Typing by DNA fingerprinting is a common tool used in bacterial biogeography and epidemiology studies. Several bacterial species can be differentiated in clonal lines associated to specific animal hosts . Single genetic differences between clonal lineages could be useful to determine the history of an infection or to find new possible borderline strains . Similarly, fingerprinting methods are frequently used to evaluate the global dispersal of environmentally relevant microbial species or lineages in a species , to correlate specific genotypes to a given environmental conditions  and to evaluate the endemicity of a given microbial type [5, 6].
Different DNA-based typing methodologies are now available and BOX-PCR is the most commonly used technique due to its simplicity, efficiency and low cost. This is a particular version of repetitive extragenic palindromic-PCR (rep-PCR)  that uses the BOX-A1R primer . BOX-PCR is a fingerprinting analysis based on the BOX dispersed-repeat motif, firstly identified in Streptococcus pneumoniae, but common in a number of bacterial species [9–11]. Since the BOX repetitive sequences are interspersed throughout the genome, BOX-PCR is a method potentially capable of simultaneously surveying many DNA regions scattered in the bacterial genome. It has been shown to have similar or even better strain differentiation power, as well as to be easier to perform, than ribosomal intergenic spacer analysis (RISA), restriction fragment length polymorphism (RFLP), amplified fragment length polymorphism (AFLP), random amplified polymorphic DNA (RAPD) and other techniques [12–14]. BOX-PCR is quicker, cheaper, and in many cases more discriminatory than pulsed field gel electrophoresis (PFGE) , despite is generally less reproducible. BOX-PCR patterns are not affected by the culture age of the strain to be analyzed  and fingerprinting output can be easily analyzed by computer assisted methods . These features make BOX-PCR a frequently used tool in biogeography studies in environmental microbiology [5, 17–20].
The current BOX-PCR technique, in which the amplified products are separated by agarose gel electrophoresis, suffers from several limitations like poor band resolution and run standardization for comparison of the different profiles in different gels. To overcome these limitations separation of fluorescent labelled products in automated DNA sequencer can be used , but this interesting improvement has been applied rarely in environmental analysis and limited to machines performing separation in long polyacrylamide gels [21, 22].
In this study we show that fluorescent BOX-PCR (F-BOX-PCR), in which the separation of PCR products is performed in an Abi-Prism 310 capillary electrophoresis system, is capable of resolving endemicity and the biogeographical repartition of different bacterial populations. We first assessed suitability and reproducibility of different electrophoretic runs of different F-BOX-PCR reactions prepared from independent extractions of DNA from eight bacterial strains exhibiting different G+C content. The power of F-BOX-PCR in resolving bacterial endemicity was assessed on a collection of Modestobacter multiseptatus strains isolated from three different microsites of an altered ancient carbonatic wall in the old city of Cagliari, Sardinia, Italy . Biogeographic segregation of different bacterial populations was tested on a collection of 45 strains of Streptococcus thermophilus isolated from the Caucasian home-made yogurt-like product Matsoni produced in different areas of the Georgian Caucasus .