, 2011). The phylogenetic composition of the extracted DNA in relation

to the original bacterial community has however received less attention. One major problem in assessing this is the fact that it is very difficult to know the true community composition. In two recent studies, it was shown that a mechanical bead-beating step during cell lysis resulted in increased complexity of extracted DNA as evidenced by an increased number of distinct bands in PCR-DGGE profiles (Ariefdjohan et al., 2010; Smith et al., 2011). The fact that different extraction procedures performed on the same fecal sample may lead to different estimations of the bacterial community composition is not surprising, but may well be disturbing for comparisons between separate studies. Within a study, it is most probable that the same DNA see more extraction method be used throughout; however, other parameters that may affect extraction, such as storage conditions of fecal samples, may vary. It is for instance common practice, mainly for practical reasons, to freeze fecal samples immediately after sampling and then collectively extract the DNA and perform downstream analysis such as sequencing or qPCR, at some later stage (Mariat et al., 2009; Santacruz et al., 2009). In this study, the effect of freezing fecal samples prior to DNA extraction was evaluated for alterations in DNA

recovery and bacterial community composition as determined by downstream quantitative PCR analysis. Fecal samples were obtained from three healthy adult volunteers (two women, one man), homogenized thoroughly in four volumes diluent (0.85% NaCl, 0.1% peptone), selleckchem centrifuged at 300 g for 2 min to remove large debris, and finally 0.5 mL of aliquots (average 8 mg dry weight) were pelleted at 10 000 g for 5 min (Fig. 1). Extraction of DNA was performed immediately with three different extraction methods (five replicates), or samples were frozen at −20 °C for 53 ± 5 days (F) prior to extraction.

Methods used for DNA extraction were M: PowerSoil® DNA Isolation kit (MO BIO Laboratories, Carlsbad), Q: QIAamp DNA Stool Mini Kit (QIAGEN, Hilden, Germany), and B: Modified QIAamp DNA Stool Mini Kit extraction procedure with the incorporation of a bead-beating step to potentially improve Atazanavir cell lysis (Leser et al., 2000). Briefly, bead-beating was performed by adding 500 μL autoclaved 0.1 mm zirconia silica beads (Biospec Products Inc., Bartlesville, OK) and 30 μL of 10% sodium dodecyl sulfate and processing for 4 min. at 30 cycles per second on a Mixer Mill MM 300 (Retsch GmbH, Haan, Germany). Extractions were performed as directed by the suppliers with minor modifications, including standardized initial sample size and elution in 200 μL, 10 mM Tris, to allow better comparison of the methods. For extractions with method M, bacterial cells were treated in a Mixer Mill MM 300 (4 min at 30 cycles per second) and not the suggested Vortex adaptor.