The pellet was resuspended in 180 μl of enzymatic lysis buffer (20 mM Tris–HCl, pH 8, 2 mM EDTA, 1.2% Triton X-100, 20 mg/ml lysozyme) and incubated at 37°C for 30 min. Glass beads (200 mg) were added and the sample was mixed by vortexing for 1 min. Total DNA was extracted CB-839 by using the DNeasy Blood & Tissue Kit (Qiagen, Hilden, Germany) following the protocol “Pretreatment for Gram-positive bacteria”. A slight modification was introduced: a centrifugation step (8000 × g for 5 min) was carried out after incubation with proteinase K to remove glass beads. DNA amounts were quantified by using NanoDrop 1000 (Thermo Scientific, Wilmington, DE). PCR-DGGE and cluster analysis Amplification reactions were performed

in a Biometra Thermal Cycler T Gradient (Biometra, Göttingen, Germany). GoTaq Flexi DNA find more Polymerase (Promega, Madison, WI) was used as thermostable DNA polymerase. The reaction mixture contained 0.5 μM of each primer, 200 μM of each dNTP, 2 mM MgCl2 solution, 1.25 U of GoTaq Flexi DNA Polymerase, 5 μl of Green GoTaq Flexi buffer 5X, and 2 μl of the bacterial DNA template

(30–40 ng) in a final volume of 25 μl. The universal primers HDA1-GCclamp and HDA2 for bacteria [39] were used to amplify a conserved region within the 16S rRNA gene. The thermocycle program consisted of the following time and temperature profile: 95°C for 5 min; 30 cycles of 95°C for 30 s, 56°C for 30 s, 72°C for 60 s; and 72°C for 8 min. The Lactobacillus genus-specific primers Lac1 and Lac2-GCclamp [40] were used to amplify a specific region of the 16S rRNA gene of lactobacilli. The amplification program was 95°C for 5 min; 35 cycles of 95°C for 30 s, 61°C for 30 s, 72°C for 60 s; and 72°C for 8 min. A volume of 8 μl of PCR samples was loaded on DGGE gels, containing 30-50% and 25-55% gradients of urea and formamide for universal bacteria and lactobacilli, respectively. DGGE analysis was performed by using the D-Code Universal Mutation System Apparatus (Bio-Rad, Los Angeles, CA), as previously described [22]. Following electrophoresis, gels were silver

stained [41] and scanned using a Molecular Imager Gel Doc XR System (Bio-Rad). DGGE gel images were analyzed using the FPQuest software version 4.5 (Bio-Rad). In order to compensate for gel-to-gel differences and external distortion to electrophoresis, Urocanase the DGGE patterns were aligned and normalized using an external reference marker. The marker for the DGGE analysis with the universal primers for bacteria contained PCR amplicons from Bacteroides, Coriobacterium, Enterococcus faecalis, Bifidobacterium bifidum, Lactobacillus casei, Acidaminococcus fermentas and Atopobium. The marker for the DGGE analysis with Lactobacillus-specific primers contained PCR amplicons from L. plantarum, L. paracasei, L. brevis, L. gasseri, L. acidophilus and L. delbrueckii subsp. bulgaricus. After normalization, bands were defined for each sample using the appropriate densitometric curve.