FIG. 1.

Experimental design for the gene expression studies. Cells of L. reuteri ATCC 55730 were diluted into MRS broth at pH 2.7 or MRS broth at pH 5.1 and incubated for 5 or 15 min. Direct microarray comparisons were performed for both time points between untreated cells at time zero, acid-treated cells at pH 2.7, and the treated control cells at pH 5.1. Four biological replicates were performed for 5-min incubation, and three biological replicates were performed for 15-min incubation. The data were analyzed with an empirical Bayes approach with respect to the three parameters pH, time, and dilution (D). Genes primarily affected by dilution were excluded from further studies.