For the rapid fingerprinting protocol, preparation of DNA from single colonies was carried out as follows. A sterile 200 μl plastic pipette tip was inserted into a single freshly grown (no longer that 72 hours of plate growth) bacterial colony, resuspended into 50 μl of sterile 5% Chelex® 100 resin solution (Sigma-Aldrich, Gillingham, UK), and then plated onto MRS agar to provide

a pure reference culture. The DNA extraction tubes were stored frozen at -20°C prior to the extraction of DNA for PCR. After thawing, the samples were boiled for 5 min and immediately placed on ice for a further 5 min; this heating and cooling cycle was repeated once to extract DNA. The resin was removed by brief centrifugation and 2 μl of the clear supernatant DNA solution used for the RAPD EPZ015666 clinical trial PCR. PCR fingerprinting SBI-0206965 nmr was carried out using a procedure that was modified from that described

[13]. RAPD primers 201 to 300 (10 μg aliquots) were purchased from the Nucleic Acid Protein Service Unit at the University of British Columbia, Vancouver, Canada http://​www.​michaelsmith.​ubc.​ca/​services/​NAPS/​. The primers that were found to be appropriate for LAB typing (272, 277 and 287; Table 1) were subsequently ordered individually in bulk from MWG Biotech (Covent Garden, London), dissolved as stocks in water at 100 pmol/μl and stored frozen. All PCR reagents were purchased from Qiagen Ltd. (Crawley, UK) and routine fingerprinting was carried out in a 25 μl reaction mixture containing: 2.5 μl PCR buffer, 5 μl Q-solution, 1.5 μl 25 mM MgCl2 (3 mM final concentration), 0.5 μl 10 mM dNTPs mixture (200 μM final concentration), 4 μl of 10 pmol/μl stock of RAPD primer, 2 μl of template DNA (approximately 40 ng) and 0.2 μl (1 unit) of Taq DNA polymerase. The PCR thermal cycles were carried out on a Flexigene Thermal Cycler (Techne Ltd., Newcastle, United Kingdom) as follows (ramping time before between temperatures): (i) 4 cycles of 94°C for 5 min., 36°C for 5 min. (70 sec. cooling time), and 72°C for 5 min. (70 sec. heating time), (ii) 30 cycles of 94°C for1 min. (55 sec. to heat from 72°C), 36°C for 1 min. (60 sec to cool), 72°C for 2 min. (70 sec.

to heat); and (iii) a final extension of 72°C for 6 min. followed by a hold at 4°C indefinitely. All reference LAB strains (Table 2) were typed in duplicate and the type strain L. acidophilus LMG 9433T was also used as an internal reproducibility control throughout all RAPD analysis, with multiple repeats performed to ensure RAPD typing was reproducible. Fingerprint profiles were separated by standard gel electrophoresis [13] using 1.5% high resolution agarose gels (Sigma-Aldrich, Poole UK). RAPD fingerprints were analysed using computer software (Gel Compar II, Appied Maths, Sint-Martens-Latem, Belgium) and fingerprint profiles compared by calculation of the Dice coefficient and clustering using the unweighted pair-group method average (UPGMA); isolates with RAPD fingerprint Dice coefficients greater than 0.