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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.