Culture-independent methods for identifying microbial communities in cheese.
This review focuses on the culture-independent methods available for the description of both bacterial and fungal communities in cheese. Important steps of the culture-independent strategy, which relies on bulk DNA extraction from cheese and polymerase chain reaction (PCR) amplification of selected sequences, are discussed. We critically evaluate the identification techniques already used for monitoring microbial communities in cheese, including PCR-denaturing gradient gel electrophoresis (PCR-DGGE), PCR-temporal temperature gradient gel electrophoresis (PCR-TTGE) or single-strand conformation polymorphism-PCR (SSCP-PCR) as well as some other techniques that remain to be adapted to the study of cheese communities. Further, our analysis draws attention to the lack of data available on suitable DNA sequences for identifying fungal communities in cheese and proposes some potential DNA targets.
Jany
Jean-Luc
JL
Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, Université Européenne de Bretagne-ESMISAB, Parvis Blaise Pascal, Technopôle de Brest Iroise, Plouzané, France. jean-luc.jany@univ-brest.fr
Barbier
Georges
G
D001419:Bacteria / Q000145:classification / Q000302:isolation & purification*; D002611:Cheese / Q000382:microbiology*; D002851:Chromatography, High Pressure Liquid; D015169:Colony Count, Microbial / Q000379:methods; D004269:DNA, Bacterial / Q000235:genetics / Q000302:isolation & purification; D004271:DNA, Fungal / Q000235:genetics / Q000302:isolation & purification; D004587:Electrophoresis, Agar Gel; D005516:Food Microbiology; D020411:Oligonucleotide Array Sequence Analysis; D010802:Phylogeny; D016133:Polymerase Chain Reaction / Q000379:methods; D012150:Polymorphism, Restriction Fragment Length; D018807:Polymorphism, Single-Stranded Conformational
D004269:DNA, Bacterial; D004271:DNA, Fungal