Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1269071 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Diatom-derived polyunsaturated aldehydes (PUAs) significantly influence marine bacterial dy-namics, yet the underlying proteomic mechanisms remain elusive. We employed high-resolution comparative proteomics to decipher the functional reprogramming of two bacterial communi-ties—one naturally associated with a PUA-producing diatom (N-community) and another with a non-PUA producer (I-community)—under ecologically relevant PUA exposure. While growth rates and cell densities remained unaffected, indicating an absence of acute toxicity, proteomics revealed pronounced community-specific reorganization. N-communities displayed stable, regula-tion-oriented adjustments consistent with physiological accommodation, whereas I-communities exhibited dose-dependent stress responses, shifting toward protein repair and antioxidant defense. Our findings demonstrate that PUAs trigger profound proteomic reprogramming conditioned by the communities' prior ecological history. This functional divergence provides a molecular basis for understanding bacterial fitness and succession during diatom blooms, where PUA-mediated in-teractions could act as a selective filter shaping the phycosphere's microbial landscape. Polyunsaturated aldehydes (PUA) produced by diatoms have been proposed to exert a wide range of effects on marine bacteria, from inhibitory or stress-inducing responses to neutral or potentially beneficial effects. However, the bacterial proteomic responses remain elusive. Here, we employed a high-resolution comparative proteomic approach to decipher the functional reprogramming of two distinct bacterial communities under ecologically relevant PUA exposure. One community was composed by bacteria naturally associated with a PUA-producing diatom (N- communy and, a second community associated with a non-PUA-producing diatom (I-community). Bacterial growth rates and final cell densities were not significantly affected by any treatment, indicating the absence of toxic effects even at high PUA concentrations. Dissolved organic carbon consumption did not provide evidence that PUA was the relevant carbon source. Interestingly, comparative proteomic analyses revealed pronounced community-specific reorganization in response to PUA expo-sure.Our results show that PUAs trigger a profound proteomic reprogramming rather than a simple stress response. While I-community prioritized antioxidant defense and protein repair, N-community showed a metabolic shift towards energy conservation. These findings suggest that the metabolic history of bacterial assemblages determines their success in the phycosphere, providing a molecular basis for microbial succession during diatom blooms.
2026-06-04 | PXD075100 | Pride
Project description:Microbiologically influenced corrosion (MIC) is recognized as a considerable threat to carbon steel asset integrity in the oil and gas industry. There is an immediate need for reliable and broadly applicable methods for detection and monitoring of MIC. Proteins associated with microbial metabolisms involved in MIC could serve as useful biomarkers for MIC diagnosis and monitoring. A proteomic study was conducted using a lithotrophically-grown bacteria Desulfovibrio ferrophilus strain IS5, which is known to cause severe electric MIC in seawater environments. Unique proteins, which are differentially and uniquely expressed during severe microbial corrosion by strain IS5, were identified. This includes the detection of a multi-heme cytochrome protein predicted to be involved in extracellular electron transfer in the presence of the carbon steel. Thus, we conclude that newly identified protein biomarker for MIC could be used to generate easy-to-implement immunoassays for reliable detection of microbiological corrosion in the field.
2021-07-30 | PXD026513 | Pride
Project description:The gut microbiome consists of trillions of bacteria, fungi, and viruses that inhabit the digestive tract. These communities are sensitive to disruption from environmental exposures ranging from diet changes to illness. Disruption of the community of lactic acid producing bacteria, Lactobaccillacea, has been well documented in mood disorders and stress exposure. In fact, oral supplement with many Lactobacillus species can ameliorate these effects, preventing depression- and anxiety-like behavior. Here, we utilize a gnotobiotic mouse colonized with the Altered Schaedler Flora to remove the two native species of Lactobaccillacea. Using this novel microbial community, we found that the Lactobacillus species themselves, and not the disrupted microbial communities are protective from environmental stressors. Further, we determine that Lactobaccillacea are maintaining homeostatic IFNγ levels which are mediating these behavioral and circuit level responses. By utilizing the Altered Schaedler Flora, we have gained new insight into how probiotics influence behavior and provide novel methods to study potential therapies to treat mood disorders.
