Search Results (230)

The global demand for Salvia miltiorrhiza Bunge in the botanical medicine market is steadily increasing. However, its production has long relied on asexual root propagation, making it highly susceptible to germplasm degradation. Transitioning to seed reproduction offers the advantage of genetic renewal, yet it is constrained by unstable seed vigor and slow seedling growth. In the present study, comprehensive physiological and microbiome analyses of S. miltiorrhiza seeds from 14 regions across 7 provinces in China were conducted to elucidate the association between the seed microbiome and vigor, and to identify plant growth-promoting (PGP) strains. The results demonstrated: (1) Seed physical traits and germination characteristics varied significantly across geographic origins. Seed vigor, exhibiting the highest coefficient of variation, served as a key parameter reflecting germination quality. (2) High-vigor seeds harbored distinct microbial communities characterized by higher diversity indices, greater network complexity, and the significant enrichment of potentially beneficial bacteria (e.g., Pseudomonas). (3) Through correlation-directed screening of isolated pure cultures, Pseudomonas mendocina P-6 and Enterobacter ludwigii BM-12 were identified as exhibiting robust, multi-trait PGP capacity. In planta validation showed that these two strains significantly promoted the growth of 1-month-old S. miltiorrhiza seedlings, increasing total fresh weight by 33.9–71.3%. This study reveals the microecological drivers of seed vigor and provides candidate strains for inoculant development, thereby supporting the sustainable, seed-based propagation of S. miltiorrhiza. Full article

To investigate how steam-explosion pretreatment affects humification during sawdust composting, an aerobic composting experiment was conducted using sawdust, chicken manure, and spent mushroom substrate as feedstocks. Two treatments were established—a steam-explosion-pretreated sawdust group (SEW) and an untreated sawdust control (CK)—each with three replicate reactors. Samples were collected dynamically at five key composting stages (initial, heating, thermophilic, cooling, and maturation) for physicochemical, enzymatic, and microbial community analyses. Linear mixed-effects model analysis revealed that enzyme activities were significantly affected by treatment, composting time, and their interaction. SEW significantly enhanced cellulase and polyphenol oxidase activities, and increased laccase and peroxidase activities at specific stages. Compared with CK (humic substances, 75.30 g/kg), SEW promoted higher humic substance accumulation (120.80 g/kg) and altered the dynamics of dissolved organic carbon. Microbial co-occurrence networks in SEW (50 nodes, 602 edges) were more complex than CK (49 nodes, 464 edges), indicating tighter microbial interactions. Path analysis revealed that HS in CK was mainly influenced by DOC and temperature, while HS in SEW was associated with enzyme activities, microbial diversity, and Pseudogracilibacillus. These results suggest that steam-explosion pretreatment enhances substrate transformation and humic substance formation during composting. Full article

Triplophysa yarkandensis (Cypriniformes: Nemacheilidae), a rare endemic fish in the Tarim River Basin, Xinjiang, China, plays a pivotal role in maintaining the stability of plateau saline–alkaline aquatic ecosystems, yet its survival is increasingly threatened by habitat salinization. However, the multi-dimensional synergistic adaptation mechanisms linking its phenotypic variation, intestinal structure, and associated microbial communities to extreme saline–alkaline stress remain poorly understood. In this study, we innovatively integrated morphological/intestinal histological characterization, 16S rRNA gene sequencing, and microbial ecological analyses (co-occurrence networks and assembly processes) to systematically decode its adaptive strategies. Results revealed that T. yarkandensis exhibits a streamlined body shape, morphological variability, and elongated intestinal villi that may support locomotion and nutrient/ion uptake under osmotic stress. Its gut exerts a stringent selective filter, driving distinct differentiation between water and gut microbial communities—with gut-enriched core taxa (Aurantimicrobium and Aestuariivirga) and functional pathways (unsaturated fatty acid biosynthesis and ABC transporters) specialized for osmoregulation. Notably, the water microbial assembly is dominated by stochastic processes, while the gut assembly relies on host-driven deterministic selection, forming a habitat-specific adaptive pattern. These findings uncover the synergistic adaptation system of host phenotype and gut microbiota for survival in extreme saline–alkaline habitats, advancing our understanding of fish–microbe co-evolution in extreme ecosystems and providing critical theoretical support for the conservation of rare plateau fish, as well as guidance for the utilization of saline–alkaline water resources in aquaculture. Full article

