Objective We compared the rhizosphere microbial interaction network structure and keystone taxon identification arising from distinct network construction algorithms, aiming to clarify the characteristics and advantages of each algorithm in inferring microbial interactions and identifying keystone taxa, thereby providing a theoretical basis for methodological selection. Methods Taking the rhizosphere microbial community of Camphora migao (a rare plant) as the model system, we constructed molecular ecological networks with three mainstream algorithms: sparse correlations for compositional data (SparCC), random matrix theory (RMT), and co-occurrence network (CoNet). We comprehensively compared network structural features and keystone taxon identification across algorithms by integrating PICRUSt2 functional prediction with keystone taxa-environmental factor correlation analysis. Results Network construction algorithms significantly influenced the topological properties of networks. SparCC generated highly modular networks (relative modularity index, RM=1.31) with distinct interaction segregation (edge connectivity=0). RMT produced a single-module structure (RM=0.78) and homogeneous connectivity (closeness centralization index=0.22). Integration of 26.0% negative correlations in CoNet reduced modularity (RM=0.95), increased network diameter (33.22 steps), and decreased robustness. Keystone taxon identification was method-dependent. Specifically, CoNet, SparCC, and RMT identified 224.00, 44.00, and 19.00 keystone taxa, respectively, with<9.2% cross-method overlap. Rhizobiales and Acidobacteriales were consistently identified as core keystone taxa by all methods, demonstrating cross-algorithm stability. The correlation analysis with environmental factors confirmed that these shared taxa significantly correlated with β-glucosidase activity, validating their role in cellulose degradation and highlighting methodological consistency in identifying key ecological processes. Conclusion The three algorithms exhibited complementary strengths: CoNet resolved complex competitive interactions; SparCC reliably assessed functional stability; RMT uncovered core functional modules. The correlation analysis with environmental factors validated the cellulose degradation function of keystone taxa, with high cross-method consistency in core ecological process identification. Our work provides a theoretical foundation for elucidating plant-microbe interactions and optimizing microbial network construction.

Objective To explore the application of hutC sequence analysis in the identification of Burkholderia cepacia complex (Bcc) at the species level. Methods We compared the sequences of hutC and the amino acid sequences of the encoded proteins and conducted phylogenetic analysis to theoretically assess the feasibility of using hutC for species-level identification of Bcc. Primers targeting the hutC of Bcc were designed, and the amplification conditions were optimized. With those of standard strains as templates, the hutC sequences of representative Bcc species were amplified. The sequencing results were compared with NCBI sequences for phylogenetic analysis to validate the theoretical hypothesis. Additionally, single nucleotide polymorphism analysis of hutC sequences was performed to identify species-level characteristic barcodes of Bcc. Results The hutC gene was relatively conserved between Bcc and non-Bcc. With the designed primers and amplification conditions, a 692 bp fragment of hutC was successfully amplified from 12 Bcc standard strains. Except for one strain with taxonomic errors, the remaining 11 strains had the comparison results consistent with those from the culture collection centers. The phylogenetic analysis based on hutC showed that different Bcc species could be clustered with high bootstrap values. A 12 nucleotide characteristic barcode of hutC was identified, which can rapidly distinguish different species of Bcc. Conclusion The gene hutC can serve as a new housekeeping gene target for accurate identification of Bcc at the complex and species levels.