2023-08-22 | GSE241110 | GEO
Project description:Root exudates contain specialised metabolites that affect the plant’s root microbiome. How host-specific microbes cope with these bioactive compounds, and how this ability shapes root microbiomes, remains largely unknown. We investigated how maize root bacteria metabolise benzoxazinoids, the main specialised metabolites of maize. Diverse and abundant bacteria metabolised the major compound in the maize rhizosphere MBOA and formed AMPO. AMPO forming bacteria are enriched in the rhizosphere of benzoxazinoid-producing maize and can use MBOA as carbon source. We identified a novel gene cluster associated with AMPO formation in microbacteria. The first gene in this cluster, bxdA encodes a lactonase that converts MBOA to AMPO in vitro. A deletion mutant of the homologous bxdA genes in the genus Sphingobium, does not form AMPO nor is it able to use MBOA as a carbon source. BxdA was identified in different genera of maize root bacteria. Here we show that plant-specialised metabolites select for metabolisation-competent root bacteria. BxdA represents a novel benzoxazinoid metabolisation gene whose carriers successfully colonize the maize rhizosphere and thereby shape the plant’s chemical environmental footprint
2024-04-05 | GSE263275 | GEO
Project description:Endothelial cell (EC)-enriched protein coding genes, such as endothelial nitric oxide synthase (eNOS), define quintessential EC-specific physiologic functions. It is not clear whether long noncoding RNAs (lncRNAs) also define cardiovascular cell-type specific phenotypes, especially in the vascular endothelium. Here, we report the existence of a set of EC-enriched lncRNAs and define a role for STEEL (spliced transcript – endothelial enriched lncRNA) in angiogenic potential, macrovascular/microvascular identity and shear stress responsiveness. STEEL is expressed from the terminus of the HOXD locus and is transcribed antisense to HOXD transcription factors. STEEL RNA increases the number and integrity of de novo perfused microvessels in an in vivo model and augments angiogenesis in vitro. The STEEL RNA is polyadenylated, nuclear-enriched and has microvascular predominance. Functionally, STEEL regulates a number of genes in diverse endothelial cells. Of interest, STEEL upregulates both eNOS and the transcription factor Kruppel-like factor 2 (KLF2), and is subject to feedback inhibition by both eNOS and shear-augmented KLF2. Mechanistically, STEEL upregulation of eNOS and KLF2 is transcriptionally mediated, in part, via interaction of chromatin-associated STEEL with the poly-ADP ribosylase, PARP1. For instance, STEEL recruits PARP1 to the KLF2 promoter. This work identifies a role for EC-enriched lncRNAs in the phenotypic adaptation of ECs to both body position and hemodynamic forces, and establishes a newer role for lncRNAs in the transcriptional regulation of EC identity.
2018-02-28 | PXD008581 | Pride
Project description:Pseudomonas aeruginosa is a pathogenic micro-organism responsible for many hospital-acquired infections. It is able to adhere to solid surfaces and develop an immobilised community or so-called biofilm. Many studies have been focusing on the use of specific materials to prevent the formation of these biofilms, but the reactivity of the bacteria in contact to surfaces remains unknown. In order to evaluate the impact of different materials on the physiology of Pseudomonas aeruginosa during the first stage of biofilm formation, i.e. adhesion, we investigated the total proteome of cells adhering to three materials: stainless steel, glass and polystyrene. Using tandem mass spectrometry performed at the PAPPSO proteomic platform, 930 proteins were identified, 70 of which were differentially expressed between the materials. Dysregulated proteins belonged to 19 PseudoCAP (Pseudomonas Community Annotation Project) functional classes, with a particular abundance of proteins involved in small molecule transport and membrane proteins. Notably, ten porins or porin precursors were under-produced in bacteria adhering to stainless steel when compared to those adhering to polystyrene and glass. Although adhesion to solid surfaces is an extracellular phenomenon, it involves not only extracellular proteins but also intracellular reactions, as observed with the dysregulation of 11 proteins involved in various metabolisms and five in protein translation. Overall, this work showed that during bacterial adhesion, P. aeruginosa senses the materials concerned and is able to modulate its physiology accordingly.
