Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1070042 | ENA |
REPOSITORIES: ENA
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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:Coral bleaching and coral reef degradation become severe as the surface seawater temperature rises. Much research to date has focused on the bacterial community composition properties within the coral holobiont, but less attention has been paid to the interactions of bacteria and corals under thermal stress. We investigated the changes of coral symbiotic bacteria and metabolites under thermal stress, and analyzed the internal relationship between bacteria and metabolites as well as their relationship with coral health. We found obvious signs of coral bleaching after heating treatment, and the interaction within symbiotic bacterial community became closer. The coral symbiotic bacterial community and metabolites changed significantly under thermal stress, and bacteria such as Flavobacterium, Shewanella and Psychrobacter increased significantly. Bacteria associated with stress tolerance, biofilm formation and mobile elements decreased, and bacterial DMSP metabolism increased slightly after heating treatment. Differential metabolites in corals after heating treatment were associated with cell cycle regulation and antioxidant. This study revealed the correlation between differential metabolites and bacterial community composition changes in corals under thermal stress, and providing valuable insight on metabolomics research of corals.
2022-10-27 | MTBLS5272 | MetaboLights
Project description:Organic matter recycling in marine systems is largely driven by microbial processes, particularly in the Arctic where primary production and inputs can be temporally offset from upper trophic level consumption. This study followed bacterial dynamics in the chlorophyll maximum of the Bering Strait and sediment-water interface of the Chukchi Sea using metaproteomic and 16S rRNA methods to measure cellular function and taxonomic composition under low and high marine-derived particulate organic matter (POM) treatments at 0°C. Parallel analysis of major organic components (lipids and amino acids) allowed a comparison of microbial-POM interactions. Over the 10 day experimental period, bacteria under both treatments showed rapid community responses and changes in proteomic expression, accompanied by small changes in the concentration and distributions of organic components. In the Bering Strait community, protein translation was an important immediate cellular response under both POM scenarios while specific metabolic processes were more distinct between treatments. For example, under both conditions, evidence for carboxylic acid metabolism increased at day 6 while carbohydrate utilization as an energy source showed unique patterns as the experiments progressed. With POM additions to the Bering Strait community, nitrogen transport and regulation went up, including nitrogen fixation and ammonia assimilation, by day 6. In addition, a number of vitamin enzymatic cofactors were enriched by this day, providing evidence for an increase in C1 metabolism at that time. Low POM conditions stimulated the cycling and synthesis of amino acids, which was not as pronounced under the high POM treatment. In the Chukchi Sea community, nitrate reduction and substrate-specific transporter activity was statistically higher than in the Bering Strait, especially under low POM conditions. Taxonomic inference revealed that a wide range of bacterial classes were associated with the shifting cellular functions, but that Alphaproteobacteria, Gammaproteobacteria and Flavobacteria controlled most of these protein abundances. Activities of all classes were highly variable, with less dominant bacterial groups exhibiting a particularly strong degree of niche separation.
2019-02-18 | PXD008780 | Pride
Project description:Manufactured nanomaterials (MNMs) are increasingly incorporated into consumer products that are disposed into sewage. In wastewater treatment, MNMs adsorb to activated sludge biomass where they may impact biological wastewater treatment performance, including nutrient removal. Here, we studied MNM effects on bacterial polyhydroxyalkanoate (PHA), specifically polyhydroxybutyrate (PHB), biosynthesis because of its importance to enhanced biological phosphorus (P) removal (EBPR). Activated sludge was sampled from an anoxic selector of a municipal wastewater treatment plant (WWTP), and PHB-containing bacteria were concentrated by density gradient centrifugation. After starvation to decrease intracellular PHB stores, bacteria were nutritionally augmented to promote PHB biosynthesis while being exposed to either MNMs (TiO2 or Ag) or to Ag salts (each at a concentration of 5 mg L-1). Cellular PHB concentration and PhyloChip community composition were analyzed. The final bacterial community composition differed from activated sludge, demonstrating that laboratory enrichment was selective. Still, PHB was synthesized to near-activated sludge levels. Ag salts altered final bacterial communities, although MNMs did not. PHB biosynthesis was diminished with Ag (salt or MNMs), indicating the potential for Ag-MNMs to physiologically impact EBPR through the effects of dissolved Ag ions on PHB producers.
2014-12-03 | GSE63781 | GEO