Dataset Information

Temporal and spatial differences in microbial composition during the manufacture of a continental-type cheese.

ABSTRACT: 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.

SUBMITTER: O'Sullivan DJ

PROVIDER: S-EPMC4357954 | biostudies-literature | 2015 Apr

REPOSITORIES: biostudies-literature

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Temporal and spatial differences in microbial composition during the manufacture of a continental-type cheese.

O'Sullivan Daniel J DJ Cotter Paul D PD O'Sullivan Orla O Giblin Linda L McSweeney Paul L H PL Sheehan Jeremiah J JJ

Applied and environmental microbiology 20150130 7

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 apparen ...[more]

PMID: 25636841

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Project description:A primary goal of modern cheese manufacturing is consistent product quality. One aspect of product quality that remains poorly understood is the variability of microbial subpopulations due to temporal or facility changes within cheese production environments. Therefore, our aim was to quantify this variability by measuring day-day and facility-facility changes in the cheese facility microbiome. In-process product (i.e., milk and cheese) and food-contact surfaces were sampled over the course of three production days at three cheese manufacturing facilities. Microbial communities were characterized using 16S rRNA metabarcoding and by plating on selective growth media. Each facility produced near-identical Cheddar cheese recipes on near-identical processing equipment during the time of sampling. Each facility also used a common pool of Lactococcus starter cultures which were rotated daily as groups of 4-5 strains and selected independently at each facility. Diversity analysis revealed significant facility-facility and day-day differences at each sample location. Facility differences were greatest on the food contact surfaces (i.e., draining-matting conveyor belts), explaining between 25 and 41% of the variance. Conversely, daily differences within each facility explained a greater proportion of the variance in the milk (20% vs. 12%) and cheese (29% vs. 20%). Further investigation into the sources of these differences revealed the involvement of several industrially relevant bacteria, including lactobacilli, which play a central role in flavor and texture development during Cheddar cheese ripening. Additionally, Streptococcus was found to contribute notably to differences observed in milk samples, whereas Acinetobacter, Streptococcus, Lactococcus, Exiguobacterium, and Enterobacteriaceae contributed notably to differences on the food contact surfaces. Facility differences in the cheese were overwhelmingly attributed to the rotation of Lactococcus starter cultures, thus highlighting circumstances where daily microbial shifts could be misinterpreted and emphasizing the importance of repeated sampling over time. The outcomes of this work highlight the complexity of the cheese facility microbiome and demonstrate daily and facility-facility microbial variations which might impact cheese product quality.

Project description:The microbial ecology of cheese involves a rich and complex interaction between starter lactic acid bacteria and nonstarter lactic acid bacteria (NSLAB), mainly originating from raw milk and/or from the environment, that can contribute to the final characteristics of cheese. The aim of the present research was the exploration of the active microbiota by RNA-based approaches during the manufacturing and ripening of a Grana-like cheese. Reverse transcriptase PCR (RT-PCR)-denaturing gradient gel electrophoresis (DGGE) and RNA-based high-throughput sequencing were applied to profile microbial populations, while the enumeration of active bacteria was carried out by using quantitative PCR (qPCR). Three different cheese productions (named D, E, and F) collected in the same month from the same dairy plant were analyzed. The application of the qPCR protocol revealed the presence of 7 log CFU/ml of bacterial load in raw milk, while, during ripening, active bacterial populations ranged from <4 to 8 log CFU/ml. The natural whey starters used in the three productions showed the same microbiota composition, characterized by the presence of Lactobacillus helveticus and Lactobacillus delbrueckii Nevertheless, beta-diversity analysis of the 16S rRNA sequencing data and RT-PCR-DGGE showed a clear clustering of the samples according to the three productions, probably driven by the different milks used. Milk samples were found to be characterized by the presence of several contaminants, such as Propionibacterium acnes, Acidovorax, Acinetobacter, Pseudomonas, and NSLAB. The core genera of the starter tended to limit the development of the spoilage bacteria only in two of the three batches. This study underlines the influence of different factors that can affect the final microbiota composition of the artisanal cheese.This study highlights the importance of the quality of the raw milk in the production of a hard cheese. Independent from the use of a starter culture, raw milk with low microbiological quality can negatively affect the populations of lactic acid bacteria and, as a consequence, impact the quality of the final product due to metabolic processes associated with spoilage bacteria.

Dataset Information

Temporal and spatial differences in microbial composition during the manufacture of a continental-type cheese.

Publications

Temporal and spatial differences in microbial composition during the manufacture of a continental-type cheese.

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