Bacterial diversity of cheonggukjang, a traditional Korean fermented food, analyzed by barcoded pyrosequencing

Cotter

et al. 2015

We sought to determine if the time, within a production day, that a cheese is manufactured has an influence on the microbial community present within that cheese. To facilitate this, 16S rRNA amplicon sequencing was used to elucidate the microbial community dynamics of brine-salted continental-type cheese in cheeses produced early and late in the production day. Differences in the microbial composition of the core and rind of the cheese were also investigated. Throughout ripening, it was apparent that cheeses produced late in the day had a more diverse microbial population than their early equivalents. Spatial variation between the cheese core and rind was also noted in that cheese rinds were initially found to have a more diverse microbial population but thereafter the opposite was the case. Interestingly, the genera Thermus, Pseudoalteromonas, and Bifidobacterium, not routinely associated with a continental-type cheese produced from pasteurized milk, were detected. The significance, if any, of the presence of these genera will require further attention. Ultimately, the use of high-throughput sequencing has facilitated a novel and detailed analysis of the temporal and spatial distribution of microbes in this complex cheese system and established that the period during a production cycle at which a cheese is manufactured can influence its microbial composition.

mentioning

confidence: 99%

Temporal and Spatial Differences in Microbial Composition during the Manufacture of a Continental-Type Cheese

Cotter

et al. 2015

“…However, the microbiota involved in buffalo mozzarella production has never been thoroughly assessed by microbial species identification, although the complexity of the microbiota is recognized on the basis of culture-based microbiological determinations (10,11,21,24). High-throughput-sequencing approaches were recently applied in a few cases to describe the microbiota of food products and have been shown to provide a thorough analysis of microbial diversity, producing much deeper output than more commonly used culture-independent approaches (1,13,16,22,23). In this study, intermediates of production of two batches of traditional mozzarella cheese were analyzed by culture-independent pyrosequencing in order to provide insights into the microbiota responsible for the production of this widely appreciated dairy product.…”

mentioning

confidence: 99%

“Remake” by High-Throughput Sequencing of the Microbiota Involved in the Production of Water Buffalo Mozzarella Cheese

Ercolini

Storia

Iacono

2012

164

127

bIntermediates of production of two batches of traditional mozzarella cheese were analyzed by culture-independent pyrosequencing. The quantitative distribution of taxa within the samples suggested that thermophilic lactic acid bacteria from the natural starter were mainly responsible for the fermentation, while microorganisms found in raw milk did not develop during fermentation. Mozzarella is perhaps the most popular nonripened cheese. Traditional mozzarella is mainly produced in southern Italy from water buffalo's milk, even though it is widely exported and also industrially produced in other countries. The technology of its manufacture has been described in detail in previous works (11,14). The cheese is made from whole raw water buffalo's milk by adding a natural whey culture (NWC) (from the batch of the previous day) as starter in a 5-h curd fermentation. The specific characteristics of the final product arise mainly from the raw materials employed, the agri-ecosystem of the area of production, and the traditional technology of the manufacturing process. The use of raw buffalo's milk and the NWC in the process have so far been recognized as strong points of traditional mozzarella production, because premium-quality products arise as result of fermentation by the specific microbiota of raw milk and NWC. Due to the use of microbiologically complex raw materials, the traditional cheese-making processes are the most difficult to control, and it is of interest to develop reliable methods to monitor the fermentation in order to standardize the process for high-quality products while preserving their typical traits. The microbiota of mozzarella cheese has been studied in the past by culture-independent fingerprinting without identification of microbial taxa (9, 14). However, the microbiota involved in buffalo mozzarella production has never been thoroughly assessed by microbial species identification, although the complexity of the microbiota is recognized on the basis of culture-based microbiological determinations (10,11,21,24). High-throughput-sequencing approaches were recently applied in a few cases to describe the microbiota of food products and have been shown to provide a thorough analysis of microbial diversity, producing much deeper output than more commonly used culture-independent approaches (1,13,16,22,23). In this study, intermediates of production of two batches of traditional mozzarella cheese were analyzed by culture-independent pyrosequencing in order to provide insights into the microbiota responsible for the production of this widely appreciated dairy product.Samples were collected in May 2012 from two dairies producing top-quality traditional water buffalo mozzarella cheese, located in the Campania region (southern Italy) in the provinces of Salerno (Batch 1) and Caserta (Batch 2), respectively. Samples of raw milk (L), natural whey cultures (NWC), curd at the beginning (C 0 ) and at end (C F ) of the ripening, and final mozzarella cheese (M) were aseptically collected, cooled at 4°C, and anal...

“…Indeed, the more traditional the manufacturing process, the more complex the microbial community in the food. In contrast, industrially obtained foods are characterized by more-simple microbial consortia (16)(17)(18).…”

Section: Hts Applications In Foodmentioning

confidence: 99%

“…However, not all of the studies report a rarefaction analysis and it is not always possible to understand how deep the sample coverage has been. For example, coverage obtained from about 1,000 reads was satisfactory to determine the microbiota of some fermented soybean products (16,17). Most samples of soft, semihard, and hard Irish cheeses were adequately covered with slightly more than 1,000 reads, while cheese rinds, which have a more complex microbiota, required more sequences to be adequately studied (15).…”

Section: Planning Sample Coverage and Taxonomic Resolution To Set Wormentioning

confidence: 99%

High-Throughput Sequencing and Metagenomics: Moving Forward in the Culture-Independent Analysis of Food Microbial Ecology

Ercolini

2013

415

229

Following recent trends in environmental microbiology, food microbiology has benefited from the advances in molecular biology and adopted novel strategies to detect, identify, and monitor microbes in food. An in-depth study of the microbial diversity in food can now be achieved by using high-throughput sequencing (HTS) approaches after direct nucleic acid extraction from the sample to be studied. In this review, the workflow of applying culture-independent HTS to food matrices is described. The current scenario and future perspectives of HTS uses to study food microbiota are presented, and the decision-making process leading to the best choice of working conditions to fulfill the specific needs of food research is described.