Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1083736 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR28223028.fastq.gz | Fastqsanger.gz |
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Project description:Mutualistic interactions with beneficial microbes can influence plant physiology far beyond the point of initial contact, yet how host plants differentiate among microbial partners, and the consequences of that discrimination, remain poorly understood. Here, we investigate how Cucumis melo responds to early seed priming with two phylogenetically related Bacillus strains: B. subtilis NCIB3610 and B. velezensis FZB42. Despite exhibiting similar colonization patterns and persistence in the root system, these strains elicit distinct, strain-specific plant responses at the developmental, metabolic, and defensive levels. B. subtilis enhances radicle elongation and drought resilience through increased starch and L-tryptophan accumulation, while B. velezensis transiently represses early growth and reprograms host transcriptome and metabolome, including jasmonate-associated gene expression and flavonoid biosynthesis. Both treatments ultimately converge on improved performance in the phyllosphere, including enhanced resistance to Botrytis cinerea and a population of Tetranychus urticae, though via divergent physiological routes. These findings reveal that plants do not merely tolerate or benefit from microbial presence, but actively engage in partner-specific programming, even among closely related beneficial strains. This capacity for functional discrimination broadens our understanding of how mutualistic interactions are shaped and diversified in plant hosts.
2026-06-11 | GSE299630 | GEO
Project description:Gut microbiome significantly influences immunotherapy responses in colorectal cancer (CRC) treatment. While individual enterobacteria have been identified as enhancers of anti-PD-1/anti-PD-L1 therapy, the synergistic effects of multiple enterobacteria remain underexplored. To fill the gap, we introduced Tumor-Suppressing Multi-Enterobacteria (TSME), a consortium of nine beneficial intestinal probiotic strains, and investigated its impact on the anti-PD-1/anti-PD-L1 therapy for microsatellite stable (MSS) CRC. Using a tumor-bearing mouse model and genomic sequencing techniques, our research demonstrated that TSME significantly improved therapy efficacy by optimizing tumor immune microenvironment. Specifically, the addition of TSME notably increased CD8+ T infiltration, modulated cytokine profiles, and up-regulated crucial immune-related pathways, including TNF and JAK-STAT. Additionally, TSME altered intestinal microbial composition, enriching beneficial bacteria such as Akkermansia and Alistipes. These findings suggest that the well-engineered multi-enterobacteria could significantly enhance the effectiveness of immunotherapy for MSS CRC by synergistically modulating the immune and microbial landscapes.
2026-04-26 | GSE271663 | GEO
Project description:This clinical trial tests whether daily fiber supplementation will change the mucosal microbiome of the colon. The microbiome are microorganisms that live in the human gut. They serve a vital role in maintaining health. Certain microbial strains are associated with the growth of colon polyps, which eventually could go on to form colon cancer. Giving dietary fiber supplements may help prevent precancerous polyps from ever developing.
| 1864 | ecrin-mdr-crc
Project description:Many Trichoderma spp. are successful plant beneficial microbial inoculants due to their ability to act as biocontrol agents with direct antagonistic activities to phytopathogens, and as biostimulants capable of promoting plant growth. This work investigates the effects of treatments with three selected Trichoderma (strains T22, TH1 and GV41) to strawberry plants on the productivity and proteome of the formed fruit. Proteomic analysis of fruits,harvested from the plants previously treated with Trichoderma and control plants was performed by using a TMT-based protein quantification strategy. Bioinformatic analysis of the differential proteins accumulation in fruits, harvested from the treated plants, revealed a central network of interacting molecular species, that demonstrated the modulation of different plant physiological processes following the microbial inoculation.
