A culture-dependent and -independent approach for the identification of lactic acid bacteria associated with the production of nem chua, a Vietnamese fermented meat product

In this study, the diversity of the native lactic acid bacteria (LAB) population in nem chua, a popular traditional Vietnamese uncooked fermented meat, was described using a combination of culture-dependent and culture-independent methods. A total of two hundred seventy-three LAB isolates were subjected to a polyphasic identification approach combining (GTG)5-PCR fingerprinting and phenylalanyl-tRNA synthase α subunit (pheS) and RNA polymerase α subunit (rpoA) gene sequence analysis. LAB associated with nem chua were identified as Lactobacillus pentosus (21%), Lactobacillus plantarum (29.7%), Lactobacillus brevis (5%), Lactobacillus paracasei (0.4%), Lactobacillus fermentum (0.7%), Lactobacillus acidipiscis (0.4%), Lactobacillus farciminis (23%), Lactobacillus rossiae (0.4%), Lactobacillus fuchuensis (0.7%), Lactobacillus namurensis (0.4%), Lactococcus lactis (0.4%), Leuconostoc citreum (9.5%), Leuconostoc fallax (1%), Pediococcus acidilactici (1%), Pediococcus pentosaceus (4%), Pediococcus stilesii (1%), Weissella cibaria (0.7%) and Weissella paramesenteroides (0.7%). Furthermore, PCR-DGGE was also applied as a culture-independent method in this study. Results indicated the presence of species of which no isolates were recovered, i.e. Lactobacillus helveticus/crispatus, Lactococcus garvieae and Vagococcus sp. Conversely, not all isolated bacteria were detected by PCR-DGGE. Principal component and discriminant analysis disclosed correlations between the different production locations and certain isolated LAB species and strains and/or DGGE bands suggesting possible influences of locally prevailing production practices on the nem chua LAB microbiota.

► High degree of LAB diversity (a total of 21 different LAB species) in nem chua ► Specific species or strains could be associated with different production practices. ► Combining culture-dependent and -independent methods is favorable. ► First step in better understanding interrelation LAB composition and nem chua ► Perspectives for developing new starter cultures for the fermentation of nem chua