Micavibrio aeruginosavorus EPB
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ABSTRACT:
PROVIDER: PRJNA163341 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Micavibrio aeruginosavorus overview
| PRJNA49897 | ENA
Project description:Micavibrio aeruginosavorus strain:HCB189 Genome sequencing
| PRJNA1283069 | ENA
Project description:Micavibrio aeruginosavorus ARL-13 genome sequencing project.
| PRJNA49751 | ENA
Project description:uncultured Micavibrio sp. overview
| PRJNA1039111 | ENA
Project description:Primary objectives: The primary objective is to investigate circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).
Primary endpoints: circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).
| 2533916 | ecrin-mdr-crc
Project description:BackgroundAlthough bacterial predators play important roles in the dynamics of natural microbial communities, little is known about the molecular mechanism of bacterial predation and the evolution of diverse predatory lifestyles.ResultsWe determined the complete genome sequence of Micavibrio aeruginosavorus ARL-13, an obligate bacterial predator that feeds by "leeching" externally to its prey. Despite being an obligate predator depending on prey for replication, M. aeruginosavorus encodes almost all major metabolic pathways. However, our genome analysis suggests that there are multiple amino acids that it can neither make nor import directly from the environment, thus providing a simple explanation for its strict dependence on prey. Remarkably, despite apparent genome reduction, there is a massive expansion of genomic islands of foreign origin. At least nine genomic islands encode many genes that are likely important for Micavibrio-prey interaction such as hemolysin-related proteins. RNA-Seq analysis shows substantial transcriptome differences between the attack phase, when M. aeruginosavorus seeks its prey, and the attachment phase, when it feeds and multiplies. Housekeeping genes as well as genes involved in protein secretion were all dramatically up-regulated in the attachment phase. In contrast, genes involved in chemotaxis and flagellum biosynthesis were highly expressed in the attack phase but were shut down in the attachment phase. Our transcriptomic analysis identified additional genes likely important in Micavibrio predation, including porins, pilins and many hypothetical genes.ConclusionsThe findings from our phylogenomic and transcriptomic analyses shed new light on the biology and evolution of the epibiotic predatory lifestyle of M. aeruginosavorus. The analysis reported here and the availability of the complete genome sequence should catalyze future studies of this organism.
| S-EPMC3189940 | biostudies-literature
Project description:Micavibrio aeruginosavorus is an obligate Gram-negative predatory bacterial species that feeds on other Gram-negative bacteria by attaching to the surface of its prey and feeding on the prey's cellular contents. In this study, Serratia marcescens with defined mutations in genes for extracellular cell structural components and secreted factors were used in predation experiments to identify structures that influence predation. No change was measured in the ability of the predator to prey on S. marcescens flagella, fimbria, surface layer, prodigiosin and phospholipase-A mutants. However, higher predation was measured on S. marcescens metalloprotease mutants. Complementation of the metalloprotease gene, prtS, into the protease mutant, as well as exogenous addition of purified serralysin metalloprotease, restored predation to wild type levels. Addition of purified serralysin also reduced the ability of M. aeruginosavorus to prey on Escherichia coli. Incubating M. aeruginosavorus with purified metalloprotease was found to not impact predator viability; however, pre-incubating prey, but not the predator, with purified metalloprotease was able to block predation. Finally, using flow cytometry and fluorescent microscopy, we were able to confirm that the ability of the predator to bind to the metalloprotease mutant was higher than that of the metalloprotease producing wild-type. The work presented in this study shows that metalloproteases from S. marcescens could offer elevated protection from predation.
| S-EPMC6145908 | biostudies-literature
Project description:Chemolithoautotrophic nitrifying bacteria release soluble organic compounds, which can be substrates for heterotrophic microorganisms. The identities of these heterotrophs and the specificities of their interactions with nitrifiers are largely unknown. In this study, we incubated nitrifying activated sludge with (13)C-labeled bicarbonate and used stable isotope probing of 16S rRNA to monitor the flow of carbon from uncultured nitrifiers to heterotrophs. To facilitate the identification of heterotrophs, the abundant 16S rRNA molecules from nitrifiers were depleted by catalytic oligonucleotides containing locked nucleic acids (LNAzymes), which specifically cut the 16S rRNA of defined target organisms. Among the (13)C-labeled heterotrophs were organisms remotely related to Micavibrio, a microbial predator of Gram-negative bacteria. Fluorescence in situ hybridization revealed a close spatial association of these organisms with microcolonies of nitrite-oxidizing sublineage I Nitrospira in sludge flocs. The high specificity of this interaction was confirmed by confocal microscopy and a novel image analysis method to quantify the localization patterns of biofilm microorganisms in three-dimensional (3-D) space. Other isotope-labeled bacteria, which were affiliated with Thermomonas, colocalized less frequently with nitrifiers and thus were commensals or saprophytes rather than specific symbionts or predators. These results suggest that Nitrospira spp. are subject to bacterial predation, which may influence the abundance and diversity of these nitrite oxidizers and the stability of nitrification in engineered and natural ecosystems. In silico screening of published next-generation sequencing data sets revealed a broad environmental distribution of the uncultured Micavibrio-like lineage.
| S-EPMC3592250 | biostudies-literature
Project description:The study is intended to collect specimens to support the application of genome analysis technologies, including large-scale genome sequencing. This study will ultimately provide cancer researchers with specimens that they can use to develop comprehensive catalogs of genomic information on at least 50 types of human cancer. The study will create a resource available to the worldwide research community that could be used to identify and accelerate the development of new diagnostic and prognostic markers, new targets for pharmaceutical interventions, and new cancer prevention and treatment strategies. This study will be a competitive enrollment study conducted at multiple institutions.
| 2140168 | ecrin-mdr-crc