Total DNA was isolated using the PowerMag soil DNA isolation kit optimized for epMotion (catalog no. 27100-4-EP; MoBio, Carlsbad, CA) according to the manufacturer’s directions and adapted for a Biomek FXp lab automation workstation (Beckman Coulter, Brea, CA). The bacterial V3-V5 16S rRNA region was amplified using the bar-coded 357F/926R primer set as used by the Human Microbiome Project (HMP) Consortium 454 sequencing protocol as described previously (34 (link)). Samples were sequenced using 454 FLX Titanium chemistry according to the manufacturer’s directions (Roche Diagnostics, Brandford, CT). Raw sequences were placed in the NCBI Sequence Read Archive (SRA) under the associated BioProject ID, PRJNA238042.
Protocol detail
Automated Soil DNA Extraction and 16S Sequencing
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Corresponding Organization :
Other organizations : University of Michigan–Ann Arbor, Essentia Health, St. Luke's Hospital
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Variable analysis
independent variables
- Bacterial V3-V5 16S rRNA region
- Not explicitly mentioned
- Total DNA isolation using the PowerMag soil DNA isolation kit
- Adaptation of the Biomek FXp lab automation workstation
- Primer set (357F/926R) used by the Human Microbiome Project (HMP) Consortium 454 sequencing protocol
- 454 FLX Titanium sequencing chemistry
- Positive controls: Not explicitly mentioned
- Negative controls: Not explicitly mentioned
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