title: Optimization of conditions for profiling bacterial populations in food by culture-independent methods.
abstract: In this study we used culture-independent methods to profile bacterial populations in food products. Denaturing gradient gel electrophoresis (DGGE) and fluorescence in situ hybridization (FISH) were employed in order to identify bacterial species without the need of isolation and biochemical identification. The protocols used to extract the DNA, subsequently subjected to PCR amplification for DGGE, as well as the hybridization procedure for FISH, were optimised. Moreover, an extensive study on the primers and probes to be used for the direct detection and identification of microorganisms commonly found in food, was carried out. Meat and cheese samples, fresh or processed, were subjected to DGGE and FISH analysis and the results obtained highlighted how the processing in food industry is decreasing the bacterial biodiversity. Not only processed cheese or meat but also fermented products were dominated by only one or few species. Lactobacillus sakei, Lactobacillus curvatus and Brochothrix thermosphacta were the main species found in meat products, while in cheese(s) Lactococcus lactis, Streptococcus thermophilus and Leuconostoc spp. were repeatedly detected. The results obtained by the two culture-independent methods used always correlated well.
authors.affiliation: Dipartimento di Valorizzazione e Protezione delle Risorse Agroforestali, University of Turin, Via Leonardo da Vinci 44, 10095, Grugliasco, Turin, Italy. lucasimone.cocolin@unito.it
authors.forename: Luca
authors.initials: L
authors.lastname: Cocolin
authors.forename: Ana
authors.initials: A
authors.lastname: Diez
authors.forename: Rosalinda
authors.initials: R
authors.lastname: Urso
authors.forename: Kalliopi
authors.initials: K
authors.lastname: Rantsiou
authors.forename: Giuseppe
authors.initials: G
authors.lastname: Comi
authors.forename: Ingrid
authors.initials: I
authors.lastname: Bergmaier
authors.forename: Claudia
authors.initials: C
authors.lastname: Beimfohr
mesh_terms: D001419:Bacteria / Q000145:classification* / Q000302:isolation & purification*; D002611:Cheese / Q000382:microbiology; D015169:Colony Count, Microbial; D004269:DNA, Bacterial / Q000032:analysis*; D016521:Electrophoresis, Gel, Pulsed-Field / Q000379:methods; D005506:Food Contamination / Q000032:analysis*; D005516:Food Microbiology; D005784:Gene Amplification; D017404:In Situ Hybridization, Fluorescence / Q000379:methods; D008460:Meat / Q000382:microbiology; D010802:Phylogeny; D016133:Polymerase Chain Reaction / Q000379:methods; D013045:Species Specificity
chemical_list: D004269:DNA, Bacterial