Bacterial and fungal communities in Austrian raw-milk hard-cheese during ripening
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PROVIDER: PRJEB40652 | ENA |
REPOSITORIES: ENA
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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:Cheese ripening involves successional changes of the rind microbial composition that harbors a key role on the quality and safety of the final products. In this study, we analyzed the evolution of the rind microbiota (bacteria and fungi) throughout the ripening of Austrian Vorarlberger Bergkäse (VB), an artisanal surface-ripened cheese, by using quantitative and qualitative approaches. The real-time quantitative PCR results revealed that bacteria were more abundant than fungi in VB rinds throughout ripening, although both kingdoms were abundant along the process. The qualitative investigation was performed by high-throughput gene-targeted (amplicon) sequencing. The results showed dynamic changes of the rind microbiota throughout ripening. In the fresh products, VB rinds were dominated by Staphylococcus equorum and Candida. At early ripening times (14-30 days) Psychrobacter and Debaryomyces flourished, although their high abundance was limited to these time points. At the latest ripening times (90-160 days), VB rinds were dominated by S. equorum, Brevibacterium, Corynebacterium, and Scopulariopsis. Strong correlations were shown for specific bacteria and fungi linked to specific ripening periods. This study deepens our understanding of VB ripening and highlights different bacteria and fungi associated to specific ripening periods which may influence the organoleptic properties of the final products.
| S-EPMC7763656 | biostudies-literature
Project description:Brevibacterium genomes from Austrian hard cheese
| PRJNA498327 | ENA
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.
2012-09-07 | E-GEOD-23987 | biostudies-arrayexpress
Project description:Metatranscriptomic analyses unravel dynamic changes in the microbial and metabolic transcriptional profiles in artisanal Austrian hard-cheeses during ripening
| PRJEB48589 | ENA
Project description:We used Affymetrix microarray analyses of thirty-two individual Vitis vinifera cv. Cabernet Sauvignon berries sampled from two clusters at fifty-percent ripening initiation. By delineating four developmental stages of ripening initiation, we demonstrate that color is a statistically significant indicator of transcriptional state during ripening initiation. We report on clustered gene expression patterns which were mined for genes annotated with signal transduction functions in order to advance regulatory network modeling of ripening initiation in grape berries. We also demonstrated that gene expression does not differ statistically significantly at a global level in berries sampled from different plants or different positions in a cluster. Experiment Overall Design: Individual grape berries were selected at 4 developmental stages along ripening initiation for RNA extraction and hybridization to Affymetrix Vitis Genome GeneChips. One goal of this study was to determine the association between the global transcriptome state and phenotypic variables frequently used in berry staging such as color and firmness, so we defined the four time-points (development series) by color/firmness combinations: green hard (GH), green soft (GS), pink soft (PS) and red soft (RS). Individual berries representing each stage were collected from either the distal or the proximal position of one cluster one each of two plants used for experiments.
2008-10-20 | E-GEOD-11406 | biostudies-arrayexpress
Project description:The cheese microbial community is dense with relatively low complexity and composed of cultivable prokaryotic and eukaryotic microorganisms. The ripening process can thus be reproduced under controlled conditions. A reduced microbial community composed of yeasts and bacteria was assembled to mimic that of smear-ripened cheese. The genomes of the microorganisms have been sequenced and annotated, which allows access to gene expression under various conditions at different ripening times. Through the use of a combined approach using omics (e.g. metatranscriptomics, volatilomics), and biochemical/microbial analyses, we have investigated the effect of a biotic perturbation, omission of some yeast, on the stability and functionality of the microbial cheese community throughout ripening.
