Ontology highlight
ABSTRACT:
PROVIDER: PRJNA775016 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The intra sub-species diversity of six strains of Lactococcus lactis subsp. lactis was investigated at the genomic level and in terms of phenotypic and transcriptomic profiles in UF-cheese model. Six strains were isolated from various sources, but all are exhibiting a dairy phenotype. Our results showed that, the six strains exhibited small phenotypic differences since similar behaviour in terms of growth was obtained during cheese ripening while only different acidification capability was detected. Even if all strains displayed high genomic similarities, sharing a high core genome of almost two thousands genes, the expression of this core genome directly in the cheese matrix revealed major strain-specific differences. This strains with the same dairy origin. Strains were cultured on skimmed raw milk ultrafiltration (UF) retentate. The UF retentate was pre-incubated overnight at 4 °C, then 45 minutes at 50 °C and homogenized during 1.5 minutes at 24 000 rpm with an ultra-turax (Imlab, France). After addition of rennet (0.3 µl ml-1), 400 g UF retentate was inoculated at 2 106 CFU/g with L. lactis subsp. lactis strains. After incubation for 8 hours at 30 °C, the cheeses were transferred at 12° C until 7 days for ripening simulation. At least three independent cultures of the six strains were performed. Total RNA was extracted from cells grown 24 hours in UF-cheese and radiolabelled cDNA were prepared and hybridized on nylon arrays. 1948 amplicons specific of Lactococcus lactis IL1403 genes were spotted twice on the array. 3 independent repetitions were performed.
2012-09-07 | E-GEOD-23987 | 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: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:Milk-derived extracellular vesicles (mEVs) have been proved to play a critical role in intercellular communication, mainly through the microRNAs (miRNAs) that they carry, to regulate biological functions of the target cells. Given miRNAs are evolutionarily conserved, EVs present in commercial milk may play a role in the physiology and health consumers. It is therefore essential to know the effects of technological treatments such as skimming and spray drying on the EV content of milk powders and on the cargo of bioactive molecules, in particular miRNAs, that they convey. Since goat’s milk or goat milk based formulas are considered as a healthy alternative for infants with cow’s milk sensitivities, including allergy, we undertook to analyze the EV content of skimmed and unskimmed goat's milk powders and to characterize their RNA content, in particular their miRNomes. mEVs were isolated using an optimized protocol based on Size Exclusion Chromatography (SEC) and compared regarding morphology, number and size by Transmission Electron Microscopy (TEM) and Nanoparticle Tracking Analysis (NTA). Their RNA and protein content were determined and their miRNomes established, using RNA sequencing. In this study we demonstrated that goat milk powders, skimmed or not upstream the spray drying treatment, contained many mEVs, ranging from 5.4 1011 to 2.5 1012 particles per mL of reconstituted milk, with an average size between 136.8 and 160.6 nm. We also demonstrated that mEVs carried significant amounts of RNA, including miRNAs. Using RT-qPCR, mRNAs encoding five of the major milk proteins were detected, suggesting that mEVs originated from mammary epithelial cells. We established the goat milk powder miRNome by identifying 351 miRNAs of which 233 are common to the 262 miRNAs previously profiled in raw goat milk. The 20 most abundant miRNAs (TOP 20) account for 80% of the total reads and the hierarchy of this TOP 20 miRNAs is somewhat overturned when comparing goat milk powder and raw goat milk. Surprisingly, whereas the comparison of raw from cow and goat milk confirmed the prevalence of miR-148a, miR-21-5p and miR-26a/miR-30a-5p, let-7a-5p and let-7f, which occupied ranks 1 and 2, respectively, in powders, were relegated to ranks 6 and 10 and 5 and 11 in raw goat and cow milk, respectively. Conversely to what was previously reported, we provide evidence that: i) EVs of typical morphology are present in goat milk powders; ii) mEVs survived the technological processes used to produce the powders; iii) their miRNA cargo is protected from degradation even though their miRNomes are not an exact mirror of miRNomes of EVs derived from fluid raw milk.
2025-01-01 | GSE254484 | GEO
Project description:In the present study we examine the changes in the expression of genes of Lactococcus lactis subspecies cremoris MG1363 during growth in milk. To reveal which specific classes of genes (pathways, operons, regulons, COGs) are important, we performed a transcriptome time series experiment. Global analysis of gene expression over time showed that L. lactis adapted quickly to the environmental changes. Using upstream sequences of genes with correlated gene expression profiles, we uncovered a substantial number of putative DNA binding motifs that may be relevant for L. lactis fermentative growth in milk. All available novel and literature-derived data were integrated into network reconstruction building blocks, which were used to reconstruct and visualize the L. lactis gene regulatory network. This network enables easy mining in the chrono-transcriptomics data. A freely available website at http://milkts.molgenrug.nl gives full access to all transcriptome data, to the reconstructed network and to the individual network building blocks. 12 time points
2012-09-12 | E-GEOD-40780 | biostudies-arrayexpress
Project description:In the present study we examine the changes in the expression of genes of Lactococcus lactis subspecies cremoris MG1363 during growth in milk. To reveal which specific classes of genes (pathways, operons, regulons, COGs) are important, we performed a transcriptome time series experiment. Global analysis of gene expression over time showed that L. lactis adapted quickly to the environmental changes. Using upstream sequences of genes with correlated gene expression profiles, we uncovered a substantial number of putative DNA binding motifs that may be relevant for L. lactis fermentative growth in milk. All available novel and literature-derived data were integrated into network reconstruction building blocks, which were used to reconstruct and visualize the L. lactis gene regulatory network. This network enables easy mining in the chrono-transcriptomics data. A freely available website at http://milkts.molgenrug.nl gives full access to all transcriptome data, to the reconstructed network and to the individual network building blocks.
2012-09-12 | GSE40780 | GEO
Project description:This SuperSeries is composed of the following subset Series: GSE23987: Transcriptomic profiles of six strains of Lactococcus lactis in ultrafiltration-cheese model GSE23990: Comparative genome hybridization profiles of six strains of Lactococcus lactis Refer to individual Series
2012-09-07 | E-GEOD-24015 | biostudies-arrayexpress
Project description:Draft genome sequences of 3 Lactococcus lactis strains isolated from raw goat milk of the Rocamadour PDO area
| PRJNA792558 | ENA
Project description:Understanding how the human gut microbiota and host are impacted by probiotic bacterial strains requires carefully controlled studies in humans, and in mouse models of the gut ecosystem where potentially confounding variables that are difficult to control in humans can be constrained. Therefore, we characterized the fecal microbiomes and metatranscriptomes of adult female monozygotic twin pairs through repeated sampling 4 weeks prior to, 7 weeks during, and 4 weeks following consumption of a commercially-available fermented milk product (FMP) containing a consortium of Bifidobacterium animalis subsp. lactis, two strains of Lactobacillus delbrueckii subsp. bulgaricus, Lactococcus lactis subsp. cremoris, and Streptococcus thermophilus. In addition, gnotobiotic mice harboring a 15-species model human gut microbiota whose genomes contain 58,399 known or predicted protein-coding genes were studied prior to and after gavage with all five sequenced FMP strains. 140 samples total. Evaluation of changes in a model community's structure over time after exposure to a consortium of 5 fermented milk product (FMP) strains.
2011-11-01 | E-GEOD-31943 | biostudies-arrayexpress