trend; however, bacterial richness declined sharply at the highest elevation.The relative abundance of the dominant phyla of both communities generally decreases as altitude rises, and altitude has a more significant role in shaping the fungal community structure. In addition, the microbial co-occurrence networks are more compact at high altitudes but looser at low altitudes, with pH and EC acting as key environmental drivers of microbial community structure.

[Objective] To investigate the species composition, dominant taxa, and diversity characteristics of bacterial communities within Spodoptera frugiperda at different developmental stages, thereby providing a scientific basis for further exploring key microorganisms associated with S. frugiperda and developing green control technologies based on symbiotic bacteria. [Methods] High-throughput sequencing of the 16S rRNA gene V1-V9 regions of bacteria from S. frugiperda at different developmental stages was performed using the PacBio sequencing platform. The structure and diversity of bacterial communities across these stages were systematically analyzed. [Results] Bacterial communities within S. frugiperda at different developmental stages were annotated at multiple taxonomic levels, resulting in 35 phyla, 72 classes, 189 orders, 322 families, 678 genera, and 1 074 species. At the phylum level, Pseudomonadota and Bacillota were consistently dominant across all developmental stages. At the genus level, Enterococcus was the dominant genus in the 2^nd to 6^th instar larvae. During the pupal stage, Providencia became the dominant genus, with a relative abundance of 78.13%. Additionally, Serratia was the dominant genus in female adults, accounting for 71.00% relative abundance, whereas Enterobacter was the dominant genus in male adults, with a relative abundance of 39.18%. Diversity analysis revealed that the egg stage exhibited the highest Shannon diversity index and Chao1 richness index among all developmental stages, whereas the pupal stage displayed the lowest levels of both bacterial diversity and species richness. Functional prediction indicated that the abundance of functional categories in bacterial communities was generally consistent across different developmental stages, with metabolic pathways showing the highest abundance. [Conclusion] The composition and diversity of bacterial communities in S. frugiperda exhibited developmental stage specificity, with the highest bacterial diversity and richness observed in the egg stage and the lowest in the pupal stage. Dominant taxa varied dynamically across developmental stages. At the genus level, Enterococcus, Providencia, Serratia, and Enterobacter were the dominant taxa and may serve as key targets for green control strategies. This study clarifies the species composition and community differences of bacteria in S. frugiperda across developmental stages, providing fundamental data for further investigating the mechanisms underlying host-symbiont interactions and developing green control technologies.

Nymphaea candida C. Presl, a rare water lily species in China, is on the brink of extinction due to its extremely low natural germination rate. Obtaining robust seedlings suitable for artificial propagation has become a key for the conservation of this species. [Objective] To isolate and identify endophytic plant growth-promoting fungi from the roots of N. candida and evaluate their growth-promoting effects on seedlings. [Methods] Pot experiments were carried out with Chaetomium globosum isolated from N. candida to assess its effects on the growth of N. candida, soil physicochemical properties, rhizosphere microbial community structure, and leaf gene expression. [Results] The application of C. globosum significantly increased the leaf length, leaf width, number of leaves, and root length of N. candida by 46.74%, 96.08%, 64.71%, and 130.13%, respectively. Moreover, the application of C. globosum significantly increased soil organic matter, alkali-hydrolyzable nitrogen content, and sucrase activity. Rhizosphere microbial community analysis indicated that the application of C. globosum specifically enriched beneficial microorganisms, including norank-p-Cryptomycota, norank-o-Monhysterida, Surirella, and norank-p-Aphelidea. Leaf transcriptome analysis further revealed that C. globosum significantly upregulated the expression of the genes related to the steroid biosynthesis pathway. [Conclusion] C. globosum effectively promotes the growth of N. candida seedlings by improving the rhizosphere microenvironment, recruiting beneficial microorganisms, and regulating steroid biosynthesis in the leaves. Thus, the endophytic plant growth-promoting fungus C. globosum might be a reliable tool for the conservation of the endangered plant species N. candida.