Helicobacter pylori infection is a major causative factor for chronic gastritis and gastric cancer, while current antibiotic therapies are facing increasingly severe resistance. Probiotics have emerged as a promising approach for anti-H. pylori research due to their high safety. Notably, certain Lactobacillus strains have been demonstrated to effectively alleviate H. pylori-induced inflammatory responses, yet their underlying molecular regulatory mechanisms remain unclear. Objective To investigate the molecular mechanism by which Lactiplantibacillus plantarum ZJ316 inhibits the H. pylori-induced inflammatory response by modulating the p38 mitogen-activated protein kinase (MAPK) signaling pathway in the host cells and assess the regulatory effect of this strain on gastric microecological homeostasis, thus providing a theoretical basis for the development of probiotic therapeutics targeting H. pylori. Methods We integrated cell experiments (human gastric adenocarcinoma cell line AGS) and animal experiments (C57BL/6 mice) and employed Western blotting (to determine the phosphorylation level of p38 MAPK), transcriptome sequencing and RT-qPCR (to analyze differential gene expression), ELISA [to determine the levels of inflammatory cytokines interleukin (IL)-8 and IL-10], 16S rRNA gene sequencing (to unveil the gastric flora structure), and hematoxylin-eosin staining (to observe gastric mucosal damage) to systematically study the intervention effect of L. plantarum ZJ316 on H. pylori infection. Results At the cellular level, L. plantarum ZJ316 inhibited H. pylori-induced p38 MAPK phosphorylation, with the inhibition rates of 21.95% and 33.72% at the time points of 1 h and 2 h, respectively (P<0.01). It down-regulated the expression of pathway genes such as MAP3K8 and FOS, and lowered the mRNA levels of the pro-inflammatory cytokines interferon-γ, tumor necrosis factor-α, and IL-6 by 43.26%, 35.95%, and 51.91%, respectively (P<0.01). The combination of this strain with adezmapimod, a p38 MAPK-specific inhibitor, further enhanced the inhibitory effect. In animal experiments, L. plantarum ZJ316 significantly attenuated gastric mucosal pathological injury and inflammatory response, and 16S rRNA gene sequencing revealed that ZJ316 reduced the relative abundance of pathogenic Pseudomonadota and significantly increased the relative abundance of Bacillota [(54.8±9.9)% vs. (27.8±5.9)%, P<0.01] in the stomach. When ZJ316 was combined with adezmapimod, the relative abundance of Bacteroidota was elevated [(58.5±5.2)% vs. (47.8±6.9)%, P<0.05], and specific beneficial genera such as Alistipes were synergistically enriched (an increase of 69.52% compared with the H. pylori group). Conclusion L. plantarum ZJ316 alleviated the inflammatory response triggered by H. pylori infection by inhibiting the p38 MAPK pathway and remodeled the gastric microecological structure. The findings provide a theoretical basis for the inhibition of H. pylori-induced inflammation by lactobacilli and the development of probiotic-based functional foods.

Objective To isolate lactic acid bacteria (LAB) with the ability to degrade milk fat, providing a theoretical foundation and technical support for dairy fermentation process optimization and probiotic development. Methods Primary screening employed media with butter as the main carbon source, followed by secondary screening using media with butter as the sole carbon source. The target strains were validated via carbon-free media. The selected strains underwent chromogenic assays for lipase characterization. Fermentation properties were assessed through viable count, acidity, acid value, and free fatty acid measurements. Probiotic potential was evaluated via acid/bile salt tolerance and cholesterol reduction assays. Results Through primary screening, secondary screening, and validation, ten strains with the ability to degrade milk fat were selected. Among them, a strain with faster growth than the others was identified as Lactobacillus delbrueckii grx601 through morphological and molecular biological characterization. This strain exhibited high lipase activity during logarithmic and stationary phases, with intracellular and extracellular enzyme activities of 14.14 U/mL and 11.45 U/mL, respectively. Enzymatic characterization showed that the optimal substrate for intracellular and extracellular lipases was p-nitrophenol palmitate, with the optimal reaction conditions of pH 7.0 and 40 ℃. The relative activity remained above 50% at 5% NaCl, which indicated certain salt tolerance. The fermentation characteristic experiment showed that L. delbrueckii grx601 significantly increased the acidity, acidity value, and free fatty acid content during the fermentation process. Moreover, the survival rates of L. delbrueckii grx601 in artificial simulated solutions with pH 3.0 and 0.30% bile salt were 83.87% and 47.70%, respectively, which indicated acid/bile salt tolerance of the strain. In addition, the cholesterol degradation rate of the strain was 7.95%. Conclusion L. delbrueckii grx601 was successfully isolated and characterized as a potent milk fat-degrading strain. Its high intra/extracellular lipase activity, favorable enzymatic properties, robust fermentation performance, and probiotic attributes (acid/bile salt tolerance, cholesterol reduction) indicate significant potential for dairy fermentation and probiotic applications.

