Whole genome sequencing of Sphingobium sp. Z007
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB12244 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Predatory bacterium Bdellovibrio bacteriovorus is ubiquitous and has a broad bacterial prey range including many antimicrobial resistant pathogens. However, it is currently unclear whether prey bacteria can evolve genetically-determined resistance against predation by B. bacteriovorus. In this project we found that the model bacterium Escherichia coli K-12 MG1655 consistently evolves resistance against B. bacteriovorus HD100 during experimental evolution. From one E. coli K-12 MG1655 ancestor eight different E. coli prey cultures were evolved each under no, low and high predatory pressure by B. bacteriovorus (for 15 evolution cycles). The ancestor (AN) as well as the eight E. coli prey lineages that evolved under high predatory pressure (H1-H8) were analysed by shot-gun proteomics. This proteomics data revealed a strong downregulation of OmpF and other structures on the prey surface. This study showed on the proteomic level what can cause resistance to predation. This will contribute to understand this ecologically important predator-prey interactions in more detail, and can advance the development of predatory bacteria as ‘living antibiotics’ to combat pathogenic bacteria.
2026-09-20 | PXD080500 | Pride
Project description: Not available
| S-EPMC7561683 | biostudies-literature
Project description:Purpose: The goal of this study was to compare gene expression in whole embryos to identify transcriptomic changes that result from maternal exposure to predation risk. Methods: Whole embryo mRNA profiles of 3 day post-fertilizationstickleback embrosof mothers exposed to simulated predation risk and control embryos were generated by RNA-sequencing of pooled embryos using Illumina Hiseq2000. The sequence reads that passed quality filters were aligned to the stickleback reference genome and analyzed at the gene level (EdgeR) and at the transcript level (Cufflinks/Cuffdiff). Subsets of embryos were also measured for embryo length and eye diameter, and data were analyzed with a general linear model (SPSS). Results: We mapped ~22 million sequence reads per sample to the stickleback reference genome (BROADS1, Ensembl database version 71.1, Feb 2006) and identified 17440 transcripts with the Tophat workflow. Differential expression analysis using both EdgeR and Cufflinks/Cuffdiff identified 455 transcripts were differentially expressed in embryos of mothers exposed to simulated predation risk as compared to control embryos, with an FDR <0.05 (Cuffdiff) or <0.10 (EdgeR). Gene ontology and pathway analysis (DAVID, IPA) of the differentially expressed gene list revealed enrichment of genes involved in growth, metabolism, neurogenesis, and epigenetics. Embryos of mothers exposed to predation risk had elevated expression of growth and metabolism genes and were also larger than control embryos, suggesting at least some of the genes differentially expressed in this study are involved in the transfer of maternal experience to offspring. Conclusions: Our results suggest that early stickleback embryos respond to maternal exposure to predation risk via changes in gene expression, and a general acceleration of the developmental program. Further study is needed to elucidate the myriad molecular interactions between genes that are differentially-regulated as a result of maternal exposure to predation risk and to understand their relationships to previously-observed maternal effects in this system. Whole embryo mRNA profiles of 3dpf stickleback embryos of mothers exposed to simulated predation risk [E] and control mothers [C] were generated by barcoded, multiplexed high-throughput RNA-sequencing on Illumina Hiseq-2000.
2014-06-07 | E-GEOD-56160 | biostudies-arrayexpress
Project description: Not available
| S-EPMC8638569 | biostudies-literature
Project description:This data set was acquired as a control set for an evolutionary study enquiring the response of Escherichia coli on the protein level to predatory pressure by Bdellovibrio bacteriovorus. Predatory bacterium Bdellovibrio bacteriovorus is ubiquitous and has a broad bacterial prey range including many antimicrobial resistant pathogens. However, it is currently unclear whether prey bacteria can evolve genetically-determined resistance against predation by B. bacteriovorus. We found that the model bacterium Escherichia coli K-12 MG1655 evolves resistance against B. bacteriovorus HD100 during experimental evolution. The experimental evolution setting showed that E. coli K-12 MG1655 lineages evolved under high predatory pressure have reduced/or no level of outer membrane porin F (OmpF) next to other changes at the outer surface on the genome and proteome level. For the latter please refer to PRIDE submission PXD080500. As a control set the proteome was analysed of markerless single gene deletion mutants of ∆ompF and ∆waaF and their reference strain E. coli BW25113 (from the KEIO library). This data set reveals the impact a single deletion has in the E. coli genome on the proteome, which is useful to assess the interconnectedness of gene regulation, the wholistic influence on the proteins, and the effect on the E. coli surface. The latter is not only useful to understand predator-prey interaction more closely, but might contribute to a better understanding of E. coli physiology overall.
2026-09-20 | PXD080501 | Pride
Project description: Not available
| BMID000000140736 | biostudies-other
Project description: Not available
| S-EPMC11026547 | biostudies-literature
Project description:An important lesson from the war on pathogenic bacteria has been the need to understand the physiological responses and evolution of natural microbial communities. Bacterial populations in the environment are generally forming biofilms subject to some level of phage predation. These multicellular communities are notoriously resistant to antimicrobials and, consequently, very difficult to eradicate. This has sparked the search for new therapeutic alternatives, including phage therapy. This study demonstrates that S. aureus biofilms formed in the presence of a non-lethal dose of phage phiIPLA-RODI exhibit a unique physiological state that could potentially benefit both the host and the predator. Thus, biofilms formed under phage pressure are thicker and have a greater DNA content. Also, the virus-infected biofilm displayed major transcriptional differences compared to an untreated control. Significantly, RNA-seq data revealed activation of the stringent response, which could slow down the advance of the bacteriophage within the biofilm. The end result would be an equilibrium that would help bacterial cells to withstand environmental challenges, while maintaining a reservoir of sensitive bacterial cells available to the phage upon reactivation of the dormant carrier population.
2017-01-20 | GSE87706 | GEO
Project description:Global transcriptional profiles of Saccharomyces cerevisiae were studied following changes in growth conditions to high hydrostatic pressure and low temperature. These profiles were quantitatively very similar, encompassing 561 co-upregulated genes and 161 co-downregulated genes. In particular, expression of the DAN/TIR cell wall mannoprotein genes, which are generally expressed under hypoxia, were markedly upregulated by high pressure and low temperature, suggesting the overlapping regulatory networks of transcription. In support of the role of the mannoproteins in cell wall integrity, cells acquired resistance against treatment with SDS, Zymolyase and lethal level of high pressure when preincubated under high pressure and low temperature. Keywords: stress response
2007-10-05 | GSE9136 | GEO