2020-06-09 | PXD016951 | Pride
Project description:Screening of beneficial bacteria in Apostichopus japonicus culture ponds
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Project description:Unlike pathogens that trigger plant defense responses, beneficial microbes are compatible with plants. One possible reason for the compatibility is that the microbial factors from beneficial microbes are inert in that they do not trigger plant defense responses. Little is known about the mechanisms underlying this seemingly inert relation. Here we report that Arabidopsis lacking the gene Growth-Promotion 1 (GP1) becomes defensive to microbial volatiles from Bacillus amyloliqueficiens strain GB03, a beneficial rhizobacterium. The gp1 mutant was isolated in a forward genetic screen for mutants that show defectiveness in GB03-triggered plant inducible vigor. GP1 encodes a stearoyl-ACP desaturase that catalyzes the desaturation of stearic acid (18:0) to oleic acid (18:1). Consistently, plant inducible vigor was also impaired by chemical enhancement of 18:1 catabolism, while genetic disruption of 18:1 catabolism largely restored the inducible vigor in gp1. When exposed to GB03-emitted microbial volatiles (GMVs), wild type plants showed transcriptional up-regulation of growth-promoting processes and down-regulation of defense responses; in contrast, the gp1 transcriptome displayed elevated defense responses when treated with GMVs. Meanwhile disruption of salicylic acid-mediated defense partially restored plant inducible vigor in gp1. Microbiota profiling revealed that GP1 dysfunction alters the assemblage of plant-associated rhizobacteria communities, including a reduction in the Bacillaceae family that is known to contain many beneficial rhizobacteria species. Consistently, gp1 mutants showed severely impaired root colonization of GB03. Our findings suggest that GP1 prevents the plant defense system from being mistakenly activated by non-pathogenic microbial factors, thereby allowing mutualistic association between the plant and beneficial microbes.
2022-10-04 | GSE139154 | GEO
Project description:The economic viability of bio-based chemical production relies on microbial strain improvement, which optimizes titer, yield, and productivity of the process. This improvement necessitates redirecting cellular metabolism towards target molecule synthesis, requiring not only heterologous gene introduction but also endogenous genomic modifications to reconfigure metabolic networks originally optimized for cellular growth. However, identifying engineering targets is complex due to the intricate nature of metabolic networks and the cumulative, interactive effects of multiple genes on compound production. Consequently, there is a critical need for technologies capable of elucidating unpredictable engineering targets and synergistic gene combinations that enhance product formation in microbial strains. This study presents an innovative, integrated methodology named Tn-MAGE for rapidly identifying unpredictable engineering targets and synergistic gene combinations to enhance microbial strain performance in compound production. Our approach synergistically combines two key strategies: (1) integration of Tn-seq with biosensor-assisted ALE in a single batch culture, and (2) utilization of MAGE for combinatorial knockout library creation coupled with biosensor-assisted high-throughput screening. This integrated Tn-MAGE methodology offers a powerful tool for discovering unpredictable targets across the genome and their combinations, facilitating the development of high-performing strains for bio-based production of valuable compounds. The versatility of this approach suggests its potential applicability in various metabolic engineering contexts, promising significant advancements in strain improvement strategies.
2025-11-22 | GSE279638 | GEO
Project description:Insufficient dietary fiber intake is strongly associated with gut microbiome dysfunction and an increased risk of noncommunicable diseases. Synergistic synbiotics, which pair defined microbial strains with their preferred carbohydrate substrates, offer a promising strategy to restore these functions. However, the rational design of such interventions remains challenging by insufficient understanding of microbial fiber-degrading capacities and the host-relevant bioactivities of fermentation-derived metabolites. Here, we identify human colonic commensal Bacteroides intestinalis (B. intestinalis) as a key microbial mediator of dietary fiber-driven metabolic, immune, and neuronal benefits. We demonstrate that the synergistic interaction between B. intestinalis and its preferred substrate, insoluble wheat arabinoxylan abundant in dietary fiber, enhances the production of anti-inflammatory, antioxidant, and anti-diabetic phenolic compounds and bile acid species. These metabolic effects are accompanied by coordinated transcriptional remodeling in the colon and spleen that improve circadian rhythm regulation, lipid metabolism, and immune defense. Importantly, these beneficial effects are preserved in conventionally raised mice with established high fat diet-induced obesity, where BI and inWAX improves glucose tolerance along with an increased production of neuroactive compounds. Our findings uncover a mechanistic framework linking B. intestinalis-mediated fiber fermentation to gut–liver–brain crosstalk and establish a rational foundation for precision synbiotic design.
2026-03-12 | GSE318341 | GEO