Prophylactic antibiotic use in intensive aquaculture promotes antimicrobial resistance, necessitating the development of microbial-based interventions. This study evaluated the individual, complementary, and synergistic effects of Bacillus subtilis natto (BSN) and Lactobacillus plantarum (LP) on the physiological performance and intestinal microecology of juvenile Japanese flounder (Paralichthys olivaceus). Over a 60-day trial, juveniles (initial weight: 5.81 ± 0.03 g) received a basal diet (CON) or a diet supplemented with 10⁷ CFU/g of BSN, LP, or both (BSN+LP). The BSN+LP consortium elicited complementary improvements in final body weight (21.39 ± 0.75 g vs. 18.66 ± 0.44 g in CON) and feed conversion efficiency (p < 0.05). Transcriptomic analysis revealed synergistic upregulation of digestive proteases (trypsin, chymotrypsin). Notably, an in pro-inflammatory markers (IL-1β, TNF-α) was counterbalanced by substantial upregulation of anti-inflammatory cytokines (IL-10, 5.65-fold; TGF-β1, 4.48-fold), suggesting the induction of mucosal tolerance rather than pathological enteritis. High-throughput 16S rRNA sequencing showed that the control cohort had a potential baseline microbial, characterized by a high relative abundance of Proteobacteria. BSN+LP administration significantly altered this microbial community into a fermentative eubiosis enriched in Firmicutes and Bacteroidota. Correlation network analyses confirmed negative interaction dynamics: increased abundance of Lactobacillus, Bacteroides, and Muribaculaceae was negatively correlated with baseline pathobiont abundance. These findings indicate that co-administration of BSN and LP hypothetically enhances metabolic energy harvest via short-chain fatty acid-producing taxa, strengthens the gut–immune axis, and competitively mitigates opportunistic pathogens. Full article

Background: Root-knot nematodes (RKNs) are destructive parasites affecting both agricultural and natural plants. Fagopyrum tataricum, a phenolic-rich edible and medicinal plant, has antidiabetic, anti-inflammatory, and anticancer properties, yet the impact of RKN infection on its rhizosphere microbiome remains unclear. Methods: We employed full-length 16S rRNA gene sequencing (FL16S) to profile bacterial communities in the rhizosphere of healthy and RKN-infected F. tataricum plants. Results: FL16S classified 78.41% of operational taxonomic units (OTUs) at the genus level and 69.18% at the species level. Healthy plants showed higher richness, diversity, and evenness, while principal co-ordinate analysis (PCoA) and PERMANOVA indicated significant RKN-associated shifts in community composition. Dominant phyla included Bacteroidota, Proteobacteria, Patescibacteria, Verrucomicrobiota, Actinobacteriota, Acidobacteriota, and Chloroflexi, with Abditibacteriota enriched in healthy and Acidobacteriota in diseased rhizospheres. At the OTU level, 66 differentially abundant taxa were identified, including nine hub OTUs in healthy plants, suggesting keystone roles in network stability. Network analyses revealed reduced diversity, interactions, and altered intra- and inter-phylum dynamics under RKN infection. Conclusions: These findings provide insight into rhizosphere microbial responses to RKN parasitism in F. tataricum and identify potential microbial biomarkers and biocontrol targets, supporting microbiome-based management strategies. Full article

