Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Construction of a dairy microbial genome catalog opens new perspectives for the metagenomic analysis of cheese microbiota

ABSTRACT: Construction of a dairy microbial genome catalog opens new perspectives for the metagenomic analysis of cheese microbiota

PROVIDER: PRJEB6314 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR699779.fastq.gz	Fastqsanger.gz
	ERR699780.fastq.gz	Fastqsanger.gz
	ERR699781.fastq.gz	Fastqsanger.gz
	ERR699782.fastq.gz	Fastqsanger.gz
	ERR699783.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 19

Similar Datasets

Construction of a dairy microbial genome catalog opens new perspectives for the metagenomic analysis of dairy fermented products.

Project description:Microbial communities of traditional cheeses are complex and insufficiently characterized. The origin, safety and functional role in cheese making of these microbial communities are still not well understood. Metagenomic analysis of these communities by high throughput shotgun sequencing is a promising approach to characterize their genomic and functional profiles. Such analyses, however, critically depend on the availability of appropriate reference genome databases against which the sequencing reads can be aligned.We built a reference genome catalog suitable for short read metagenomic analysis using a low-cost sequencing strategy. We selected 142 bacteria isolated from dairy products belonging to 137 different species and 67 genera, and succeeded to reconstruct the draft genome of 117 of them at a standard or high quality level, including isolates from the genera Kluyvera, Luteococcus and Marinilactibacillus, still missing from public database. To demonstrate the potential of this catalog, we analysed the microbial composition of the surface of two smear cheeses and one blue-veined cheese, and showed that a significant part of the microbiota of these traditional cheeses was composed of microorganisms newly sequenced in our study.Our study provides data, which combined with publicly available genome references, represents the most expansive catalog to date of cheese-associated bacteria. Using this extended dairy catalog, we revealed the presence in traditional cheese of dominant microorganisms not deliberately inoculated, mainly Gram-negative genera such as Pseudoalteromonas haloplanktis or Psychrobacter immobilis, that may contribute to the characteristics of cheese produced through traditional methods.

| S-EPMC4320590 | biostudies-literature

Transcriptomic profiles of six strains of Lactococcus lactis in ultrafiltration-cheese model

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

Gene expression of the bacterium Glutamicibacter arilaitensis when grown with Penicillium in cheese

Project description:RNA-seq was used in combination with various analytical chemistry approaches to identify the chemical and genetic basis of pigment production of the bacterium Glutamicibacter arilaitensis when growing on cheese. This bacterium commonly found in cheese rinds where it co-occurs with Penicillium species and other molds. Pinkish-red pigments are produced by the bacterium in response to growth with Penicillium. Both chemical analyses and RNA-seq point to coproporphyrin III as the major metabolite leading to pigment formation.

2018-04-01 | GSE112092 | GEO

Anabolic effects of cheddar cheese consumption in human skeletal muscle

Project description:The goal of this project was to use a randomized, cross over design to determine the amino acid blood and muscle response to the acute ingestion of cheddar cheese in comparison to that of bovine milk and to investigate the skeletal muscle mTORC1 response.

2021-01-31 | GSE163279 | GEO

Transcription profiling by array of Staphylococcus aureus grown in cheese matrix in mixed culture with Lactococcus lactis

Project description:Effect of the presence of Lactococcus lactis on Staphylococcus aureus transcriptome in cheese matrix. S. aureus was co-cultured with L. lactis LD61 in cheese matrix during 7 days. RNA samples were extracted at different time points (6 h, 8 h, 10 h, 24 h and 7 days) in order to monitor the dynamic response of S. aureus MW2 in cheese matrix in presence of L. lactis

2011-07-01 | E-MEXP-2842 | biostudies-arrayexpress

Cheese

Project description:Cheese Raw sequence reads

| PRJNA930577 | ENA

Staphylococcus hominis strain:cheese | isolate:cheese

Project description:Staphylococcus hominis strain:cheese | isolate:cheese Genome sequencing

| PRJNA488059 | ENA

Macrococcoides caseolyticum strain:cheese | isolate:cheese

Project description:Macrococcoides caseolyticum strain:cheese | isolate:cheese Genome sequencing

| PRJNA488264 | ENA

Mammaliicoccus sciuri strain:cheese | isolate:cheese

Project description:Mammaliicoccus sciuri strain:cheese | isolate:cheese Genome sequencing