BACKGROUND:The pattern-forming bacterium Paenibacillus vortex is notable for its advanced social behavior, which is reflected in development of colonies with highly intricate architectures. Prior to this study, only two other Paenibacillus species (Paenibacillus sp. JDR-2 and Paenibacillus larvae) have been sequenced. However, no genomic data is available on the Paenibacillus species with pattern-forming and complex social motility. Here we report the de novo genome sequence of this Gram-positiv ...[more]
Project description:The transcriptome of EHEC grown in vitro with or without Symbioflor® was analyzed using RNA-seq. The analysis revealed downregulation of several virulence-associated genes in the presence of Symbioflor®, including virulence key genes (e.g., LEE, flagellum, quorum-sensing). EHEC were grown on LB medium, either with or without Symbioflor added.
Project description:Transcriptional profiling of the bacteria Paenibacillus vortex comparing control untreated cells with kanamycin treated cells after 18 hours of exposure. Goal was to determine the effect of the antibiotic kanamycin in concentration which affect the colony morphology on global bacteria gene expression. Two-condition experiment, control cells vs. kanamycin treated cells. Biological replicates: 2 control replicates, 2 treated replicates. Pooling of 5 technical replicates for each biological replicate.
Project description:Escherichia coli O157:H7 is an important food-borne pathogen that can cause hemorrhagic colitis (HC) and hemolytic-uremic syndrome (HUS) in humans. pO157_Sal, a novel conjugative plasmid is present in a Chinese O157:H7 outbreak strain Xuzhou21. Here we investigated the phenotypic and transcriptional differences between the wild type strain Xuzhou21 and the pO157_Sal cured mutant strain Xuzhou21m. RNA-seq analysis found that all 52 ORFs encoded on pO157_Sal were transcribed. 168 chromosomal and pO157 genes were differentially expressed (≥2 fold difference) between Xuzhou21 and Xuzhou21m. Sixty-seven and 101 genes were up-regulated and down-regulated respectively by pO157_Sal including genes related to stress response, adaption and virulence. The plasmid-cured mutant grew slower than wild type in M9 medium under the condition of high NaCl or presence of sodium deoxycholate (NaDC), corroborating with the RNA-seq data. Seven differentially expressed genes are associated with NaDC resistance, including the adenine-specific DNA-methyltransferase gene (dam), multidrug efflux system subunit gene mdtA, hyperosmotically inducible periplasmic protein gene osmY and oxidation-reduction related genes while two differentially expressed genes (osmY and pspD) are likely to be related to resistance to osmotic pressure. A number of differentially expressed genes were virulence associated including four genes encoding T3SS effectors from the chromosome and ehxD from pO157. These findings demonstrated that the plasmid pO157_Sal affects the chromosome and pO157 genes transcription and contributes to the enhanced ability to resist stress. We conclude that pO157_Sal plays an important role in regulating global gene expression and affects virulence and adaptation of E.coli O157:H7. The total mRNA extracted from Escherichia coli O157:H7 Xuzhou21 and its plasmid cured strain Xuzhou21m were sequenced using Illumina.
Project description:In prokaryotes and eukaryotes, cell-cell communication and recognition of self are critical to coordinate multicellular functions. While kin and kind discrimination are increasingly appreciated to shape naturally occurring microbe populations, the underlying mechanisms that govern these interbacterial interactions are insufficiently understood. Here we identify a mechanism of interbacterial signal transduction that is mediated by contact-dependent growth inhibition (CDI) system proteins. CDI systems have been characterized by their ability to deliver a polymorphic protein toxin into the cytoplasm of a neighboring bacterium, resulting in growth inhibition or death unless the recipient bacterium produces a corresponding immunity protein. Using the model organism Burkholderia thailandensis, we show that delivery of a catalytically active CDI system toxin to immune (self) bacteria results in gene expression and phenotypic changes within the recipient cells. Termed contact-dependent signaling (CDS), this response promotes biofilm formation and other community-associated behaviors. Examination of wild-type Burkholderia thailandensis and two mutant strains, each in triplicate (9 samples total). mutant BtEKA contains two amino acid substitutions (E3064A and K3066A) within the coding sequence of gene Bth_I2723. In mutant PS12-WT, the native promoter of gene Bth_I2723 has been replaced with the strong constitutive promoter of the E264 rpsL gene, PS12.
Project description:In this work the genomic expression of two Burkholderia cenocepacia clonal variants (IST439 and IST4113) were compared. These isolates were collected from a chronically colonized cystic-fibrosis patient that has died from the cepacia syndrome. IST439 was the first B. cenocepacia isolate recovered from the patient and it is thought to have initiated the infection while the IST4113 isolate was recovered three years later, after a period of exacerbated infection that compelled the patient to hospitalization and intravenous therapy with gentamicine and ceftazidime. Among other phenotypic differences, IST4113 is much more resistant to a wide range of antimicrobials tested with very different biological targets
Project description:Purpose : The goal of this study was to use RNA Seq to define the regulon of the transciption factor Anr by comparing global transcriptional profiles of Pseudomonas aeruginosa strain PAO1 and a clinical isolate with their isogenic ∆anr mutants, grown in colony biofilms at 1% oxygen. Methods : mRNA profiles were generated for laboratory strain PAO1 and for a clinical isolate J215, as well as for ∆anr derivatives of each strain, in duplicate, by deep sequencing. Strains were grown for 12 hours in colony biofilms at 1% O2, 5% CO2 prior to RNA harvest. Ribosomal and transfer RNAs were removed using the MICROBExpress kit (Life Technologies). mRNA reads were trimmed and mapped to the PAO1 NC_002516 reference genome from NCBI using the ClC Genomics Workbench platform and defaut parameters. mRNA profiles of 12 hour colony biofilms were generated for P. aeruginosa strains PAO1 WT, PAO1 ∆anr, clinical isolate J215, and J215 ∆anr, each in duplicate, by deep sequencing using Illumina HiSeq.