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Table 1 in vitro biofilm analyses parameters used in this study to test reproducibility

From: An in vitrobiofilm model system maintaining a highly reproducible species and metabolic diversity approaching that of the human oral microbiome

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
  1. CDM, chemically defined medium; DGGE, denaturing gradient gel electrophoresis; WGS, whole genome shotgun.