Ontology highlight
ABSTRACT:
PROVIDER: PRJNA952943 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The aim of the study was to carry out a CGH study utilizing a set of 39 diverse Bacillus isolates. Thirty four B. cereus and five B. anthracis strains and isolates were chosen so as to represent different lineages based on previous characterizations, including MLEE and MLST (Helgason, Okstad et al. 2000; Helgason, Tourasse et al. 2004). They represent the spectrum of B. cereus phenotypic diversity by including soil, dairy and periodontal isolates in addition to virulent B. anthracis strains.
2009-11-25 | GSE19068 | GEO
Project description:Staphylococcus aureus is recognized worldwide as a major pathogen causing clinical or subclinical intramammary infections in all the dairy species (sheep, goats and cows). The present study was designed to comparatively investigate 65 S. aureus isolates recovered from dairy sheep and S. aureus suclinical mastitis from cows (n=21) and goats (n=22), for the presence of 190 putative virulence determinants with a single-dye DNA microarray and PCR. The probes (65 mer) were mainly designed from the S. aureus Mu50. The extracted DNA of each strain was labelled with Cy5. The microarray results were validated with PCR.The genomic comparative study with the DNA microarrays showed lineage and species specificity genes leading to the host-specific pathogenic traits of S. aureus in dairy species.
2008-07-01 | E-TABM-288 | biostudies-arrayexpress
Project description:Experimental evolution is a powerful approach to study how ecological forces shape microbial genotypes and phenotypes, but to date strains were predominantly adapted to conditions specific to laboratory environments. The lactic acid bacterium Lactococcus lactis naturally occurs on plants and in the dairy environment and it is generally believed, that dairy strains originate from the plant niche. Here we investigated the adaptive process from the plant to the dairy niche and show that during the experimental evolution of a L. lactis plant isolate in milk, several mutations are selected that affect amino acid metabolism and transport. Three independently evolved strains were characterized by whole genome re-sequencing, revealing 4 to 28 mutational changes in the individual strains. Two of the adapted strains showed clearly increased acidification rates and yields in milk, and contained three identical point mutations. Transcriptome profiling and extensive phenotyping of the wild-type plant isolate compared to the evolved mutants, and a "natural" dairy isolate confirmed that major physiological changes associated with improved performance in the dairy environment relate to nitrogen metabolism. The deletion of a putative transposable element led to a significant decrease of the mutation rate in two of the adapted strains. These results specify the adaptation of a L. lactis strain isolated from mung bean sprouts to growth in milk and they demonstrate that niche-specific adaptations found in environmental microbes can be reproduced by experimental evolution. Multiple loop design with 12 samples and 16 dual label arrays. Each sample is hybrdized at least on two different arrays and with both dyes.
2010-06-24 | E-GEOD-20373 | biostudies-arrayexpress
Project description:Experimental evolution is a powerful approach to study how ecological forces shape microbial genotypes and phenotypes, but to date strains were predominantly adapted to conditions specific to laboratory environments. The lactic acid bacterium Lactococcus lactis naturally occurs on plants and in the dairy environment and it is generally believed, that dairy strains originate from the plant niche. Here we investigated the adaptive process from the plant to the dairy niche and show that during the experimental evolution of a L. lactis plant isolate in milk, several mutations are selected that affect amino acid metabolism and transport. Three independently evolved strains were characterized by whole genome re-sequencing, revealing 4 to 28 mutational changes in the individual strains. Two of the adapted strains showed clearly increased acidification rates and yields in milk, and contained three identical point mutations. Transcriptome profiling and extensive phenotyping of the wild-type plant isolate compared to the evolved mutants, and a "natural" dairy isolate confirmed that major physiological changes associated with improved performance in the dairy environment relate to nitrogen metabolism. The deletion of a putative transposable element led to a significant decrease of the mutation rate in two of the adapted strains. These results specify the adaptation of a L. lactis strain isolated from mung bean sprouts to growth in milk and they demonstrate that niche-specific adaptations found in environmental microbes can be reproduced by experimental evolution.
2010-03-03 | GSE20373 | GEO
Project description:In both beef and dairy cattle, the majority of embryo loss occurs in the first 14 days following insemination. During this period, the embryo is completely dependent on its maternal uterine environment for development, growth and ultimately survival, therefore an optimum uterine environment is critical to embryo survival. We used microarrays to assess endometrial gene expression in high and low fertility heifers during the mid-luteal phase of the estrous cycle.
2011-06-10 | GSE29853 | GEO
Project description:Methicillin-resistant Staphylococcus aureus (MRSA) is the causative agent of serious hospital- and community-associated infections. Due to the global rise in community-associated MRSA, the respective lineages are increasingly introduced into hospitals. This raises the question whether and, if so, how they adapt to this new environment. The present study was aimed at investigating how MRSA isolates of the USA300 lineage, infamous for causing infections in the general population, have adapted to the hospital environment. To this end, a collection of community- and hospital-associated USA300 isolates was compared by RNA-sequencing. Here we report that merely 460 genes were differentially expressed between these two epidemiologically distinct groups, including genes for virulence factors, oxidative stress responses and the purine, pyrimidine and fatty acid biosynthetic pathways. Differentially regulated virulence factors included leukotoxins and phenol-soluble modulins, implicated in staphylococcal escape from immune cells. We therefore investigated the ability of the studied isolates to survive internalization by human neutrophils. This showed that the community-associated isolates have the highest neutrophil-killing activity, while the hospital-associated isolates are better adapted to intra-neutrophil survival. Importantly, the latter trait protects internalized staphylococci against a challenge with antibiotics. We therefore conclude that prolonged intra-neutrophil survival serves as a relatively simple early adaptation of S. aureus USA300 to the hospital environment where antibiotic pressure is high.
2016-11-02 | GSE89394 | GEO
Project description:In both beef and dairy cattle, the majority of embryo loss occurs in the first 14-16 days following insemination. During this period, the embryo is completely dependent on its maternal uterine environment for development, growth and ultimately survival, therefore an optimum uterine environment is critical to embryo survival. We used microarrays to assess endometrial gene expression in high and low fertility heifers during the late-luteal phase of the estrous cycle.
2013-08-22 | GSE50091 | GEO