2018-10-24 | PXD006881 | Pride
Project description:Determine in the context of a controlled crossover diet-intervention trial the role of taurocholic acid metabolism by gut bacteria in African American subjects at elevated risk for colorectal cancer (CRC). Two isocaloric diets, an animal-based diet high in taurine and saturated fat (HT-HSAT) and a plant-based, low in taurine and low saturated fat (LT-LSAT) will be used to determine the extent to which the relationship between diet (independent variable) and mucosal markers of CRC risk including epithelial proliferation, oxidative stress, DNA damage, and primary and secondary bile acid pools and biomarkers of inflammation (dependent variables) is explained by the abundance of sulfidogenic bacteria and hydrogen sulfide (H2S) concentrations &/or deoxycholic acid (DCA) and DCA-producing bacteria clostridium scindens (mediator variables).
| 2274903 | ecrin-mdr-crc
Project description:The response of soil microbial community to climate warming through both function shift and composition reorganization may profoundly influence global nutrient cycles, leading to potential significant carbon release from the terrain to the atmosphere. Despite the observed carbon flux change in northern permafrost, it remains unclear how soil microbial community contributes to this ecosystem alteration. Here, we applied microarray-based GeoChip 4.0 to investigate the functional and compositional response of subsurface (15~25cm) soil microbial community under about one year’s artificial heating (+2°C) in the Carbon in Permafrost Experimental Heating Research site on Alaska’s moist acidic tundra. Statistical analyses of GeoChip signal intensities showed significant microbial function shift in AK samples. Detrended correspondence analysis and dissimilarity tests (MRPP and ANOSIM) indicated significant functional structure difference between the warmed and the control communities. ANOVA revealed that 60% of the 70 detected individual genes in carbon, nitrogen, phosphorous and sulfur cyclings were substantially increased (p<0.05) by heating. 18 out of 33 detected carbon degradation genes were more abundant in warming samples in AK site, regardless of the discrepancy of labile or recalcitrant C, indicating a high temperature sensitivity of carbon degradation genes in rich carbon pool environment. These results demonstrated a rapid response of northern permafrost soil microbial community to warming. Considering the large carbon storage in northern permafrost region, microbial activity in this region may cause dramatic positive feedback to climate change, which is important and necessary to be integrated into climate change models.
2016-02-22 | GSE77866 | GEO
Project description:An important goal for many nutrition-based microbiome studies is to identify the metabolic function of microbes in complex microbial communities and its impact on host physiology. This research can be confounded by poorly-understood effects of community composition and host diet on the metabolic traits of individual taxa. Here, we investigated these multi-way interactions by constructing and analyzing metabolic models comprising every combination of five bacterial members of the Drosophila gut microbiome (from single taxa to the five-member community of Acetobacter and Lactobacillus species) under three nutrient regimes. We show that the metabolic function of Drosophila gut bacteria is dynamic, influenced by community composition and responsive to dietary modulation. Furthermore, we show that ecological interactions such as competition and mutualism identified from the growth patterns of gut bacteria are underlain by a diversity of metabolic interactions, and show that the bacteria tend to compete for amino acids and B vitamins more frequently than for carbon sources. Our results reveal that in addition to fermentation products such as acetate, intermediates of the tricarboxylic acid (TCA) cycle including 2-oxoglutarate and succinate are produced at high flux and cross-fed between bacterial taxa suggesting important roles for TCA cycle intermediates in modulating Drosophila gut microbe interactions and the potential to influence host traits. These metabolic models provide specific predictions of the patterns of ecological and metabolic interactions among gut bacteria under different nutrient regimes, with potentially important consequences for overall community metabolic function and nutritional interactions with the host.
2021-07-01 | MODEL2002040003 | BioModels