Background and Objectives: Gastric cancer remains a leading cause of cancer-related mortality worldwide and develops through complex interactions between environmental factors, microbial dysbiosis, and host molecular pathways. Although Helicobacter pylori infection is a well-established risk factor, emerging evidence suggests that broader alterations in the gastric microbiome may also contribute to carcinogenesis. However, the associations between gastric cancer-associated microbial taxa and host gene expression profiles remain insufficiently characterized. This study aimed to identify host gene signatures associated with gastric cancer-related microbial taxa through a descriptive analysis integrating microbiome-derived taxa with transcriptome data. Materials and Methods: Microbial taxa associated with gastric cancer were systematically retrieved from the Disbiome database. Taxon set enrichment analysis (TSEA) was performed using the MicrobiomeAnalyst platform to identify host genes associated with gastric cancer-associated taxa. Importantly, TSEA relies on healthy reference data from the Human Microbiome Project and does not establish gastric cancer-specific interactions or causal relationships. Gene expression levels were subsequently evaluated using The Cancer Genome Atlas (TCGA) PanCancer stomach adenocarcinoma (STAD) dataset by comparing tumor and matched normal gastric tissues. Gene interaction network and transcription factor (TF) enrichment analyses were conducted to explore predicted regulatory relationships. Results: Among 64 microbial taxa associated with gastric cancer, 43 were reported as elevated. After removing overlapping taxa across studies, 37 elevated and 21 reduced taxa were retained for analysis. TSEA identified 11 host genes associated with gastric cancer-related microbial taxa. Transcriptomic analysis demonstrated significant downregulation of DPP6 and DLG2, while KDM4D, USP34, and VDR were significantly upregulated in gastric cancer tissues compared with normal controls. Network and TF enrichment analyses revealed predicted co-expression and co-localization patterns among these genes, suggesting their potential involvement in immune-related processes, epigenetic regulation, and cellular organization. Conclusions: This descriptive study identifies distinct host gene expression signatures associated with gastric cancer-associated microbial dysbiosis. This study is purely associative and hypothesis-generating; no causal or mechanistic inferences are made. TSEA used healthy reference data and therefore does not reflect gastric cancer-specific host–microbe interactions. The findings provide a basis for future hypothesis-driven research but require validation in independent cohorts. Full article

Schizopygopsis younghusbandi is an endemic and economically important fish in the Qinghai-Xizang Plateau, but its aquaculture is limited by harsh environmental conditions and incomplete understanding of host–microbiome–environment interactions. This study applied metagenomic sequencing to examine how different culture environments affect growth, water microbial communities, and gut microbiome network stability. Three-year-old juveniles (initial body weight 50.57 ± 1.88 g) were reared for 90 days in five systems: conventional pond (P), wetland (WL), concrete tank (G), river (R), and recirculating aquaculture system (RC). No significant differences in initial body weight or length were observed among groups (p > 0.05). Fish in the RC system achieved the highest final body weight, weight gain rate, and specific growth rate (p < 0.05), while survival rates were highest in the river and RC groups and lowest in ponds (p < 0.05). Microbial diversity and community composition differed significantly among culture modes, with bacterial and protozoan communities showing the strongest environmental responsiveness. Co-occurrence network analyses revealed that RC and G systems exhibited higher network complexity, density, and proportion of positive correlations, reflecting enhanced microbial interaction and ecological stability, whereas the WL system showed reduced network connectivity. Correlation analysis indicated that bacterial abundance was positively associated with total nitrogen, total phosphorus, and dissolved oxygen (p < 0.05), highlighting environmental regulation of microbial assemblages. Overall, the aquaculture environment shapes gut microbial networks, which closely relate to growth performance. Recirculating aquaculture systems can mitigate growth limitations in plateau fish by stabilizing the environment and reinforcing gut microbial communities, providing a sustainable strategy for high-altitude aquaculture development. Full article

Inland waters are critical nodes in the global nitrogen cycle, where microbial processes govern transformations that impact water quality and ecosystem functioning. Inland waters are critical nodes in the global nitrogen cycle, where microbial processes govern transformations that impact water quality and ecosystem functioning. To systematically map the knowledge structure and to identify evolving trends in this field, a bibliometric analysis was conducted using CiteSpace on 2459 publications from the Web of Science Core Collection (1990–2024). The results reveal a significant increase in publications after 2010, peaking at 228 in 2024, with China (1541 articles) and the Chinese Academy of Sciences (776 articles) being the leading country and institution, respectively. Keyword co-occurrence and cluster analyses identify a core conceptual framework centered on microbial communities, nitrogen transformation processes (e.g., denitrification, anammox), and aquatic habitats (e.g., lakes, rivers). Based on keyword emergence and temporal trends, the analysis suggests an evolution in research focus across four dimensions: research subjects (from microbial biomass to keystone taxa), core questions (from process rates to predictive manipulation), methodological tools (from culturing to multi-omics), and mechanistic understanding (from linear pathways to complex networks). These observed patterns indicate a progressive refinement of the field. The findings provide a structured overview of the literature and may inform future research directions, but should be interpreted as bibliometric trends rather than definitive conclusions about the state of the science. Full article

