Background: Small untranslated RNAs (sRNAs) seem to be far more abundant than previously believed. The number of sRNAs confirmed in E. coli through various approaches is above 70, with several hundred more sRNA candidate genes under biological validation. Although the total number of sRNAs in any one species is still unclear, their importance in cellular processes has been established. However, unlike protein genes, no simple feature enables the prediction of the location of the corresponding sequences in genomes. Several approaches, of variable usefulness, to identify genomic sequences encoding sRNA have been described in recent years.

Lactococcus lactis is used extensively for the production of various cheeses. At every stage of cheese fabrication, L. lactis has to face several stress-generating conditions that result from its own modification of the environment as well as externally imposed conditions. We present here the first in situ global gene expression profile of L. lactis in cheeses made from milk concentrated by ultrafiltration (UF-cheeses), a key economical cheese model. The transcriptomic response of L. lactis was analyzed directly in a cheese matrix, starting from as early as 2 h and continuing for 7 days. The growth of L. lactis stopped after 24 h, but metabolic activity was maintained for 7 days. Conservation of its viability relied on an efficient proteolytic activity measured by an increasing, quantified number of free amino acids in the absence of cell lysis. Extensive downregulation of genes under CodY repression was found at day 7. L. lactis developed multiple strategies of adaptation to stressful modifications of the cheese matrix. In particular, expression of genes involved in acidic-and oxidativestress responses was induced. L. lactis underwent unexpected carbon limitation characterized by an upregulation of genes involved in carbon starvation, principally due to the release of the CcpA control. We report for the first time that in spite of only moderately stressful conditions, lactococci phage is repressed under UF-cheese conditions. Lactic acid bacteria, particularly Lactococcus lactis, have a long history of use in milk fermentation, from small-scale traditional operations to well-controlled industrial applications. Recent developments of molecular tools have unraveled the genetics, physiology, and metabolism of this economically very important microorganism. However, interpretation has always been limited by the lack of knowledge regarding in situ bacterial physiology. Technological properties (e.g., acidification, proteolytic or lipolytic activity, and bacteriocin production) can easily be shown and quantified in vitro but have hardly ever been verified in a complex solid matrix, due to local intrinsic factors. There have been several successful attempts to measure the DNA and rRNA extracted directly from a solid food (or environmental) matrix in order to estimate either the predominant species and/or the overall level of metabolic activity of the species (11,33). In a few cases, the expression of genes of technological interest from extracted mRNAs has been checked (42). The global gene or protein expression of L. lactis has been characterized in milk (15, 34) but not directly in cheese, the corresponding solid dairy matrix.Over the last few years, functional-genomics approaches, including transcriptomics, have been increasingly used to obtain global gene expression profiles, thereby providing a comprehensive view of microorganism physiology. So far, such global approaches in food microbiology and in situ have been poorly documented. Recently, Bachmann et al. presented the genetic responses of L. lactis in mixed cu...