Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1074261 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:RNASeq of roots from two genotypes of Arabidopsis thaliana plants, Col-0 and myb36-2 grown axenically or with a 41 member bacterial Synthetic Community (SynCom) to explore the interaction between the root diffusion barriers and the root microbiome.
2020-11-01 | GSE151376 | GEO
Project description:The experiment was designed to test the interactions of Spartina alterniflora, its microbiome, and the interaction of the plant-microbe relationship with oil from the Deepwater Horizon oil spill (DWH). Total RNA was extracted from leaf and root microbiome of S. alterniflora in soils that were oiled in DWH oil spill with or without added oil, as well as those grown in unoiled soil with or without added oil. The work in its entirety characterizes the transport, fate and catabolic activities of bacterial communities in petroleum-polluted soils and within plant tissues.
2020-04-10 | GSE148431 | GEO
Project description:Development of cereal crops with high nitrogen-use efficiency (NUE) is a priority for worldwide agriculture. In addition to conventional plant breeding and genetic engineering, the use of the plant microbiome offers another approach to improve crop NUE. To gain insight into the bacterial communities associated with sorghum lines that differ in NUE, a field experiment was designed comparing 24 diverse sorghum lines under sufficient and deficient nitrogen (N). Amplicon sequencing and untargeted gas chromatography-mass spectrometry (GC-MS) were used to characterize the bacterial communities and the root metabolome associated with sorghum genotypes varying in sensitivity to low N. We demonstrated that N stress and sorghum type (energy, sweet, and grain sorghum) significantly impacted the root-associated bacterial communities and root metabolite composition of sorghum. We found a positive correlation between sorghum NUE and bacterial richness and diversity in the rhizosphere. The greater alpha diversity in high NUE lines was associated with the decreased abundance of a dominant bacterial taxa, Pseudomonas. Multiple strong correlations were detected between root metabolites and rhizosphere bacterial communities in response to low-N stress. This indicates that the shift in the sorghum microbiome due to low-N is associated with the root metabolites of the host plant. Taken together, our findings suggest that host genetic regulation of root metabolites plays a role in defining the root-associated microbiome of sorghum genotypes differing in NUE and tolerance to low-N stress.
2023-08-29 | MSV000092783 | MassIVE
Project description:Project Description: The interaction between microorganisms and plants plays a key role in plant development and environmental adaptation. Among these microorganisms, plant growth-promoting bacteria (PGPB) enhance agricultural productivity sustainably. Beyond direct effects on plant physiology, epigenetic modifications such as DNA methylation regulate gene expression and adaptive responses. This study investigates how DNA hypomethylation influences early interactions between maize (Zea mays) and the PGPB Herbaspirillum seropedicae, focusing on plant growth, metabolism, and root microbiome. Treatment with the hypomethylating agent 5-azacytidine (5-azaC) did not affect bacterial growth but induced notable phenotypic changes in maize, particularly in root morphology. Inoculation with H. seropedicae enhanced plant growth across biometric parameters. Microscopy revealed bacterial colonization primarily in root mucilage, with higher bacterial accumulation in 5-azaC-treated roots. Global methylation analysis indicated that H. seropedicae modulates cytosine methylation similarly to 5-azaC, suggesting a role in epigenetic regulation. Gene expression analysis of DNA methylation machinery supports hypomethylation as a driver of plant-microbe interactions. Root microbiome profiling showed that 5-azaC significantly altered microbial composition, whereas bacterial inoculation partially restored it toward control profiles. Proteomic analysis identified 1,818 proteins, highlighting significant shifts in metabolic pathways, especially carbon metabolism and the citric acid cycle. These findings demonstrate that DNA hypomethylation, combined with bacterial interaction, profoundly impacts cellular and metabolic processes, offering new insights into early plant-microbe interactions. This knowledge may contribute to developing sustainable agricultural practices through epigenetic and microbial modulation.
2026-05-05 | PXD077098 | Pride
Project description:Bariatric surgical procedures such as sleeve gastrectomy (SG) provide effective type 2 diabetes remission in human patients. Previous work demonstrated that gastrointestinal levels of the bacterial metabolite lithocholic acid (LCA) are decreased after SG in mice and humans. Here, we show that LCA worsens glucose tolerance and impairs whole body metabolism. We also show that taurodeoxycholic acid (TDCA), which was the only bile acid whose concentration was increased in the murine small intestine post-SG, suppresses the bacterial bile acid-inducible (bai) operon and production of LCA both in vitro and in vivo. Treatment of diet-induced obese (DIO) mice with TDCA reduces LCA levels and leads to microbiome-dependent improvements in host glucose handling. Moreover, TDCA abundance is decreased in small intestinal tissue from T2D patients. This work has revealed that TDCA is an endogenous inhibitor of LCA production and suggests that TDCA may contribute to the glucoregulatory effects of bariatric surgery.
2024-07-21 | GSE262065 | GEO
Project description:Both microbiological and genomics approaches demonstrated the significant PGP potential and stability of bacterial consortia SAB, which outperformed its members. Phenotypic data indicated that SAB treatment positively impacted shoot and root biomass growth. Furthermore, greenhouse experiments confirmed the consistent and significant performance of SAB treatment on choy sum plants in various soil conditions. Transcriptomics data of boht root and shoot at two different time point revealed that SAB triggered a parallel activation of growth and defense response in shoot that by pass the growth defense tread-off through microbiome mediated signaling and beneficial services.
2026-01-01 | GSE285600 | GEO
Project description:The gut microbiome is significantly altered in inflammatory bowel diseases, but the basis of these changes is not well understood. We have combined metagenomic and metatranscriptomic profiling of the gut microbiome to assess changes to both bacterial community structure and transcriptional activity in a mouse model of colitis. Gene families involved in microbial resistance to oxidative stress, including Dps/ferritin, Fe-dependent peroxidase and glutathione S-transferase, were transcriptionally up-regulated in colitis, implicating a role for increased oxygen tension in gut microbiota modulation. Transcriptional profiling of the host gut tissue and host RNA in the gut lumen revealed a marked increase in the transcription of genes with an activated macrophage and granulocyte signature, suggesting the involvement of these cell types in influencing microbial gene expression. Down-regulation of host glycosylation genes further supports a role for inflammation-driven changes to the gut niche that may impact the microbiome. We propose that members of the bacterial community react to inflammation-associated increased oxygen tension by inducing genes involved in oxidative stress resistance. Furthermore, correlated transcriptional responses between host glycosylation and bacterial glycan utilisation support a role for altered usage of host-derived carbohydrates in colitis. Complementary transcription profiling data from the mouse hosts have also been deposited at ArrayExpress under accession number E-MTAB-3590 ( http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-3590/ ).
2015-05-22 | E-MTAB-3562 | biostudies-arrayexpress
Project description:Arabidopsis root bacterial microbiome Metagenome
| PRJNA400677 | ENA
Project description:We combined an experimental microbiome of 11 bacterial strains isolated from the gut of native Caenorhabditis elegans. C. elegans were maintained on the experimental microbiome, Escherichia coli OP50 (control food source), or OP50 supplemented with cell-free media (CFM) from the experimental microbiome. For each of the three feeding conditions, RNA-seq was performed for wildtype (N2) worms or transgenic worms expressing amyloid beta 1-42 in their body wall muscle (GMC101).
2022-06-23 | E-MTAB-10693 | biostudies-arrayexpress