Background: Prostate cancer (PCa) arises from complex interactions among host genetics, androgen signaling, and microbial communities. Emerging genomic evidence supports the presence of microbial consortia within prostate tissue, suggesting that microbial genes, metabolites, and host–microbe interactions may contribute to chronic inflammation, oncogenic signaling, and therapeutic resistance. Methods: We conducted a narrative review using targeted searches of PubMed and Google Scholar for studies published between 2020 and 2025, complemented by selected mechanistic reports published in March 2026. Human studies and experimental research providing mechanistic insights into prostate models were prioritized. Due to the heterogeneous methodologies, evidence was synthesized qualitatively, with an emphasis on genomic and signaling perspectives. Results: Low-biomass microbial DNA is consistently detected in prostate tissue. Proteomic analyses of Corpora amylacea suggest a “fossil record” of past infections through sequestered microbial DNA and antimicrobial proteins, potentially priming tissue for long-term carcinogenic processes, although contamination remains a key limitation. Recurrent bacterial and viral signals, including Cutibacterium acnes, Escherichia coli, Pseudomonas, Acinetobacter, human papillomavirus, Epstein–Barr virus, and cytomegalovirus, appear to converge on a restricted set of tumor-relevant pathways, including TLR–NF-κB, MAPK, PI3K/AKT/mTOR, cGAS–STING, and p53/pRb disruption. These interactions may promote cytokine production, oxidative stress, DNA damage, epithelial–mesenchymal transition, extracellular matrix remodeling, immune evasion, and resistance to therapy. The gut–prostate axis further links intestinal dysbiosis and microbial metabolites with systemic IGF-1 signaling and castration resistance. Conclusions: Microbial genomic consortia in the prostate and gut may shape inflammatory, metabolic, and immune networks that influence PCa initiation and progression. However, most available data remain correlative and are limited by low-biomass sampling, contamination risk, and heterogeneous study designs. Future research should prioritize rigorous contamination control, longitudinal and prostate-specific mechanistic studies, and integrated multi-omic approaches to clarify causality and identify actionable microbial targets for prevention, diagnosis, and therapy. Full article

Intensive ornamental planting is increasingly prevalent in urban green spaces, yet its effects on soil microbial community assembly and interaction networks remain poorly understood. Here, we examined shifts in soil properties, microbial diversity, community composition, and interaction networks across successive planting cycles. Bacterial alpha-diversity remained relatively stable, whereas fungal communities showed pronounced sensitivity to early planting stages. Beta-diversity analyses revealed that bacterial community composition was jointly influenced by planting stage and site type, while fungal communities were primarily structured by site characteristics. Co-occurrence network analysis revealed contrasting reassembly trajectories between microbial groups. Bacterial networks exhibited increasing complexity and modularity, indicating enhanced interaction intensity and competitive structuring under intensive management. In contrast, fungal networks displayed reduced connectivity but maintained or recovered modular organization, suggesting structural buffering. Notably, keystone taxa remained taxonomically conserved, indicating that network reorganization was driven by interaction rewiring rather than species turnover. We propose a dual-speed reassembly framework in which bacteria function as fast-responding components with dynamic interaction networks, whereas fungi act as slow-buffering, structurally persistent elements. This decoupling of short-term functional responsiveness and long-term stability provides new insights into how intensive management reshapes soil microbiomes in botanical garden ecosystems. Full article

