Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genome heterogeneity in Lactobacillus helveticus: Rethinking a “niche specialist”*

ABSTRACT: 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.

ORGANISM(S): Lactobacillus helveticus Lacticaseibacillus paracasei ATCC 334

PROVIDER: GSE23660 | GEO | 2013/08/16

SECONDARY ACCESSION(S): PRJNA130859

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Genome heterogeneity in Lactobacillus helveticus: Rethinking a “niche specialist”*

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

Transcriptional Profile of Lactobacillus helveticus grown in milk vs. MRS medium

Project description:L. helveticus is used to modulate cheese flavor and as a starter organism in certain cheese varieties. Our group has compiled a draft (4x) sequence for the 2.4 Mb genome of an industrial strain L. helveticus CNRZ32. The primary aim was to investigate expression of 168 completely sequenced genes during growth in milk and MRS medium using microarrays. Oligonucleotide probes against each of the completely sequenced genes were compiled on maskless photolithography-based DNA microarrays. Additionally, the entire draft genome sequence was used to produce tiled microarrays where the non-interrupted sequence contigs were covered by consecutive 24-mer probes. Keywords: growth conditions response

2007-02-14 | GSE7005 | GEO

Discovery-driven target selection from six milk-derived ingredients for consensus detection of casein and whey milk allergens

Project description:Milk is one among the most common food allergens and the proteins representing caseins and whey fractions of milk have been characterized as the major triggers for allergic responses in susceptible individuals. Milk or milk-derived ingredients- varying in their casein and whey protein content and composition- are present as an ingredient in many foods. This project was designed to identify candidate target peptides for casein and whey fractions of milk which can be used for milk allergen detection from foods irrespective of the type of ingredients used in them.

2020-06-05 | PXD016429 | Pride

Proteomic analysis of Late Neolithic pottery residues from Poland

Project description:The detection of dairy processing is pivotal to our understanding of ancient subsistence strategies. This culinary process is linked to key arguments surrounding the evolution of lactase persistence in prehistory. Despite extensive evidence indicating the presence of dairy products in ceramics in the European Neolithic, questions remain about the nature and extent of milk (and lactose) processing and consumption. In order to investigate past patterns of dairy processing, here we analyse ancient proteins identified from Late Neolithic Funnel Beaker ceramics, scrutinising the principle that curd and whey proteins partition during the production of dairy foods from milk. Our results indicate the presence of casein-rich dairy products in these vessels suggesting the creation of curd-enriched products from raw milk. Moreover, this analysis reveals the use of multiple species for their dairy products in the Late Neolithic Funnel Beaker culture, adding to a growing body of evidence that multiple taxa were exploited for dairying in the Neolithic. Alongside palaeoproteomic analysis we also apply lipid residue analysis, with discrepancies in these two approaches suggesting that effects from isotope mixing may be underestimating the frequency of milk use in prehistoric pottery, highlighting the utility of a multi-stranded approach.

2023-05-10 | PXD037912 | Pride

Proteomic analysis of Late Neolithic pottery from Poland and modern replica cheesemaking vessels

2023-05-10 | PXD037913 | Pride

Sheep’s Milk: a deep exploration of the low-abundance proteome

Project description:In the last years the amount of ovine milk production, mainly used to formulate a wide range of different and exclusive dairy products often categorized as gourmet food, is progressively increasing. Taking also into account that sheep milk (SM) also appears to be potentially less allergenic than cow’s one, an in-depth information about its protein composition is essential to improve the comprehension of its potential benefits for human consumption and the role of milk components during cheese-making processes. The present work reports the results of an in-depth characterization of SM whey proteome, carried out by coupling the Combinatorial Peptide Ligand Library (CPLL) technology applied at three different pH values with SDS-PAGE and high resolution UPLC-nESI MS/MS analysis. This approach allowed the identification of 949 unique species that, to our knowledge, represent the largest description so far of the SM proteome. Particularly, this massive identification has expanded literature data about sheep whey proteome by 223 novel proteins previously undetected, many of which are involved in the defence/immunity mechanisms or in the nutrient delivery system. A comparative analysis of the proteins here identified with the inventory of the gene products discovered in cow’s milk whey to date, evidenced that about 50% of the identified components appear to be unique of sheep whey milk proteome and include a heterogeneous group of components which seem to have health-promoting benefits.

2016-12-07 | PXD004556 | Pride

Gene expression profile of probiotic Lactobacillus casei Zhang during the late stage of milk fermentation

Project description:Lactobacillus casei Zhang is a probiotic bacterium isolated from koumiss in Inner Mongolia of China that has been commercially used as a starter in the manufacture of dairy products. To study the gene expression profiles of L. casei Zhang during growth in milk, a whole-genome microarray was used. Compared to L. casei Zhang grown to late logarithmic phase in milk, 61 genes were significantly up-regulated (>5 fold) in stationary phase, whereas 26 genes were down-regulated. Collectively, these data showed that the majority of the identified genes was involved in carbohydrate metabolism and energy production, followed by genes involved in nucleotide metabolism, inorganic ion transport, amino acid transport and metabolism, chaperone, etc. This study demonstrates the fundamental effects of cultural conditions on the transcriptome of L. casei Zhang. Moreover, it improves the understanding of the growth and survival mechanism of the bacterium during the late stage of milk fermentation. L. casei Zhang was grown in milk for 14h (late logarithmic phase) or 18h (stationary phase). 2 biological replicates each.

2011-12-31 | E-GEOD-24597 | biostudies-arrayexpress

Streptococcus thermophilus LMD-9

Project description:Used in the manufacture of fermented dairy foods, such as yogurt and mozzarella cheese.

| PRJNA13773 | ENA

Gene expression profile of probiotic Lactobacillus casei Zhang during the late stage of milk fermentation

2011-12-31 | GSE24597 | GEO

RNA-Seq data from dairy goat milk somatic cells in response to fish oil diet induced milk fat depression

Project description:Dietary supplementation with fish-oil modulates ruminant milk composition towards a healthier fatty acid profile for consumers, but it also causes milk fat depression (MFD). Because the dairy goat industry is mainly oriented towards cheese manufacturing, MFD can elicit economic losses. There is large individual variation in animal susceptibility with goats more (RESPO+) or less (RESPO−) responsive to diet-induced MFD. Thus, we used RNA-Seq to examine gene expression profiles in mammary cells to elucidate mechanisms underlying MFD in goats and individual variation in the extent of diet-induced MFD.

2022-12-11 | E-MTAB-11581 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data