Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1193017 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR31567382_1.fastq.gz | Fastqsanger.gz | |||
| SRR31567382_2.fastq.gz | Fastqsanger.gz | |||
| SRR31567383_1.fastq.gz | Fastqsanger.gz | |||
| SRR31567383_2.fastq.gz | Fastqsanger.gz |
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Project description:Analysis of Lactobacillus plantarum stains isolated from different cheese type
2017-07-12 | GSE101169 | GEO
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.
2012-09-07 | GSE23990 | GEO
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.
2012-09-07 | GSE23987 | GEO
Project description:Lactobacillus helveticus is a rod-shaped lactic acid bacterium that is widely used in the manufacture of fermented dairy foods and for production of bioactive peptides from milk proteins. Although L. helveticus is commonly associated with milk environments, phylogenetic studies show it is closely related to an intestinal species, Lactobacillus acidophilus, which has been shown to impart probiotic health benefits to humans. This relationship has fueled a prevailing hypothesis that L. helveticus is a highly specialized derivative of L. acidophilus which has adapted to acidified whey. However, L. helveticus has also been sporadically recovered from non-dairy environments, which argues the species may not be as highly specialized as is widely believed. This study employed genome sequence analysis and comparative genome hybridizations to investigate genomic diversity among L. helveticus strains collected from cheese, whey, and whiskey malt, as well as commercial cultures used in manufacture of cheese or bioactive dairy foods. Results revealed considerable variability in gene content between some L. helveticus strains, and indicated the species should not be viewed as a strict dairy-niche specialist. In addition, comparative genomic analyses provided new insight on several industrially and ecologically important attributes of L. helveticus that may facilitate commercial strain selection.
2013-08-16 | GSE23660 | GEO
Project description:Lactobacillus helveticus is a rod-shaped lactic acid bacterium that is widely used in the manufacture of fermented dairy foods and for production of bioactive peptides from milk proteins. Although L. helveticus is commonly associated with milk environments, phylogenetic studies show it is closely related to an intestinal species, Lactobacillus acidophilus, which has been shown to impart probiotic health benefits to humans. This relationship has fueled a prevailing hypothesis that L. helveticus is a highly specialized derivative of L. acidophilus which has adapted to acidified whey. However, L. helveticus has also been sporadically recovered from non-dairy environments, which argues the species may not be as highly specialized as is widely believed. This study employed genome sequence analysis and comparative genome hybridizations to investigate genomic diversity among L. helveticus strains collected from cheese, whey, and whiskey malt, as well as commercial cultures used in manufacture of cheese or bioactive dairy foods. Results revealed considerable variability in gene content between some L. helveticus strains, and indicated the species should not be viewed as a strict dairy-niche specialist. In addition, comparative genomic analyses provided new insight on several industrially and ecologically important attributes of L. helveticus that may facilitate commercial strain selection. 42 samples were hybridized to the microarray chip, which contains probe sequences from L. helveticus CNRZ32. CNRZ32 was also hybridized and used as the reference sample. Data from the microarray was statistically analyzed using the R software. Samples were compared to the reference (CNRZ32) to investigate genome diversity amoung L. helveticus strains,
2013-08-16 | E-GEOD-23660 | biostudies-arrayexpress
Project description:Lactobacillus casei is remarkably adaptive to diverse habitats. To understand the evolution and adaptation of Lb. casei strains isolated from different environments, the gene content of 22 Lb. casei strains isolated from various habitats (cheeses, n=8; plant materials, n=8; and human sources, n=6) were examined by comparative genome hybridization with an Lb. casei ATCC 334-based microarray.
2009-03-17 | GSE15030 | GEO
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 M17. At least three independent cultures of the six strains were performed. Genomic DNA was extracted from cells grown overnight on M17 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-23990 | biostudies-arrayexpress
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.
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Project description:Helicobacter pylori, which is known as pathogens of various gastric diseases, have many types of genome sequence variants. That is part of the reason why pathogenesis and infection mechanisms of the H. pylori-driven gastric diseases have not been well clarified yet. Here we performed a large-scale proteome analysis to profile the heterogeneity of the proteome expression of 7 H. pylori strains by using LC/MS/MS-based proteomics approach combined with a customized database consisting of non-redundant tryptic peptide sequences derived from full genome sequences of 52 H. pylori strains. The non-redundant peptide database enabled us to identify more peptides in the database search of MS/MS data, compared with a simply merged protein database. Using the approach we performed proteome analysis of genome-unknown strains of H. pylori in as large-scale as genome-known ones. Clustering of the H. pylori strains using the proteome profiling slightly differed from the genome profiling and more clearly divided the strains into two groups based on the isolated area. Furthermore, we also identified phosphorylated proteins and sites of the H. pylori strains and obtained phosphorylation motif located in the N-terminus, which are commonly observed in bacteria.
2018-12-28 | PXD011364 | JPOST Repository