Monitoring of the microbiota of fermented sausages by culture independent rRNA-based approaches

In Italy, fermented sausages (called "salami") are consumed in large quantities. Salami samples from a local meat factory in the area of Torino were analyzed at 0, 3, 7, 30 and 45 days of ripening. Swab samples from the production environment were also collected at the beginning of the experiment. The diversity of metabolically active microbiota occurring during the natural fermentation of salami was evaluated by using RT-PCR-DGGE coupled with RNA-based pyrosequencing of the 16S rRNA gene. A culture-dependent approach was also applied to identify and characterize isolated Staphylococcaceae and LAB populations. Staphylococcus succinus, Staphylococcus xylosus and Lactobacillus sakei were the species most frequently isolated during the maturation time. Rep-PCR analysis showed that S. succinus and S. xylosus isolated from swabs and salami samples clustered together, suggesting possible contamination during the production process. RT-PCR-DGGE and rRNA-based pyrosequencing showed that the metabolically active populations were dominated by S. succinus, Lb. sakei and Leuconostoc carnosum. In this specific case study, only a few species belonging to Staphylococcaceae, Lactobacillaceae and Leuconostocaceae may be metabolically active and contribute to determine the final characteristics of the products.