The brush was removed and discarded. The sample in 80% ethanol was divided evenly into 2 sterile Corex® tubes and centrifuged in a refrigerated Sorvall SS-34 rotor at 16,000 × g for 30 min. Following centrifugation, supernatants were discarded. One pellet was suspended in 5 ml of ice-cold 80% ethanol and Selleck XMU-MP-1 archived at -20°C. The second pellet beta-catenin inhibitor was suspended in 1 ml phosphate buffered saline (PBS) for DNA extraction. Approximately 0.25 ml of the sample was added to each of 4
MoBio PowerBead tubes. The samples were shaken vigorously in a Bead Beater (BioSpec Products, Bartlesville, OK) for 1.5-2 min at 4°C, and then extracted according to manufacturer’s instructions. After purification, the concentration of community DNA was determined spectrophotometrically using a Nanodrop (Thermo Scientific, Wilmington, DE). Selleck MK-8776 Fifty percent of the yield was immediately archived at -80°C; the remaining DNA was used for polymerase chain reaction (PCR) amplification and 454 pyrosequencing. 454 pyrosequencing For 454 Flx sequencing, community template DNAs were amplified with primers designed by the Ribosomal Database Project (RDP) at Michigan State University . The forward primer contains the Flx-specific terminal sequence (5′-GCCTCCCTCGCGCCATCAG-3′)
followed by a six base tag and then the 16S rRNA-specific 3′ terminus of the composite primer (5′-AYTGGGYDTAAAGNG-3′). The reverse primer was composed of four variants targeting the same 16S rRNA region to maximize coverage of the database (R1 = /5′/TACNVGGGTATCTAATCC; R2 = /5′/TACCRGGGTHTCTAATCC; R3 = /5′/TACCAGAGTATCTAATTC; R4 = /5′/CTACDSRGGTMTCTAATC). The 3′ terminus of the forward primer is at E. coli position 578 and Pyruvate dehydrogenase the 3′ terminus of the reverse primer is at position 785. Pilot scale (25 μl) PCR reactions for optimization were followed by 2-3 preparative 50 μl amplification
reactions. High fidelity Taq (Invitrogen Platinum) was used with MgSO4 (2.5 mM), the vendor supplied buffer, BSA (0.1 mg/ml), dNTPs (250 μM) and primers (1 μM). A three minute soak at 95°C was followed by 30 cycles of 95°C (45 s), 57°C (45 s) and 72°C (1 min) with a final 4 min extension at 72°C. PCR products were agarose gel purified (2% metaphor in TAE) and bands were extracted with a QIAquick Gel Extraction Kit (Qiagen, Valencia, CA). Gel extracted material was further purified with a Qiagen PCR Cleanup kit. Quantification of purified PCR product was with PicoGreen using Qubit (Invitrogen, Carlsbad, CA). The PCR products from 20 to 40 samples were combined in equal mass amounts and loaded into a Roche GS Flx system using vendor specified chemistries. Sequence analysis tools All sequences derived from 454 Flx sequencing were processed through the RDP pyrosequencing pipeline [15–17]. Initial processing included screening and removing short reads (those lacking both primer sequences) and low quality reads (any with errors in the primer sequence).