[Frontiers in Bioscience 14, 4673-4684, January 1, 2009] 4673 Bifidobacteria: from ecology to genomics Francesca Turroni 1 , Douwe van Sinderen 2 , Marco Ventura 1 1 Department of Genetics, Biology of Microorganisms, Anthropology and Evolution University of Parma, Italy, 2 Alimentary Pharmabiotic Centre and Department of Microbiology, Bioscience Institute, National University of Ireland, Western Road, Cork, Ireland TABLE OF CONTENTS 1. Abstract 2. Introduction 3. Bifidobacteria and ecology 4. Bifidobacteria and their role in the human gut 5. Bifidobacteria and health-promoting effects 5.1. Modulation of harmful intestinal microflora 5.2. Immune modulation 5.3. Allergic disease 5.4. Acute gastro-enteritis and diarrhoea caused by viral and bacterial infections 5.5. Lactose intolerance 5.6. Inflammatory bowel disease 5.7. Constipation 6. Genomics and bifidobacteria 7. Plasmids in bifidobacteria 8. Bifidobacteria and genetic adaptation to the human gut 9. Bifidobacteria and prebiotics 9.1. Fructo-oligosaccharides (FOS) 9.2. β-galactosidases 9.3. Arabinoxylan and arabinogalactan 9.4. α-Galacto-oligosaccharides and galactomannan 9.5. Starch 9.6. Mucin 10. Bifidobacterial genomics: biosynthetic and metabolic capabilities 11. Bifidobacteria genomics and host interactions 12. Functional genomics and bifidobacteria 13. Acknowledgments 14. References 1. ABSTRACT Bifidobacteria are high G+C Gram positive bacteria belonging to the phylum Actinobacteria. In recent years bifidobacteria have attracted a lot of attention because of their perceived positive contribution to the functionality of the human gastro intestinal tract. For this reason, scientific research on these bacteria has been rapidly expanding, in particular in areas such as genomics, molecular ecology and genetics. Ecological studies together with genome-based sequencing efforts have provided scientific evidence for the considerable contribution of bifidobacteria to the human gut microbiome. Furthermore, bifidobacterial genomics has revealed various genetic adaptations of these bacteria to the gastrointestinal niche. 2. INTRODUCTION Bifidobacteria represent high G+C Gram positive microorganisms belonging to the Actinobacteria phylum. The Bifidobacterium genus forms a coherent phylogenetic unit within the Actinobacteria as illustrated by the 16S rDNA sequences of its members, which share over 93% similarity (1). Notably, recent evidence from several taxonomic attempts (e.g. phylogenetic trees from concatenated sequences as well as from protein indel analyses) has demonstrated that bifidobacteria are related to the Micrococcineae order (e.g., Tropheryma, Leifsonia and Kinenococcus) where they form a deep branching lineage within the Actinobacteria phylum (2; 3).