The gradient was disassembled into %G+C fractions with 5 G+C% intervals PND-1186 in vitro using perfluorocarbon (fluorinert) as a piston. In the procedure, the highest %G+C fraction is collected last, exposing it to the most turbulence. The DNA quantification during the dismantlement was based on A280, as described by Apajalahtiand

colleagues [41], to avoid background. The DNA fractions were desalted with PD-10 columns according to the manufacturer’s instructions (Amersham Biosciences, Uppsala, Sweden). For the unfractioned DNA sample, faecal microbial DNA of the same healthy individuals was pooled (n = 22; there was an insufficient amount of faecal DNA left for one of the individuals). Amplification of the 16S rRNA genes, cloning and sequencing The 16S rRNA gene from each of the seven DNA fractions was amplified, cloned and sequenced, as in the study by Kassinen and colleagues [21]. To maximize the recovery of different phylotypes, two

universal primer pairs were used independently for all samples. The first primer pair corresponded to Escherichia coli 16S rRNA gene positions 8–27 and 1492–1512, with Sotrastaurin clinical trial sequences 5′-AGAGTTTGATCCTGGCTCAG-3′ [42] and 5′-ACGGCTACCTTGTTACGACTT-3′ [43], respectively. The second primer pair corresponded to E. coli 16S rRNA gene positions 7–27 and 1522–1541, with sequences 5′-GAGAGTTTGATYCTGGCTCAG-3′ and 5′-AAGGAGGTGATCCARCCGCA-3′ [44], respectively. The 50-μl PCR reactions contained 1 × DyNAzyme™ Buffer (Finnzymes, Espoo, Finland), 0.2 mM of each dNTP, 50 pmol of primers, 1 U of DyNAzyme™ II DNA Polymerase Napabucasin cost (Finnzymes, Espoo, Finland), 0.125 U of why Pfu DNA polymerase (Fermentas, Vilnius, Lithuania) and 10 μl of desalted fractioned DNA template (containing less than 2 ng/μl of DNA) or pooled extracted DNA from the faecal samples. The thermocycling conditions consisted of 3 min at 95°C, followed by a variable number of cycles of 30 s at 95°C, 30 s at 50°C, 2 min at 72°C and a final extension of 10 min at 72°C. The number of PCR cycles used for each fraction was optimized to the minimum amount of cycles which resulted in a visually detectable band of the PCR product on ethidium bromide stained agarose gel. A protocol of 27, 20, 25 and 30 cycles

was applied to %G+C fraction 25–30, 30–60, 60–65 and 65–75, respectively. The 16S rRNA gene from the unfractioned pooled faecal DNA sample was amplified using 20 PCR cycles. The amplifications were performed using 15 reactions, and the products were pooled, concentrated using ethanol precipitation, and eluted with 50 μl of deionized MilliQ water (Millipore, Billerica, MA, USA). The precipitated PCR products were purified with the QIAquick PCR Purification Kit (Qiagen, Hilden, Germany), or using the QIAquick Gel Extraction Kit (Qiagen, Hilden, Germany) after excising from 1.25% SeaPlaque agar (Cambrex, East Rutherford, NJ, USA), and eluted in 35 μl of elution buffer. The concentration of the purified amplicons was estimated with serially diluted samples on 0.