Colorectal cancer (CRC), a common malignant neoplasm of the digestive system globally, demonstrates pathological progression that is intricately linked not only to dysbiosis of the gut microbiota but also to the oral microbial ecosystem. The emerging concept of the “oral-gut axis” offers novel insights into the regulation of microbial interactions across different organs. Recent research indicates that Peptostreptococcus, a predominant genus within the oral microbiome, exhibits spatiotemporal correlations with the initiation and progression of CRC. This genus may influence intestinal microecological changes and CRC pathogenesis through the “oral-gut axis”. We explore the microbial interactions between oral and intestinal ecosystems, examining the multidimensional associations between specific Peptostreptococcus species (such as P. stomatis and P. anaerobius) and CRC development. Key considerations include the population heterogeneity of these species among CRC patients with varying clinical profiles, their dynamic evolution during the adenoma-carcinoma sequence, and their spatial distribution across different pathological stages. We synthesize mechanistic evidence illustrating the role of Peptostreptococcus in promoting tumorigenesis by enhancing cancer cell proliferation, inducing epithelial-mesenchymal transition, and remodeling the tumor microenvironment. Additionally, this article assesses the clinical potential of Peptostreptococcus as predictive biomarkers and therapeutic targets for CRC. Finally, we propose future directions for the development of targeted microbial intervention strategies against oral-derived pathogens, with the aim of stimulating scientific interest and encouraging further investigation in this emerging research area.

Objective Developing plant-microbe combined techniques is significant for addressing the problem of declining cropland quality in China and enriching the approaches for biological remediation of degraded soils. Methods The plant growth-promoting traits of Burkholderia sp. YQ9 were determined by assessing its cellulase, protease, and ammonia production. Subsequently, a pot experiment was conducted to evaluate the effects of different dilutions of Burkholderia sp. YQ9 inoculant and culture medium on the growth of white clover (Trifolium repens) and the physicochemical properties of the rhizosphere soil. Furthermore, high-throughput sequencing was employed to analyze the impacts of different treatments on the structure of the rhizosphere microbial community. Results Burkholderia sp. YQ9 exhibited plant growth-promoting traits, being capable of producing cellulase, protease, and ammonia. White clover improved the pH environment of the rhizosphere soil. Application of the original inoculant of Burkholderia sp. YQ9 promoted white clover growth, significantly enhancing the content of soluble protein and soluble sugar in the shoots and leaves, as well as the levels of available phosphorus and available potassium in the rhizosphere soil, thereby facilitating organic matter decomposition. Analysis of microbial alpha diversity in the rhizosphere soil revealed that both the original inoculant of Burkholderia sp. YQ9 and the culture medium significantly reduced the richness, diversity, and evenness of both fungal and bacterial communities in the rhizosphere soil and altered the composition of the soil microbial community. The correlation analysis further indicated that the microbial community in the rhizosphere soil was correlated with white clover growth and soil physicochemical properties. Conclusion Burkholderia sp. YQ9 not only promoted the growth of white clover but also modified the composition of the rhizosphere microbial community and improved the soil fertility. These findings provide microbial augmentation-based technical support for enhancing cropland quality.

Objective To investigate the mechanism by which the endophytic fungus Trichoderma harzianum Rifai help the seedlings of the rare medicinal plant Camphora migao (H. W. Li) Y. Yang, Bing Liu & Zhi Yang to defend against drought stress. Methods We simulated different drought stress gradients using the potted weighing method after inoculation of C. migao seedlings with T. harzianumvia rhizosphere injection and investigated the plant growth, physiological, and biochemical indexes. Results Under different drought conditions, inoculation with T. harzianum significantly increased the growth indexes such as biomass, plant height, and root growth of C. migao seedlings, compared with the uninoculated control group. Furthermore, T. harzianum significantly increased the activities of antioxidant enzymes and the content of osmotically regulation substances, reduced the malondialdehyde content, and elevated the content of photosynthetic pigments in the seedling leaves, which effectively mitigated the drought stress effects on the growth and development of C. migao seedlings. Conclusion T. harzianum improved the physiological responses of C. migao seedlings to drought stress by regulating osmotic balance and maintaining the stability of antioxidant system.

