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opencc-by-4.0Dec 2021View details →

Supplementary data of endogenous starter culture and cheese metagenomes

The first description of the virome composition in Brazilian artisanal Canastra cheese and the phage-bacterial interactions in this food system. Here you can access the contigs that compose the 16 metagenome-assembled genomes (MAG) explored in paper and their spacers sequences.

Figure 5. Sensory score and period of storage for processed cheese-Time-Delay Artificial Neural Network Computing Models for Predicting Shelf Life of Processed Cheese

R2 was found to be 96.5 percent of the total variation as explained by sensory scores. Period of storage (days) for which the processed cheese has been in the shelf can be determined based on sensory score (Fig. 5).

Figure 4. Comparison of ASS and PSS for multilayer model R-Time-Delay Artificial Neural Network Computing Models for Predicting Shelf Life of Processed Cheese

TDNN models with single and multi layers were developed taking soluble nitrogen, pH, standard plate count, yeast & mould count, spore count as input parameters, and sensory score as output parameter for predicting the shelf life of processed cheese stored at 30o C. Mean Square Error, Root Mean Square Error, Coefficient of Determination and Nash - Sutcliffo Coefficient were used in order to compare the prediction ability of the developed TDNN models. Regression equations were developed for predicting the shelf life of processed cheese, which came out as 28.25 days. Since, predicted value is close to the experimentally determined shelf life of 30 days, hence from the study it can be concluded that TDNN artificial neural network models are quite efficient in predicting shelf life of processed cheese.

Figure 2. Training pattern of TDNN models-Time-Delay Artificial Neural Network Computing Models for Predicting Shelf Life of Processed Cheese

The Neural Network Toolbox under MATLAB software was used for developing the TDNN models. Training pattern of TDNN models is presented in Fig.2.

Figure 1. Inputs and output parameters for TDNN models-Time-Delay Artificial Neural Network Computing Models for Predicting Shelf Life of Processed Cheese

The data consisted of 36 samples, which were divided into two subsets, i.e., 30 used for training the network and 6 for testing the TDNN models. Soluble nitrogen, pH, standard plate count, yeast & mould count, and spore count were taken as input parameters, and sensory score as output parameter for developing TDNN single and multilayer models (Fig.1).

Figure 3. Comparison of ASS and PSS single layer model-Time-Delay Artificial Neural Network Computing Models for Predicting Shelf Life of Processed Cheese

opencc-by-4.0May 2017View details →

Tomographic X-ray data of carved cheese

This is an open-access dataset of tomographic X-ray data of a carved cheese. The dataset consists of <ul> <li>the X-ray sinogram of a single 2D slice of the cheese slice with three different resolutions, and</li> <li>the corresponding measurement matrices modeling the linear operation of the X-ray transform.</li> </ul> Each of the sinograms was obtained from a measured 360-projection fan-beam sinogram by down-sampling and taking logarithms. The original (measured) sinogram is also provided in its original form and resolution. Documentation of the dataset is available at <a href="https://arxiv.org/abs/1705.05732">arxiv.org/abs/1705.05732</a>. See also <a href="https://www.fips.fi/dataset.php">www.fips.fi/dataset.php</a>.

opencc-by-4.0Mar 2024View details →

Supplement: Genomic and phenotypic imprints of microbial domestication on cheese starter cultures

This data repository contains the latest version of the supplemental data, code and figures for the following manuscript: Vincent Somerville, Nadine Thierer, Remo S. Schmidt, Alexandra Roetschi, Laurianne Braillard, Monika Haueter, Hélène Berthoud, Noam Shani , Ueli von Ah, Florent Mazel & Philipp Engel 2024. “Genomic and phenotypic imprints of Neolithic domestication on Cheese Starter cultures”  All additional genomic data is stored under the following Bioprojects on NCBI: PRJNA717134 PRJNA1048529 PRJNA1083966 PRJNA1157897

opencc-by-4.0Oct 2022View details →

Supplement: Extensive diversity and rapid turnover of phage defense repertoires in cheese-associated bacterial communities

