Table 3.

Molecular approaches used in discrimination among the genus Lactobacillus.

Methods Used	Comments	Species Identified and Source	Reference
23S rDNA probe	Probes unequivocally differentiated L. acidophilus and L. plantarum isolates.	L. acidophilus, L. pentosus, L. plantarum species isolates from feed supplements or starter products	[92]
Ribotyping	Good discrimination at strains level based upon differences in rRNA.	Some L. paracasei ss. paracasei strains as the dominant ones from raw milk cheeses	[93]
RAPD	Good discrimination at strains level.	L. plantarum 2035 and L. plantarum ACA-DC 2640 isolated from Feta cheese	[94]
Species-specific PCR (plantaricin biosynthesis protein gene)	Rapid and preliminary screening of L. plantarum from large vegetable samples before performing a battery of phenotypic and molecular methods.	L. plantarum from vegetable samples	[95]
Species-specific PCR using 16S rRNA or unique genes primers	Successful in the species detected in 17 products matched those indicated on their labels, whereas the remaining products contained species other than those appearing on the label.	Some Lactobacillus spp., 19 probiotics and 12 dairy products	[96]
Genus- and species-specific PCR, multiplex PCR, real-time HRM analysis, RFLP-PCR, rep-PCR, RAPD-PCR, AFLP-PCR, and proteomic methods such as MALDI-TOF MS typing and SDS-PAGE fingerprinting	Multiplex PCR and MALDI-TOF MS were the most valuable methods to identify the tested bacteria at the species level. At the strain level, the AFLP-PCR method showed the highest discriminatory power.	L. casei group, two international collections of microorganisms—the Japan Collection of Microorganisms (JCM) and Belgian Coordinated Collections of Microorganisms (BCCM)	[97]
Comparative sequence analysis, stretches of rec A gene	Successful in a clear separation of all type strains in distinct branches; identification of L. casei ATCC 393 and L. casei ATCC 334 as L. zeae and L. paracasei, respectively.	L. casei, L. paracasei (both subspecies), L. rhamnosus, L. zeae, strains from a commercial probiotic product.	[98]
16S ARDRA, RAPD, Eco RI ribotyping	13 wine strains typed as L. paracasei/casei, based on similar band pattern as L. paracasei type strain and L. casei ATCC 334.	L. casei/L. paracasei from wine	[99]
PFGE	Good discrimination at strain level based upon different bacterial strains.	The strains of L. plantarum isolated from the different fermented foods	[100]
One-step PCR-based, using 16S rRNA genes primers	Successful differentiation among 10 common lactic acid bacteria at the species level.	L. delbrueckii and others from fermented milk	[101]
16S ARDRA, ribotyping, RAPD	Only RAPD and ribotyping could discriminate between the type strains of both species.	L. plantarum, L. pentosus, Wine isolates	[99]
PCR-ARDRA (Taq I), RAPD	ARDRA and RAPD approaches may demonstrate a robust efficiency in the discrimination of unknown isolates.	L. acidophilus, L. planetarum, and L. fermentum from abomasums driven rennet	[102]
Repetitive-element PCR	Could rapidly and easily differentiate L. brevis species at strains level.	The closely related strains of L. brevis species	[103]
Multi-locus sequence typing (MLST) and multiplex RAPD-PCR	Targeting different genetic variations under the combination of MLST and multiplex-RAPD analysis	L. sanfranciscensis, Chinese traditional sourdoughs	[104]
PCR-DGGE, length-heterogeneity PCR (LH-PCR)	Good discrimination at strains level.	Type and reference strains of L. brevis DSMZ 20556 and L. plantarum DSMZ 2601	[105]
FISH	Rapid and accurate way to identify and quantify bacterial species.	L. plantarum (Probiotic products)	[106]