Table 1.
in vitro biofilm analyses parameters used in this study to test reproducibility
| Goal | Samples and number of replicate wells | Incubation conditions prior to DNA extraction | Community profile technique |
|---|---|---|---|
| Address batch and well reproducibility |
Batch 1 × 1 |
Step I: 16 hrs growth in SHI medium |
16S-454 pyrosequencing |
| Batch 2 × 2 | |||
| Batch 3 × 3 | |||
| Saliva × 3 |
Step II: 2 hrs starvation in CDM |
||
| No incubation | |||
| Address reproducibility between research laboratories |
With sucrose × 2 without sucrose × 2 |
16 hrs growth in SHI medium with or without sucrose |
DGGE |
| Address temporal taxonomic diversity during biofilm development | Time course (hrs) = 3,6,9,12,16,48 | 48 hrs growth in SHI medium | WGS metagenomes Illumina HiSeq |
CDM, chemically defined medium; DGGE, denaturing gradient gel electrophoresis; WGS, whole genome shotgun.