Genomics of LAB and dairy associated species

5.1. Introduction 5.2. Genomics of LAB species 5.2.1. Next Generation Sequencing of strains, dairy starter genomics 5.2.2. Pacific Bioscience single-molecule real-time sequencing technology. 5.2.3. Illumina MySeq and HiSeq 2000. 5.2.4. Ion Torrent platform 5.3. NGS platform applied to sequencing of microbial communities. Metagenomics. 5.3.1. Pangenomics 5.3.2. -Omic technologies: transcriptomics, proteomics, functional genomics, systems biology. 5.4. Metabolomics and proteomics 5.4.1. Subcellular localization (SLC). Secretion systems for secreted proteins 5.4.2. Interactome for cell adhesion and pathogen exclusion. 5.4.3. LAB peptidome 5.5. Comparative genomics of dairy associated bacteria. The Lactobacillus genus complex, Streptococci/Lactococci, Enterococci, Propionibacteria and Bifidobacteria 5.5.1. Comparative genomics of Lb. rhamnosus and Lb. casei 5.5.2. Lb. casei core genome and ecotype differences in dairy adapted strains. 5.6. Clustered Regularly Spaced Palindromic Repeats (CRISPR) in adaptive immunity 5.7. Regulation of carbon metabolism 5.7.1. Transcriptional and post-transcriptional regulation in carbon metabolism 5.7.2. Two-component systems and phosphorylation in sugar substrate regulation 5.7.3. Regulatory RNAs and alternative sigma factors in gene expression 5.8. Conclusions