Metabarcoding of experimental cheese
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB36799 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR3931210_1.fastq.gz | Fastqsanger.gz | |||
| ERR3931210_2.fastq.gz | Fastqsanger.gz | |||
| ERR3931220_1.fastq.gz | Fastqsanger.gz | |||
| ERR3931220_2.fastq.gz | Fastqsanger.gz | |||
| ERR3931230_1.fastq.gz | Fastqsanger.gz |
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Project description:Studies of food microorganism domestication can provide important insight into adaptation mechanisms and lead to commercial applications. Penicillium roqueforti is a fungus with four genetically differentiated populations, two of which were independently domesticated for blue cheese-making, with the other two populations thriving in other environments. Most blue cheeses are made with strains from a single P. roqueforti population, whereas Roquefort cheeses are inoculated with strains from a second population. We made blue cheeses in accordance with the production specifications for Roquefort-type cheeses, inoculating each cheese with a single P. roqueforti strain, using a total of three strains from each of the four populations. We investigated differences between the cheeses made with the strains from the four P. roqueforti populations, in terms of the induced flora, the proportion of blue color, water activity and the identity and abundance of aqueous and organic metabolites as proxies for proteolysis and lipolysis as well as volatile compounds responsible for flavor and aroma. We found that the population-of-origin of the P. roqueforti strains used for inoculation had a minor impact on bacterial diversity and no effect on the abundance of the main microorganism. The cheeses produced with P. roqueforti strains from cheese populations had a higher percentage of blue area and a higher abundance of the volatile compounds typical of blue cheeses, such as methyl ketones and secondary alcohols. In particular, the Roquefort strains produced higher amounts of these aromatic compounds, partly due to more efficient proteolysis and lipolysis. The Roquefort strains also led to cheeses with a lower water availability, an important feature for preventing spoilage in blue cheeses, which is subject to controls for the sale of Roquefort cheese. The typical appearance and flavors of blue cheeses thus result from human selection on P. roqueforti, leading to the acquisition of specific features by the two cheese populations. These findings have important implications for our understanding of adaptation and domestication, and for cheese improvement.
2021-10-06 | MTBLS1509 | MetaboLights
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
Project description:Purpose: The goal of this study is to compare differences between Penicillium roqueforti conidia from various conditions shown to affect heat-resistance to identify genes possibly related to heat-resistance using RNA-seq. Methods: mRNA from Penicillium roqueforti conidia produced at different temperatures (15C, 25C or 30C) and different cultivation times (3, 5, 7 or 10 days) was extracted, in triplicate, and sequenced with Illumina NextSeq500. The sequence reads that passed quality filters were analyzed using Hisat2 followed by Cufflinks. Results: we mapped about 19 million sequence reads per sample to the Penicillium roqueforti genome (build LCP96 04111) and identified 9723 transcripts in the conidia. Data analysis revealed a subset of 33 genes showing increased expression in culture conditions that increase heat-resistance. Conclusions: Our study generated insight into multiple genes that are likely involved in the heat-resistance of Penicillium roqueforti.
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Project description:Population genomics of Penicillium roqueforti
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Project description:Population genomics of Penicillium roqueforti
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Project description:shotgun sequencing of cheese production facility and associated samples
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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:Paleofeces are an important source of information to study the evolution of dietary habits and human health. The UNESCO World Heritage region of Hallstatt-Dachstein/Salzkammergut is one of Europe’s oldest cultural and industrial landscapes; its underground salt mines dating back at least to the 14th century BC are one of the few archaeological sites where paleofeces are well preserved. The high salt concentrations and the constant annual temperature at around 8°C inside the isolated Hallstatt mines have perfectly preserved organic archaeological artefacts (e.g. paleofeces, clothing, mining tools) that provide unique insights into the daily life of a progressive community in Hallstatt. Here we subjected human paleofeces dated from the Bronze Age to early Modern Times to an in-depth microscopic, metagenomic and proteomic analysis. This allowed us to reconstruct the diet of the former population and gain insights into their ancient gut microbiome composition. Our dietary survey identified bran and glumes of different cereals as one of the most prevalent plant fragments. This highly fibrous, carbohydrate-rich diet was supplemented with proteins from broad beans and occasionally with fruits, nuts, or animal food. Linked to these traditional dietary habits all ancient miners up to the early Modern times have gut microbiome structures akin to modern non-Westernized individuals which may indicate a shift in the gut community composition of modern Westernized populations due to quite recent dietary and lifestyle changes. When we extended our microbial survey to fungi present in the paleofeces, we observed in one of the Iron Age samples a high abundance of Penicillium roqueforti and Saccharomyces cerevisiae DNA. Genome-wide analysis indicates that both fungi were involved in food fermentation and provide the first molecular evidence for blue cheese and beer consumption during Iron Age Europe.
2021-11-02 | PXD027613 | Pride