Application of molecular identification tools for Lactobacillus, with a focus on discrimination between closely related species: A review

Lactobacillus is among the most important GRAS food lactic acid bacteria, with nearly 140 species at present, mostly of industrial importance. Being part of the natural flora of a range of food products like raw milk, fermented dairy products, fruits, vegetables, meat products they also serve as starters for a number of fermented food products either to enhance the quality or to add health benefits. These groups of economically important species are often alike in phenotypic and physiological characteristics, probably due to their co-evolution in the same ecological niches; hence they are difficult to be differentiated. This demands advanced methods for their proper identification and characterization. With the advancement of molecular biology, a range of DNA-based molecular techniques has replaced the largely cumbersome phenotypic methods. This review summarizes the various molecular techniques available for detection and identification within the genus Lactobacillus, with special emphasis on the four groups of closely resembling species: L. casei group, L. acidophilus group, L. delbrueckii subspecies, and L. plantarum group. This review also provides insights into current trends for alternative molecular markers other than 16S rRNA to resolve the ambiguity within phylogenetically close species in the genus Lactobacillus.