Transcriptional Profile of Lactobacillus helveticus grown in milk vs. MRS medium
Ontology highlight
ABSTRACT:
ORGANISM(S): Lactobacillus helveticus CNRZ32 Lactobacillus helveticus
PROVIDER: GSE7005 | GEO | 2007/02/14
SECONDARY ACCESSION(S): PRJNA99253
REPOSITORIES: GEO
Similar Datasets
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:This experiment was designed to identify transcribed regions of japonica subspecies of the rice genome. A series of high-density oligonucleotide tiling arrays that represent sense and antisense strands of the entire nonrepetitive sequence of all the 12 chromosomes were designed to measure genome-wide transcription. A total of 12253842 36mer oligonucleotide probes positioned every 46 nt on average were used for this purpose. The probes were synthesized via maskless photolithography at a feature density of approximately 389,000 probes per slide. The arrays were hybridized with fluorescence-labeled cDNA reverse-transcribed from equal amounts of four selected poly(A)+ RNA population (seedling root, seedling shoot, panicle, and suspension cultured cells). Keywords: tiling array, genome-wide transcription
2007-02-21 | GSE6996 | GEO
Project description:This experiment was designed to identify transcribed regions of indica rice genome. A series of high-density oligonucleotide tiling arrays that represent sense and antisense strands of the entire nonrepetitive sequence of the chromosome were used to measure transcriptional activities. A total of 838,816 36mer oligonucleotide probes, positioned every 46 nt on average, were designed to interrogate the indica genome, respectively. The probes were synthesized via maskless photolithography at a feature density of approximately 389,000 probes per slide. The arrays were hybridized with fluorescence-labeled cDNA reverse-transcribed from equal amounts of four selected poly(A)+ RNA populations, namely, seedling roots, seedling shoots, panicles, and suspension cultured cells of the respective rice subspecies. Keywords: genome tiling experiments
2005-10-15 | GSE3452 | GEO
Project description:This experiment was designed to identify transcribed sequences across the human genome, particularly those distinct from previously annotated genes. To measure global transcriptional activity a series of high-density oligonucleotide tiling arrays was constructed to represent sense and antisense strands of the entire nonrepetitive sequence of the genome (1.5 Gb). A total of 51,874,388 36mer oligonucleotide probes, positioned every 46 nt on average, were synthesized via maskless photolithography at a feature density of approximately 390,000 probes per slide. The arrays were hybridized to fluorescence-labeled cDNA reverse-transcribed from triple-selected poly (A)+ liver tissue RNA. Keywords = transcription Keywords = gene expression Keywords = human Keywords: other
2004-10-29 | GSE1904 | GEO
Project description:This experiment was designed to identify transcribed sequences across the human genome, particularly those distinct from previously annotated genes. To measure global transcriptional activity a series of high-density oligonucleotide tiling arrays was constructed to represent sense and antisense strands of the entire nonrepetitive sequence of the genome (1.5 Gb). A total of 51,874,388 36mer oligonucleotide probes, positioned every 46 nt on average, were synthesized via maskless photolithography at a feature density of approximately 390,000 probes per slide. The arrays were hybridized to fluorescence-labeled cDNA reverse-transcribed from triple-selected poly (A)+ liver tissue RNA. Keywords = transcription Keywords = gene expression Keywords = human
2004-10-29 | E-GEOD-1904 | biostudies-arrayexpress
Project description:This experiment was designed to identify transcribed regions of both japonica and indica rice chromosome 10. A series of high-density oligonucleotide tiling arrays that represent sense and antisense strands of the entire nonrepetitive sequence of the chromosome were used to measure transcriptional activities. A total of 750,282 and 838,816 36mer oligonucleotide probes, positioned every 46 nt on average, were designed to interrogating the japonica and the indica chromosome, respectively. The probes were synthesized via maskless photolithography at a feature density of approximately 389,000 probes per slide. The arrays were hybridized with fluorescence-labeled cDNA reverse-transcribed from equal amounts of four selected poly(A)+ RNA populations, namely, seedling roots, seedling shoots, panicles, and suspension cultured cells of the respective rice subspecies. Keywords: other
2005-04-09 | GSE2500 | GEO
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. Comparative genome hybridization was performed against an Affymetrix custom microarray designed to include 2,661 (97%) chromosomal and 17 (85%) plasmid CDSs predicted to occur in Lb. casei ATCC 334, as well as all predicted CDSs in the draft Lb. helveticus CNRZ 32 genome. CDSs that were not included in the microarray design were all transposase-encoding genes.
2010-06-21 | E-GEOD-15030 | biostudies-arrayexpress
Project description:Genomic rearrangement, often driven by insertion sequence (IS) elements, is one of the major processes in the evolution of prokaryotes. Sequence analysis of 16S rRNA of Lactobacillus helveticus, an organism that evolved in a dairy environment and Lactobacillus acidiophilus an organism that evolved associated with the gastrointestinal tract (GIT) demonstrated 98.4% identity suggesting that they divergently evolved from a common ancestor. Moreover, complete genome sequence analysis of both organisms has demonstrated a remarkable degree of gene synteny (75% homologous genes) despite the presence of an exceptionally high number and diversity of IS elements in the Lb. helveticus genome. Array based comparative genomic hybridization (aCGH) performed on nine strains of Lb. helveticus revealed sixteen clusters of open reading frames (ORFs) flanked by IS elements. Four of these ORFs are associated with restriction/modification which may have played a role in accelerated evolution of strains in a commercially intensive ecosystem undoubtedly challenged through successive phage attack. Furthermore, analysis of the IS-flanked clusters demonstrated that the most frequently encountered IS were also those most abundant in the genome (IS1201, ISL2, ISLhe1, ISLhe2, ISLhe65 and ISLhe63). These findings contribute to the overall viewpoint on a versatile character of IS elements and the role they may play in bacterial genome plasticity.
2009-06-12 | GSE16553 | GEO
Project description:Genomic rearrangement, often driven by insertion sequence (IS) elements, is one of the major processes in the evolution of prokaryotes. Sequence analysis of 16S rRNA of Lactobacillus helveticus, an organism that evolved in a dairy environment and Lactobacillus acidiophilus an organism that evolved associated with the gastrointestinal tract (GIT) demonstrated 98.4% identity suggesting that they divergently evolved from a common ancestor. Moreover, complete genome sequence analysis of both organisms has demonstrated a remarkable degree of gene synteny (75% homologous genes) despite the presence of an exceptionally high number and diversity of IS elements in the Lb. helveticus genome. Array based comparative genomic hybridization (aCGH) performed on nine strains of Lb. helveticus revealed sixteen clusters of open reading frames (ORFs) flanked by IS elements. Four of these ORFs are associated with restriction/modification which may have played a role in accelerated evolution of strains in a commercially intensive ecosystem undoubtedly challenged through successive phage attack. Furthermore, analysis of the IS-flanked clusters demonstrated that the most frequently encountered IS were also those most abundant in the genome (IS1201, ISL2, ISLhe1, ISLhe2, ISLhe65 and ISLhe63). These findings contribute to the overall viewpoint on a versatile character of IS elements and the role they may play in bacterial genome plasticity. 2164 ORFs of Lb. helvetiucs DPC4571 spotted on the array in duplicate. Two arrays per each strain.
2010-05-18 | E-GEOD-16553 | biostudies-arrayexpress