Bacterial metatranscriptome analysis of a probiotic yogurt using an RNA-Seq approach

We describe one of the first metatranscriptome analyses of a probiotic-containing yogurt using an RNA-Seq approach. The mRNA from three yogurt samples, representing two different flavors and two time points for one flavor, was extracted and sequenced with the ABI SOLiD 4 sequencing platform. To help understand the molecular basis for survival of these organisms in fermented milk, the highly expressed genes were functionally annotated and analyzed. The most highly expressed genes across all samples belonged to categories of protein translation, carbohydrate transport and metabolism, and amino acid transport and metabolism. Differential mRNA abundance was compared for flavor and storage time for organisms with high sequencing coverage. In all organisms, protein metabolism, and more specifically ribosomal protein components, were the most represented in differentially expressed mRNA transcripts between flavors and storage time comparisons. Further analysis showed that the probiotic strain was capable of adapting to its environment.