Cluster analysis of the DGGE patterns was performed using the FPQ

Cluster analysis of the DGGE patterns was performed using the FPQuest software. Sequencing of DGGE fragment The DNA fragment of interest was excised from the denaturing gel with a sterile scalpel, washed once in 1X PCR buffer, and incubated in 20 μl of the same buffer overnight at 4°C. Two μl of the buffer solution were used as a template for PCR reaction. Reamplification of the 16S rRNA region was conducted

as described above by employing the primers Lac1 and Lac2 (without the GC-clamp). The re-amplified fragment was purified using the Wizard SV Gel and PCR Clean-up system (Promega), and then subjected to automated sequence analysis of both DNA strands with Lac1 and Lac2. BigDye terminators (ABI-PerkinElmer, Foster City, CA) were used with a 377 sequencer (ABI). Sequence identity was determined by comparison with the rRNA gene sequences deposited in GenBank database using BLAST algorithm (http://​www.​ncbi.​nlm.​nih.​gov/​BLAST). AR-13324 chemical structure Quantitative real-time PCR Quantitative PCR was performed in a LightCycler instrument (Roche, Mannheim, Germany) and SYBR Green I fluorophore was used to correlate the amount of PCR CBL0137 purchase product with the fluorescence

signal. Each DNA sample was amplified with different genus- or species-specific primer sets targeted to 16S rRNA gene or 16S-23S rRNA spacer region: Bact-0011f/Lab-0677r [42] for click here Lactobacillus, Bif164/Bif662 [43] for Bifidobacterium, Th1/Th2 [44] for Streptococcus thermophilus, F-GV1/R-GV3 [45] for Gardnerella vaginalis, c-Atopo-f/c-Atopo-r [46] for Atopobium, g-Prevo-f/g-Prevo-r [47] for Prevotella, VeilloF/VeilloR [48] for Veillonella. Amplifications were carried out in a final volume of 20 μl containing 0.5 μM of each primer, 4 μl of LightCycler-FastStart DNA Master SYBR Green I (Roche) and either 2 μl

of template or water (no-template control). The thermal cycling conditions were as PLEKHM2 follows: an initial denaturation step at 95°C for 10 min followed by 30 (Lactobacillus, Atopobium, G. vaginalis and Veillonella), 35 (Prevotella) or 40 (Bifidobacterium, S. thermophilus) cycles of denaturation at 95°C for 15 s; primer annealing at 63°C (Lactobacillus, S. thermophilus), 62°C (Veillonella), or 60°C (Bifidobacterium, Atopobium, Prevotella, G. vaginalis ) for 20 s; extension at 72°C for 45 s (Lactobacillus, Atopobium, Prevotella, G. vaginalis, Veillonella), 30 s (Bifidobacterium), or 15 s (S. thermophilus) and a fluorescence acquisition step at 85°C (Lactobacillus, Atopobium, G. vaginalis, Veillonella, S. thermophilus), 87°C (Prevotella) or 90°C (Bifidobacterium) for 5 s. DNAs extracted from L. acidophilus NCFM, B. longum NCC2705, G. vaginalis ATCC 14018, Prevotella bivia ATCC 29303, Veillonella parvula ATCC 10790, Atopobium vaginae ATCC BAA-55 and S. thermophilus ATCC 19258 were used as standards for PCR quantification.

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