About this Book

The economic importance of lactic acid bacteria (LAB) for the food industry and

their implication in health and disease has rendered them attractive models for

research in many laboratories around the world. Over the past three decades,

molecular and genetic analysis of LAB species provided important insights into the

biology and application of starter and probiotic LAB and in the virulence of LAB

pathogens. The knowledge obtained prepared LAB researchers for the forthcoming

opportunities provided by the advent of microbial genomics. Today, developments

in next-generation sequencing technologies have rocketed LAB genome research

and the sequences of several hundreds of strains are available.

This flood of information has revolutionized our view of LAB. First of all, a detailed

picture has emerged about the evolutionary mechanisms allowing LAB to inhabit

the very diverge ecological niches in which they can be found. Adaptation of LAB to

nutrient-rich environments has led to degenerative evolution processes that resulted

in shortening of chromosomes and simplified metabolic potential. Gene acquisition

through horizontal transfer, on the other hand, is also important in shaping LAB gene

pools. Horizontally acquired genes have been shown to be essential in technological

properties of starters and in probiosis or virulence of commensals. Progress in

bioinformatics tools has allowed rapid annotation of LAB genomes and the direct

assignment of genetic traits among species/strains through comparative genomics.

In this way, the molecular basis of many important traits of LAB has been elucidated,

including aspects of sugar fermentation, flavor and odor formation, production of

textural substances, stress responses, colonization of and survival in the host, cell-tocell

interactions and pathogenicity. Functional genomics and proteomics have been

employed in a number of instances to support in silico predictions. Given that the

costs of advanced next-generation methodologies like RNA-seq are dropping fast,

bottlenecks in the in silico characterization of LAB genomes will be rapidly overcome.

Another crucial advancement in LAB research is the application of systems biology

approaches, by which the properties and interactions of components or parts of a

biological system are investigated to accurately understand or predict LAB behavior.

Practically, systems biology involves the mathematical modeling of complex biological

systems that can be refined iteratively with wet-lab experiments. High-throughput

experimentation generating huge amounts of data on the properties and quantities

of many components such as transcripts, enzymes and metabolites has resulted

in several systems models of LAB. Novel techniques allow modelling of additional levels of complexity including the function of small RNAs, structural features of

RNA molecules and post-translational modifications. In addition, researchers

have started to apply systems approaches in the framework of LAB multispecies

ecosystems in which each species or strain is considered as a part of the system.

Metatransciptomics, metaproteomics and metametabolomics offer the means to

combine cellular behavior with population dynamics in microbial consortia.