Table 2.
Characteristics of mechanical pretreatment according to the DNA pretreatment/extraction protocol used by each participating center.
| Participating Center | Center 1 | Center 2 | Center 3 | Center 4 | Center 5 | |
|---|---|---|---|---|---|---|
| Abbreviated Name of DNA Extraction System | EM | IN | QF | QP | ZR | MPG |
| Commercial name of mechanical lysis matrix (company) |
Tube Lysing Matrix E® (MP Biomedicals) |
GB05® (Next Advance) in 1.5 mL polypropylene tube (Eppendorf) |
BeadTubes®, QIAamp PowerFecal DNA kit® (Qiagen) | R BashingBead Lysis Tube®, kit Quick DNA Fecal/Soil Microbe Microprep kit® (ZymoResearch) |
MagnaLyser Green Tubes® (Roche Diagnostics) |
|
| Diameter of beads | Mix of three types beads: −1.4 ± 0.2 mm ceramic spheres (64% ZrO2, 33% SiO2) −0.112 ± 0.038 mm silica spheres −one 4 mm glass bead |
0.5 mm | 0.7 mm | Mix of two types beads: 0.1 and 0.5 mm |
1.4 mm | |
| Chemical composition of beads | Glass beads | Garnet beads | ZR BashingBead TM: ultra-high density beads are fracture resistant, chemically inert | Ceramic beads | ||
| Duration of grinding | 1 min | 3 min | 10 min | 45 s | 1 min | |
| Speed of grinding | 6 m/s | 30 Hz (1800 oscillations/min) |
3200 rpm | 7000 rpm | 3500 rpm | |
| Homogenizer system (company) |
High-speed benchtop homogenizer FastPrep 24 (MP Biomedicals) |
High-speed benchtop homogenizer TissueLyser® II (Qiagen) |
Vortex homogenizer Vortex-Genie 2® (Scientific industries) |
High-speed benchtop homogenizer MagnaLyser® (Roche Diagnostics) |
||
| Lysis buffer (company) [volume] |
Nuclisens® easyMAG® Lysis buffer (bioMérieux) [1 mL] |
Nuclisens® easyMAG Lysis buffer (bioMérieux) [800 µL] |
PowerBead Solution QIAamp PowerFecal DNA kit (Qiagen) [750 µL] |
BashingBead Buffer®, Quick DNA Fecal/Soil Microbe Microprep kit (ZymoResearch) [750 µL] |
Bacterial Lysis Buffer (Roche Diagnostics) [500 µL] |
|
EM, Nuclisens® EasyMAG®, bioMérieux; IN, ELITE InGenius®; ELITechGroup; QF, QIAamp Fast DNA Stool Mini Kit®, Qiagen; QP, QIAamp Power Fecal DNA Kit®, Qiagen; ZR, Quick DNA Fecal/Soil Microbe Miniprep®, ZymoResearch; MPG, MagnaPure 96® with grinding, Roche Diagnostics.