Culture-independent methods for identifying microbial communities in cheese

Jany, Jean‐Luc; Barbier, Georges

doi:10.1016/j.fm.2008.06.003

Cited by 153 publications

(110 citation statements)

References 102 publications

Supporting

Mentioning

110

Contrasting

Order By: Relevance

“…Besides culturing, a vast array of molecular techniques is now applied to address the question of microbial diversity and population dynamics throughout the cheese manufacturing and ripening processes (25). However, despite the increasing number of polyphasic studies, including both culture-dependent and culture-independent approaches, to our knowledge no data on 16S rRNA-based pyrosequencing of the microbiome of traditional cheeses have been published.…”

Section: Discussionmentioning

confidence: 99%

“…In addition to conventional microbial characterization, a vast array of culture-independent molecular techniques is now available to address the diversity and evolution of microbial populations throughout cheese manufacture and ripening (25). Among others, techniques such as denaturing gradient gel electrophoresis (DGGE) (40), single-strand conformation polymorphism (SSCP) (14), fluorescent in situ hybridization (FISH) (18), length heterogeneity-PCR (LH-PCR) (29), quantitative real-time PCR (qPCR) (21), and terminal-restriction fragment length polymorphism (T-RFLP) (3) complement classic culturing techniques, providing a more complete picture of the cheese ecosystem.…”

mentioning

confidence: 99%

See 1 more Smart Citation

Biodiversity in Oscypek, a Traditional Polish Cheese, Determined by Culture-Dependent and -Independent Approaches

Alegría

Szczęsny

Mayo

et al. 2012

Appl Environ Microbiol

132

View full text Add to dashboard Cite

Oscypek is a traditional Polish scalded-smoked cheese, with a protected-designation-of-origin (PDO) status, manufactured from raw sheep's milk without starter cultures in the Tatra Mountains region of Poland. This study was undertaken in order to gain insight into the microbiota that develops and evolves during the manufacture and ripening stages of Oscypek. To this end, we made use of both culturing and the culture-independent methods of PCR followed by denaturing gradient gel electrophoresis (PCR-DGGE) and pyrosequencing of 16S rRNA gene amplicons. The culture-dependent technique and PCR-DGGE fingerprinting detected the predominant microorganisms in traditional Oscypek, whereas the next-generation sequencing technique (454 pyrosequencing) revealed greater bacterial diversity. Besides members of the most abundant bacterial genera in dairy products, e.g., Lactococcus, Lactobacillus, Leuconostoc, Streptococcus, and Enterococcus, identified by all three methods, other, subdominant bacteria belonging to the families Bifidobacteriaceae and Moraxellaceae (mostly Enhydrobacter), as well as various minor bacteria, were identified by pyrosequencing. The presence of bifidobacterial sequences in a cheese system is reported for the first time. In addition to bacteria, a great diversity of yeast species was demonstrated in Oscypek by the PCR-DGGE method. Culturing methods enabled the determination of a number of viable microorganisms from different microbial groups and their isolation for potential future applications in specific cheese starter cultures.

show abstract

Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

Biodiversity in Oscypek, a Traditional Polish Cheese, Determined by Culture-Dependent and -Independent Approaches

Alegría

Szczęsny

Mayo

et al. 2012

Appl Environ Microbiol

132

View full text Add to dashboard Cite

show abstract

“…In metagenomics, the amplified fragments are shorter, ranging from 200 to 400 bp, but contain nine hypervariable regions (V1-V9) [41], which compensate the lack of information due to the small sequence size by a high rate of mutation. In most studies, the V3 region located in the 5' part of the gene is chosen [42]. However, the phylogenetic information is sometimes insufficient to achieve species identification.…”

Section: Exploring Bacterial Communities By 16s Pcr-ttgementioning

confidence: 99%

Bacterial Biodiversity in Midguts of Anopheles Mosquitoes, Malaria Vectors in Southeast Asia

Manguin¹,

Ngo²,

Tainchum³

et al. 2013

Anopheles Mosquitoes - New Insights Into Malaria Vectors

View full text Add to dashboard Cite

“…PCR-based molecular profiling techniques targeting either particular populations or select taxonomic communities are also routinely used and have been extensively reviewed (8)(9)(10). PCR-based methods cannot, however, provide comprehensive coverage of total microbial populations.…”

mentioning

confidence: 99%

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

O’Sullivan

Cotter

O’Sullivan

et al. 2015

Appl Environ Microbiol

View full text Add to dashboard Cite

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.

show abstract

Culture-independent methods for identifying microbial communities in cheese

Abstract: 1 2This review focuses on the culture-independent methods available for the description of both 3 bacterial and fungal communities in cheese. Important steps of the culture-independent 4 strategy, which relies on bulk DNA extraction from cheese and polymerase chain reaction 5

Cited by 153 publications

References 102 publications

Biodiversity in Oscypek, a Traditional Polish Cheese, Determined by Culture-Dependent and -Independent Approaches

Biodiversity in Oscypek, a Traditional Polish Cheese, Determined by Culture-Dependent and -Independent Approaches

Bacterial Biodiversity in Midguts of Anopheles Mosquitoes, Malaria Vectors in Southeast Asia

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

Contact Info

Product

Resources

About