Amplified fragment length polymorphism (AFLP™) is a PCR based DNA fingerprinting technique that generates band profiles via the selective amplification of restriction fragments of whole genomic DNA. The method can be used both for identification and typing.
At BCCM/LMG, AFLP™ is provided as a customer service for accurate identification of lactic acid bacteria (LAB) and bifidobacteria at the (sub)species level. AFLP™ DNA fingerprints are generated for (unknown) isolates and compared to profiles of LAB and Bifidobacterium strains available in elaborated in-house reference databases, covering most currently described taxa of these groups of bacteria. Compared to sequence analysis of housekeeping gene(s), AFLP™ is sometimes more suitable for identification at the subspecies level, e.g. AFLP™ enables identification of Lactococcus lactis strains at the subspecies level. For high-resolution identification of starter cultures, feed inoculants, probiotic cultures, food spoilers, etc AFLP™ is a valuable approach.
Next to identification, AFLP™ is also suitable for typing of LAB and bifidobacteria, as well as other bacteria at the intraspecies to strain level. When multiple selective primer combinations are used, AFLP™ may approach the resolution offered by PFGE in cases of monitoring, epidemiology, authenticity verifications, etc.
For data processing and interpretation, GeneMapper v4.0 (Applera, USA) and BioNumerics v7 (Applied Maths, Belgium) software are used.
The service report provided to customers includes detailed technical information on the used restriction enzymes and primers and scientific conclusions of the analysis. Additionally, in a typing report dendrograms with digitized profiles constructed with BioNumerics software and/or comparisons constructed with GeneMapper software are included. The latter type of comparison is more suitable for making conclusions at the intraspecies level.
Cleenwerck I, De Wachter M, González Á, De Vuyst L & De Vos P. 2009. Differentiation of species of the family Acetobacteraceae by AFLP DNA fingerprinting and reclassification of Gluconacetobacter kombuchae as Gluconacetobacter hansenii. Int J Syst Evol Microbiol 59: 1771-1786. doi: 10.1099/ijs.0.005157-0
Vancanneyt M, Huys G, Lefebvre K, Vankerckhoven V, Goossens H, Swings J. 2006. Intraspecific genotypic characterization of Lactobacillus rhamnosus strains intended for probiotic use and isolates of human origin. Appl Environ Microb 72:5376-5383. doi: 10.1128/AEM.00091-06