Background Phages are key drivers of genomic diversity in bacterial populations as they impose strong selective pressure on the evolution of bacterial defense mechanisms across closely related strains. The pan-immunity model suggests that such diversity is maintained because the effective immune system of a bacterial species is the one distributed across all strains present in the community. However, only few studies have analyzed the distribution of bacterial defense systems at the community-level, mostly focusing on CRISPR and comparing samples from complex environments. Here, we studied 2778 bacterial genomes and 188 metagenomes from cheese-associated communities, which are dominated by a few bacterial taxa and occur in relatively stable environments. Results We corroborate previous laboratory findings that in cheese-associated communities nearly identical strains contain diverse and highly variable arsenals of innate and adaptive (i.e., CRISPR-Cas) immunity systems suggesting rapid turnover. CRISPR spacer abundance correlated with the abundance of matching target sequences across the metagenomes providing evidence that the identified defense repertoires are functional and under selection. While these characteristics align with the pan-immunity model, the detected CRISPR spacers only covered a subset of the phages previously identified in cheese, providing evidence that CRISPR does not enable complete immunity against all phages, and that the innate immune mechanisms may have complementary roles. Conclusions Our findings show that the evolution of bacterial defense mechanisms is a highly dynamic process and highlight that experimentally tractable, low complexity communities such as those found in cheese, can help to understand ecological and molecular processes underlying phage-defense system relationships. These findings can have implications for the design of robust synthetic communities used in biotechnology and the food industry.

opencc-by-4.0Oct 2016View details →

Cheese bacteria genomes

Annotated complete genomes from cheese-associated bacteria, used for analysis in Bonham et. al. Extensive Horizontal Gene Transfer in Cheese-Associated Bacteria http://dx.doi.org/10.1101/079137 Includes many previously published genomes, including those from Almeida et. al. BMJ Genomics 2014

dryad36/100

Soil microbiome dataset from the University of Wisconsin Arlington and Lancaster agricultural research stations and cheese maker and vegetable processor wastewater land application sites

Cheese making and vegetable processing are trillion-dollar industries globally. However, they generate immense volumes of high nitrogen wastewater that must be processed safely and cost effectively. Land application systems are frequently used by rural medium and smaller processing facilities that lack ready access to wastewater resource recovery facilities. This study utilized soil microbial data to determine system differences leading to high denitrification rates observed in incubation studies in agricultural soil collected from University of Wisconsin Agricultural Research Stations (ARS), Arlington and Lancaster stations, compared to industry cheese making and vegetable processing land application water treatment facilities. It was hypothesized that decade long frequent treatment with facility wastewater would alter the microbial communities in the system soils, but this is not the case. No clear correlations were found between soil denitrification rates and biotic or abiotic system factors and the microbial communities observed in the industry systems are similar to the ARS soils under agricultural production and to literature reported denitrifying systems such as wetlands and wastewater resource recovery facilities. Knowing that land application system management does not alter the microbial biome will allow any management advances that increase denitrification efficiency in other denitrifying systems to be readily applied to industry wastewater land application facilities.

opencc-zeroApr 2024View details →

openmit-licenseOct 2024View details →

Code and Data for Manuscript "How raw milk-based adjunct cultures influence the microbial diversity in cheese"

This repository contains the data and code used in the study "How raw milk-based adjunct cultures influence the microbial diversity in cheese" by Dreier et al. (2024). The study investigates the impact of raw milk-based adjunct cultures (NMAC) on the microbial diversity of cheese. The data includes 16S rRNA gene amplicon sequences from cheese samples, as well as metadata and code used for data analysis.

opencc-by-4.0Nov 2020View details →

Meta-Analysis on the Effect of Biopreservatives on Staphylococcus aureus in Cheese

Recording of the talk “Meta-analysis on the effect of biopreservatives on Staphylococcus aureus in cheese” presented by Ursula Gonzales-Barron at the 71st Annual Meeting of the European Federation of Animal Science, EAAP, Online virtual meeting (1-4 Dec 2020).

opencc-by-4.0Oct 2020View details →

Meta-regression Models Describing the Effects of Essential Oils and Added Lactic Acid Bacteria on Staphylococcus aureus Inactivation in Cheese

