Published Research

Journal :  in : PROBIOTICS AND PREBIOTICS : SCIENTIFIC ASPECTS, ED. G.W. TANNOCK, PUBL. CAISTER ACADEMIC PRESS, 2005, Chapter 5, pp. 97-128

Publication Name :  BEYOND GENOME SEQUENCES : APPROACHES TO GENOME-WIDE ANALYSIS OF GUT BACTERIA

Authors :  ARIGONI F., FISSEHA M.

Keywords :  ANALYSIS, BACTERIA, BIFIDOBACTERIUM, GASTROINTESTINAL TRACT, GENOME, INTERACTION, LACTOBACILLUS, MICROORGANISM, PATHOGEN

Summary :  The human gastrointestinal (GI) tract is a complex ecosystem that is composed of hundreds of different bacterial species that together play an important role in the physiology of their host. Understanding how different species of the gut microbiota interact with each other and how they individually or collectively contribute to our health remains a challenge for the future. One major difficulty is the definition and measurement of a healthy status and the correlation of this to the presence or absence of certain species within the GI tract, bearing in mind that the microbiota varies among individuals. A better understanding of the biology of the organisms found in the GI tract and of how they have adapted to co-exist and interact with their host will undoubtedly help us to appreciate the impact they have on human physiology. Here, we will review how genome sequencing of various gut-associated organisms has revealed the ways in which the microbiota have adapted to their specific environments, and we will highlight how genome analysis allows us to generate hypotheses about the molecular basis of the interplay between host and microbes. This will be illustrated with the recently completed genomes of microorganisms that can be detected in the human GI tract, namely Bifidobacterium longum NCC2705, Lactobacillus acidophilus NCFM, Bacteroides thetaiotaomicron VPI-5482, Lactobacillus johnsonii NCC533 and Lactobacillus plantarum WCFS1. Because many questions related to hostpathogen interactions are akin to those raised for beneficial microbes, we will discuss a number of functional genomics approaches that have been applied to the study of pathogens and that could also be relevant to the study of non-pathogenic bacteria found in the intestine. Finally, we will review the way in which genome-wide approaches have recently been used to identify Lactobacillus reuteri and L. plantarum genes induced in the mouse GI tract.



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