[Frontiers in Bioscience 14, 1362-1386, January 1, 2009]

Genomic features of Lactobacillus species

Yong Jun Goh, Todd R. Klaenhammer

Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC 27695

TABLE OF CONTENTS

1. Abstract
2. Introduction
3. Genome overview
3.1. Genome statistics
3.2. Metabolic and biosynthetic capabilities
4. Genome feature highlights and functional genomics
4.1. Environmental response and adaptation
4.1.1. Transcriptional regulation
4.1.2. Acid stress response and adaptation
4.1.3. Osmotic and oxidative stress responses
4.1.4. Bile stress response and tolerance
4.2. Interaction with the environments: cell surface factors
4.3. Polysaccharides biosynthetic gene clusters
4.4. Metabolism of unusual carbohydrates
4.5. Bacteriocin biosynthesis and immunity
4.6. Oxalate catabolism
5. The Lactobacillus mobilome
6. Comparative genomics
7. Genome evolution and diversity
8. Future perspective
9. Acknowledgments
10. References

1. ABSTRACT

As member of the lactic acid bacteria (LAB), the genus Lactobacillus represents a diverse number of species that play significant roles in the biopreservation of foods and commensals common within the human gastrointestinal (GI) tract. Certain species of Lactobacillus, particularly those of human origin, have been used as probiotic bacteria due to their health-promoting effects. A recent explosion of genomic information on lactobacilli has expanded our knowledge of metabolic capabilities and key gene features that are predicted to play important roles in niche adaptation and function. This review provides an overview of probiotic-related genome features and functional genomic studies that have linked genes to traits. Interspecies heterogeneity and niche-specialized adaptation among lactobacilli, as revealed by comparative genome analysis, are also discussed.