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Annu. Rev. Microbiol. 2009.63:269-290. Downloaded from www.annualreviews.org by Universidad Autonoma de Coahuila on 01/25/13. For personal use only.

Probiotic and Gut Lactobacilli andBifidobacteria: Molecular Approaches to Study Diversity and Activity
Michiel Kleerebezem1,2,3 and Elaine E. Vaughan4
1

TI Food & Nutrition, 2 NIZO food research, 6710 BA Ede, The Netherlands; email: Michiel.Kleerebezem@nizo.nl

3

Laboratory for Microbiology, Wageningen University, 6703 HB Wageningen, The Netherlands Unilever Research & Development, 3133 AT, Vlaardingen, The Netherlands;email: Elaine.Vaughan@Unilever.com

4

Annu. Rev. Microbiol. 2009. 63:269–90 First published online as a Review in Advance on June 5, 2009 The Annual Review of Microbiology is online at micro.annualreviews.org This article’s doi: 10.1146/annurev.micro.091208.073341 Copyright c 2009 by Annual Reviews. All rights reserved 0066-4227/09/1013-0269$20.00

Key Words
Lactobacillus, Bifidobacterium, gutmicrobiota, prebiotic

Abstract
Lactobacilli and bifidobacteria have traditionally been recognized as potential health-promoting microbes in the human gastrointestinal tract, which is clearly reflected by the pre- and probiotic supplements on the market. Bacterial genomics of lactobacilli and bifidobacteria is initiating the identification and validation of specific effector molecules that mediatehost health effects. Combined with advanced postgenomic mammalian host response analyses, elucidations of the molecular interactions and mechanisms that underlie the host-health effects observed are beginning to be gathered. These developments should be seen in the complexity of the microbiota-host relationships in the intestine, which through the new metagenomic era has regained momentum and willundoubtedly progress to functional microbiomics and host response analyses within the next decade. Taken together, these developments are anticipated to dramatically alter the scope and impact of the probiotic field, offering tremendous new opportunities with accompanying challenges for research and industrial application.

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Contents
INTRODUCTION . . . . . . . . . . . . . . . . . . ECOLOGYOF PROBIOTIC/GUT LACTOBACILLI AND BIFIDOBACTERIA . . . . . . . . . . . . . . . Human Gut Microbiome Members . . . . . . . . . . . . . . . . . . . . . . . Metagenomic Insights . . . . . . . . . . . . . . FUNCTIONAL GENOMICS . . . . . . . . Genomics of Lactobacilli and Bifidobacteria . . . . . . . . . . . . . . . Adaptation to the Gut Niche . . . . . . . Probiotic Effector Molecules . . . . . . .MOLECULAR HOST RESPONSES . . . . . . . . . . . . . . . . . . . . . FUTURE PROSPECTS AND PERSPECTIVES . . . . . . . . . . . 270

271 272 273 274 274 277 278 281 282

INTRODUCTION
The probiotic potential of the intestinal and dairy species of lactobacilli and bifidobacteria was first researched over a hundred years ago. At that time the yearning to understand microbial ecology of these groups inthe human intestine was linked to the aspiration to manage and maintain human health. This subject still has a fascination for today’s researchers more than ever, stimulated by the same motivation to promote health as well as a genuine curiosity for the world we inhabit, and in this case, the world that inhabits us. The link between lactobacilli and human health was first proposed in the late 1800sby Metchnikoff, who devoted the last decade of his life to this research (35). Bifidobacteria were first isolated from human infant feces and described in the 1900s by Tissier (109, 110), and became associated with a healthy intestinal tract owing to their numerical dominance in human breastfed infants compared with formula-fed infants that suffered more diarrhea. In the twenty-first century,...