The mycoheterotrophic plant Monotropa uniflora relies on fungal symbionts for carbon and nutrient acquisition. However, its interactions with other microbial groups, beyond ectomycorrhizal fungi, remain unexplored. Here, we characterized bacterial and fungal communities associated with M. uniflora across two compartments: ectomycorrhizospheric soil linked to the mycorrhizal network and the surface-sterilized lower stem endosphere. Microbial community composition was assessed using high-throughput amplicon sequencing of the bacterial 16S rRNA gene and the fungal ITS region. Fungal richness was consistently higher in ectomycorrhizospheric soil than in the stem endosphere, whereas bacterial alpha diversity showed no consistent differences between compartments. Multivariate analyses suggested compartment-associated patterns in both bacterial and fungal community composition. Ectomycorrhizospheric soil was dominated by saprotrophic fungal taxa and bacterial groups with predicted metabolic potential, including taxa associated with iron, sulfur and nitrogen cycling. In contrast, the lower stem endosphere was enriched in bacterial taxa commonly associated with anaerobic and nitrogen-related metabolisms. Functional predictions further suggested an increase of carbon fixation-related pathways in rhizosphere-associated bacterial communities. Together, these results indicate that M. uniflora is associated with distinct and structured microbial assemblages across soil and internal plant compartments, highlighting the predicted functional potential of bacterial communities in nutrient- and carbon-related processes in mycoheterotrophic plant–soil systems alongside fungal partners. Full article

Environmental pH plays a critical role in microbial fermentation processes. Weizmannia coagulans attracts particular attention for exceptional acid tolerance and lactic acid productivity. Yet acidic stress impacts on its cell division regulation remain unclear. Here, a critical pH value (pH 4.20) for growth inhibition of the Gram-positive bacterium Weizmannia coagulans strain BC99 was first established. Transcriptomic analysis of metabolic pathways was then performed. The multi-layered regulatory network underlying acid stress-induced cell division was elucidated. Integrated transcriptomic and physiological analyses reveal that acid stress triggers multigene expression reprogramming. This drives core metabolic network reorganization, coordinately regulating division processes. RNA-seq analysis demonstrated acid stress triggered differential expression of division genes (FtsZ/Q downregulation), ATP synthase suppression, and peptidoglycan transport reduction, while enhancing membrane rigidification (Cfa) and magnesium homeostasis (CorA). The PhoPR dual-component system emerged as a central regulator, inhibiting septal assembly via RipA hydrolase and RpsU ribosomal suppression while rerouting carbon flux to glycolysis, elucidating bacterial acid adaptation mechanisms. Collectively, these adaptive changes prioritize cell survival over active proliferation under acidic conditions. This study provides molecular insights into how W. coagulans preserves viability under acid stress, offering a theoretical basis for optimizing its performance in probiotic applications. Full article

Castanopsis hystrix (C. hystrix) is one of the most dominant and ecologically important species in subtropical evergreen broad-leaved forests of China. Interactions between its root and rhizosphere microorganisms play a pivotal role in nutrient acquisition and in mediating plant response s to environmental stresses. In this study, high-throughput 16S ribosomal RNA (16S rRNA) sequencing combined with untargeted metabolomics was employed to systematically characterize the rhizosphere microbial community and root exudates in C. hystrix. The results showed that, compared with non-rhizosphere soil, bacterial diversity in the rhizosphere of C. hystrix was significantly reduced, while several specialized and potentially efficient taxa were selectively enriched, particularly Candidatus_Solibacter, Candidatus_Xiphinematobacter, and Candidatus_Koribacter, thereby reshaping a distinct rhizosphere-specific community structure. Metabolomic analyses further revealed that 129 metabolites were significantly enriched in the rhizosphere, including four major classes of compounds associated with plant stress resistance: lipids and lipid-like molecules, organoheterocyclic compounds, organic acids and derivatives, and phenylpropanoids and polyketides. The enrichment of these metabolites likely contributes substantially to stress tolerance in C. hystrix. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis identified six defense-related metabolic pathways, including pyrimidine metabolism, steroid biosynthesis, nucleotide metabolism, plant hormone signal transduction, ATP-binding cassette transporter (ABC transporters), and the biosynthesis of various plant secondary metabolites. Further correlation analysis and co-occurrence network analysis suggested that C. hystrix may potentially influence the enrichment of beneficial microorganisms through rhizosphere metabolites selectively, which could reduce the reliance on external nutrient acquisition and enhance the stress resilience of C. hystrix. Our study provides a comprehensive perspective for elucidating rhizosphere interaction networks and their ecological functions in C. hystrix, thereby enhancing our understanding of the environmental adaptability of dominant tree species in subtropical forests. Full article