Recording of the talk “Meta-regression models describing the effects of essential oils and added lactic acid bacteria on Staphylococcus aureus inactivation in cheese”, presented by Beatriz Nunes Silva at the 2020 International Association for Food Protection Annual Meeting, IAFP, Online virtual meeting (26-28 Oct 2020).

opencc-by-4.0Jan 2021View details →

Protocol for DNA Extraction from Cheese

Video demonstrating the protocol for DNA extraction from cheese based on PowerFood Microbial DNA isolation kit MO BIO, according to Yang et al. (2016) procedure. Training video elaborated within the ArtiSaneFood project.

opencc-by-4.0Feb 2022View details →

Dataset related to article "Functional characterization and immunomodulatory properties of Lactobacillus helveticus strains isolated from Italian hard cheeses "

This record contains raw datarelated to article "Functional characterization and immunomodulatory properties of Lactobacillus helveticus strains isolated from Italian hard cheeses " Lactobacillus helveticus carries many properties such as the ability to survive gastrointestinal transit, modulate the host immune response, accumulate biopeptides in milk, and adhere to the epithelial cells that could contribute to improving host health. In this study, the applicability as functional cultures of four L. helveticus strains isolated from Italian hard cheeses was investigated. A preliminary strain characterization showed that the ability to produce folate was generally low while antioxidant, proteolytic, peptidase, and β-galactosidase activities resulted high, although very variable, between strains. When stimulated moDCs were incubated in the presence of live cells, a dose-dependent release of both the pro-inflammatory cytokine IL-12p70 and the anti-inflammatory cytokine IL-10, was shown for all the four strains. In the presence of cell-free culture supernatants (postbiotics), a dose-dependent, decrease of IL-12p70 and an increase of IL-10 was generally observed. The immunomodulatory effect took place also in Caciotta-like cheese made with strains SIM12 and SIS16 as bifunctional (i.e., immunomodulant and acidifying) starter cultures, thus confirming tests in culture media. Given that the growth of bacteria in the cheese was not necessary (they were killed by pasteurization), the results indicated that some constituents of non-viable bacteria had immunomodulatory properties. This study adds additional evidence for the positive role of L. helveticus on human health and suggests cheese as a suitable food for delivering candidate strains and modulating their anti-inflammatory properties.

opencc-by-4.0Sep 2022View details →

Supplementary informations of endogenous starter culture and cheese metagenomes

The first description of the virome composition in Brazilian artisanal Canastra cheese and the phage-bacterial interactions in this food system. Here you can access supplemental methods and results (docx) and supplemental data (MAGs contigs, novel 987 group phage contigs, and MAGs spacers).

opencc-zeroJun 2022View details →

Supplementary information for: Monitoring cheese ripening by single-sided NMR

Supplementary information for: Monitoring cheese ripening by single-sided NMR Raw experimental data used to create the manuscript. Data structure: Each folder contains the date of acquisition. Inside folders are CPMG, DT2, and T1T2 experiments with suffix showing the position of the acquired region in micrometers.

opencc-zeroDec 2020View details →

Mould for brus-type cheese

A wooden form that consists of four elements, a board, a rim made of a shank and two flat, round wooden discs with patterns cut out using the woodcarving technique for stamping the so-called cyfry on the cheese. With these moulds, large rennet cheeses called bruski were shaped. The name of these products comes from their shape (large, round, with two flattened sides), resembling stones for brusenie, i.e. sharpening. This type of cheese was made in the Tatra Mountains in 2nd half of 19th century at Hala (meadow) Pyszna, and during the period just before World War I, also at Hala Kondratowa. Some sources go as far as to limit the production of bruski in the Tatra Mountains to the area of these two mountain pastures. ID no.: E/4284/a,b,c,d/MT Time of creation: 1850–1914 Museum: The Dr. Tytus Chałubiński Tatra Museum in Zakopane https://muzea.malopolska.pl/en/objects-list/1784 Digitalisation: Digitalisation: RDW MIC, Virtual Małopolska project Source: Objaverse 1.0 / Sketchfab