2024-04-29 | MTBLS6968 | MetaboLights
Project description:Extending ripening of hard cheeses well beyond the traditional ripening period is becoming increasingly popular, although little is known about the actual evolution of their characteristics. The present work aimed at investigating selected traits of Parmigiano Reggiano cheese ripened for 12, 18, 24, 30, 40 and 50 months. Two cheeses per each ripening period were sampled. Although moisture constantly decreased and was close to 25% in 50-month cheeses, with a parallel increase in cheese hardness, several biochemical changes occurred involving the activity of both native and microbial enzymes. Capillary electrophoresis demonstrated degradation of ?s1- and ?-casein, indicating residual activity of both chymosin and plasmin. Similarly, continuous release of free amino acids supported the activity of peptidases deriving from lysed bacterial cells. Volatile flavor compounds, such as short-chain fatty acids and some derived ketones, alcohols and esters, evaluated by gas chromatography with solid-phase micro-extraction, accumulated as well. Cheese microstructure was characterized by free fat trapped in irregularly shaped areas within a protein network, with native fat globules being no longer visible. This study showed for the first time that numerous biochemical and structural variations still occur in a hard cheese at up to 50 months of aging, proving that the ripening extension deserves to be highlighted to the consumer and may justify a premium price.
| S-EPMC7143483 | biostudies-literature
Project description:Abstract This study aimed to compare the three strains of Listeria monocytogenes survival in raw milk cheese and pasteurized milk cheese and to suggest the effect of milk microbiota on survival. L. monocytogenes cell counts decreased in all cheese as ripening time increased, and the survival rate was different for the strains of L. monocytogenes. Furthermore, L. monocytogenes survived longer in raw milk cheese than in pasteurized milk cheese. The difference of bacterial survival in each cheese was independent of Aw or the Lactobacillus spp. populations in cheeses; there was no difference in Aw or Lactobacillus spp. populations in all cheeses. The richness of microbiota in raw milk was little higher than in pasteurized milk, and five phyla (Chloroflexi, Cyanobacteria, Deinococcus–Thermus, Lentisphaerae, and Verrucomicrobia) were present only in raw milk. Also, organic acid?producing bacteria were presented more in pasteurized milk compared with raw milk; thus, the growth of L. monocytogenes was slower in pasteurized milk. In conclusion, differences in the microbial community of milk can affect the growth of L. monocytogenes. Making cheese using raw milk is a risk of L. monocytogenes infection; thus, efforts to prevent growth of L. monocytogenes such as the use of appropriate food additives are required. Cell counts of L. monocytogenes in all cheese samples were decreased as ripening time increased. Five phyla (Chloroflexi, Cyanobacteria, Deinococcus–Thermus, Lentisphaerae, and Verrucomicrobia) were only existed in raw milk; therefore, the different composition of microbiome between raw milk and pasteurized milk could be affected to the L. monocytogenes survival.
| S-EPMC7500772 | biostudies-literature
Project description:Aside from their amino acid content, dairy proteins are valuable for their ability to carry encrypted bioactive peptides whose activities are latent until released by digestive enzymes or endogenous enzymes within the food. Peptides can possess a wide variety of functionalities, such as antibacterial, antihypertensive, and antioxidative properties, as demonstrated by in vitro and in vivo studies. This phenomenon raises the question as to what impact various traditional cheese-making processes have on the formation of bioactive peptides in the resulting products. In this study, we have profiled the naturally-occurring peptides in two hard and two soft traditional cheeses and have identified their known bioactive sequences. While past studies have typically identified fewer than 100 peptide sequences in a single cheese, we have used modern instrumentation to identify between 2900 and 4700 sequences per cheese, an increase by a factor of about 50. We demonstrated substantial variations in proteolysis and peptide formation between the interior and rind of each cheese, which we ascribed to the differences in microbial composition between these regions. We identified a total of 111 bioactive sequences among the four cheeses, with the greatest number of sequences, 89, originating from Mimolette. The most common bioactivities identified were antimicrobial and inhibition of the angiotensin-converting enzyme. This work revealed that cheese proteolysis and the resulting peptidomes are more complex than originally thought in terms of the number of peptides released, variation in peptidome across sites within a single cheese, and variation in bioactive peptides among cheese-making techniques.
2020-12-23 | PXD021426 | Pride