Quantitative microbial risk assessment (QMRA) has become a central framework for evaluating foodborne microbial hazards by integrating microbiological data, exposure assessment, dose–response modelling, and probabilistic simulation. Over the past three decades, its rapid expansion has created challenges in obtaining a coherent overview of the field’s structure, dominant themes, and research trajectories. This study presents a bibliometric and systematic review of QMRA research in food safety. Bibliographic data were retrieved from the Scopus database (search conducted in January 2026), including peer-reviewed articles published in English between 1995 and 2024, and analysed using performance analysis and science mapping techniques to assess publication trends, influential contributors, collaboration patterns, and thematic evolution. Risk of bias assessment was not applicable due to the bibliometric nature of the study. The results indicate steady long-term growth of QMRA research, based on a final dataset of 186 articles across multiple journals and countries, with a concentrated influence structure dominated by a limited number of specialised journals, institutions, and research groups. International collaboration is particularly strong within European networks. Thematic analysis identifies probabilistic exposure assessment, Monte Carlo simulation, predictive microbiology, and dose–response modelling as the methodological core, with a primary focus on major foodborne pathogens such as Campylobacter, Salmonella, Listeria monocytogenes, and Escherichia coli. Persistent emphasis on uncertainty, cross-contamination, and dose–response relationships highlights key methodological challenges. Limitations include reliance on a single database and potential exclusion of studies using alternative terminology. These findings provide a structured overview of the QMRA landscape and identify priorities for methodological refinement and future application in food safety risk assessment. This study received no external funding and was not prospectively registered. Full article

Soil fumigation effectively mitigates replanting obstacles induced by intensive cultivation, yet its non-targeted biocidal effects can suppress beneficial microbial activity, potentially compromising agricultural sustainability. Microbial inoculation, as a strategy to supplement beneficial microorganisms, is often employed to restore soil microbial communities. However, in practice, commonly used exogenous microbial consortia exhibit poor adaptability in non-native environments, frequently resulting in limited efficacy. To address this limitation, we propose an ecological intervention based on the reintroduction of indigenous cultivable microorganisms: cultivable microbial communities were isolated from healthy adjacent soils and inoculated into fumigated soils affected by replanting obstacles. The experimental soil consisted of black soil under continuous cropping, collected from Northeast China. The three treatments were continuous cropping soil (control), fumigated continuous cropping soil and fumigated continuous cropping soil after inoculation of indigenous cultivable microorganisms. Using high-throughput sequencing and agronomic–chemical analyses, combined with cross-domain networks and procrustes analysis, we systematically assessed the ecological effects of this approach on microbial restoration and the alleviation of replanting obstacles. The results showed that indigenous cultivable microorganism inoculation significantly increased the richness of bacterial and fungal communities in fumigated soils within 21 days, extending microbial richness and diversity. Furthermore, inoculation accelerated the reconstruction of dominant microbial community structures, with the relative abundance of dominant species reaching up to 80%. Positive synergistic interactions between bacteria and fungi increased by approximately 10%, enhancing network stability. Key bacterial taxa, such as Paenibacillus and Mycobacterium, were significantly correlated with available potassium and phosphorus content, while Micromonospora, Massilia, and Flavisolibacter influenced plant fresh weight, total nitrogen, and potassium accumulation. Key fungal taxa, such as Cryptococcus and Phialemonium, were significantly associated with soil organic matter stability, maize photosynthetic efficiency, plant dry weight, and total phosphorus content. This study confirms the ecological adaptability and functionality of indigenous cultivable microorganisms in soil ecosystem restoration, offering a low-risk, highly effective localized intervention strategy for sustainable agriculture. Full article