Objective To investigate the effect of inoculating the associative nitrogen-fixing bacteria strain Paraburkholderia RBCS-17 on the root-associated bacterial community of sugarcane. Methods We employed 16S rRNA gene high-throughput sequencing combined with QIIME 2-based bioinformatics analysis to investigate the effects of inoculating Paraburkholderia RBCS-17 on the alpha diversity, beta diversity, composition, and co-occurrence network of the root-associated bacterial community of sugarcane. Results Inoculating Paraburkholderia RBCS-17 did not significantly affect the diversity but significantly changed the structure of the root-associated bacterial community. Further studies showed that the inoculation significantly increased the relative abundance of Burkholderia, Dyella, and Pseudomonas, while reducing the relative abundance of certain potentially detrimental bacteria such as Ralstonia. In addition, the inoculation altered the key module composition of the bacterial co-occurrence network in sugarcane roots, which suggested that inoculation might influence potential bacterial interactions. Conclusion Inoculating the associative nitrogen-fixing bacterial strain Paraburkholderia RBCS-17 modified the root-associated bacterial community structure of sugarcane, promoting the enrichment of potentially beneficial bacteria while suppressing potentially harmful ones. These findings provide new insights into the intricate interactions among associative nitrogen-fixing bacteria, host plants, and indigenous bacteria.

Objective To isolate multifunctional phosphate-solubilizing bacteria (PSB) exhibiting psychrophilic adaptation and saline-alkaline tolerance in response to the ecological challenge of phosphorus limitation in saline-alkaline soils in cold regions, evaluate their phosphate-solubilizing efficiency and environmental adaptability, and preliminarily investigate their phosphate-solubilizing mechanisms. Methods We used an inorganic phosphorus-selective medium to isolate bacterial strains from saline-alkaline soils in Baicheng, Jilin Province. The phosphate-solubilizing capacity was quantitatively determined through the molybdenum-antimony colorimetric method. Taxonomic identification was performed through morphological characterization and phylogenetic analysis based on 16S rRNA gene sequences. The phosphate solubilization conditions were optimized via multi-parameter gradient optimization. HPLC was employed to quantify organic acid metabolites. Phenol-sulfuric acid assay and crystal violet staining were employed to characterize biofilm formation and extracellular polysaccharide (EPS) synthesis. Results The isolated strain Pseudomonas psychrophila MPP2402 demonstrated broad-spectrum environmental adaptability, maintaining stable growth at 5-30 ℃, pH 7.0-10.0, and 0.2-0.8 mol/L NaCl. The strain achieved 574.66 mg/L soluble phosphorus (14.8% increase) under optimal conditions: 15 ℃, pH 7.0, 0.4 mol/L NaCl, 1% inoculum density, and 5 g/L Ca₃(PO₄)₂. MPP2402 may exert the phosphate-solubilizing effect through the secretion of organic acids such as succinic acid (51.53 μg/mL), oxalic acid (22.84 μg/mL), tartaric acid (15.11 μg/mL), and malic acid (5.93 μg/mL), which worked in concert to solubilize phosphate. Additionally, the strain utilized EPS to construct a biofilm barrier and regulated the viable count in adverse environments such as low-temperature and saline-alkaline conditions. Conclusion The successful isolation of MPP2402 establishes a foundational resource for developing efficient saline-alkaline tolerant microbial agents and improving soil nutrient management in cold-region ecosystems.

Pseudomonas aeruginosa (PA) is a major cause of hospital-acquired infections. It can survive in a variety of extreme environments, and is highly resistant to antibiotics. PA can attack immunocompromised populations to cause severe infections, being a major cause of mortality in clinical practice. Therefore, rapid diagnosis of PA is critical for infection control. Conventional detection techniques such as plate assays, immunoassays, and nucleic acid assays have excellent accuracy and sensitivity, while they are costly and time-consuming. In recent years, novel biosensing technologies have achieved ultrasensitive and precise detection of PA by integrating various biorecognition elements and signal enhancement strategies, providing an efficient, convenient, and cost-effective solution for the rapid identification, treatment, and control of PA. In this paper, we systematically review the principles, application progress, and challenges of magnetic separation biosensing technologies based on electrochemical, optical, CRISPR/Cas12a system, and magnetic nanoparticles, and provide future research directions, aiming to promote the innovation and clinical application of the technologies for rapid detection of PA.