Chapter 1
Molecular Methods in Microbial Ecology
Erwin G. Zoetendal and Roderick I. Mackie
It is now generally accepted in microbial ecology that cultivation-based approaches provide an incomplete picture of microbial diversity in the gastrointestinal (GI) tract because only a minority of microbes can be obtained in culture. Therefore, the application of molecular approaches, especially those focused on 16S ribosomal RNA (rRNA) sequence diversity, have become popular as they enable researchers to bypass the cultivation step. These approaches have provided considerable information about microbial ecosystems, including the GI tract. This chapter will summarize the different approaches and their impact on our knowledge of the ecology of the GI tract and provide guidelines for future research directions with a focus on pre- and probiotics.
Chapter 2
Taxonomy of Lactobacilli and Bifidobacteria
Franco Dellaglio and Giovanna E. Felis
The genera Lactobacillus and Bifidobacterium contain a large number of species and strains that exhibit important properties in an applied context, especially in the area of food and probiotics. An updated list of species belonging to those two genera, their phylogenetic relationships and other relevant taxonomic information is reviewed in this chapter. The conventional nature of taxonomy is explained, and some basic concepts and terms will be presented for readers who are not familiar with this important and fast-evolving area, the importance of which is often underestimated. It is explained that the analysis of biodiversity and its cataloguing, i.e. taxonomy, constitutes the basis for applications and scientific communication: reliable identification and correct naming of bacterial strains are not only the primary aims of taxonomic studies but also fundamental elements in an applied context for the tracking of probiotic strains and non-fraudulent labelling of fermented milks and pharmaceutical products containing probiotic microorganisms. A number of freely available resources have been listed, and their use is suggested for people concerned with different aspects of taxonomy. Some perspectives in taxonomy have been outlined, in particular considering the role of culture-independent analyses to reveal the still unknown and uncultured microorganisms. Finally, the impact of the availability of whole-genome sequences in taxonomy is briefly explained; these sequences are expected to give insights into bacterial evolution, which will surely have implications for taxonomy even if the analysis of data for lactic acid bacteria is at only its very beginning.
Chapter 3
The Microecology of Lactobacilli in the Gastrointestinal Tract
Jens Walter
The majority of studies on intestinal lactobacilli, especially in the last two decades, have been focused on the behaviour of lactobacilli introduced into the gastrointestinal tract as probiotics and their in vitro characterization. Research on the ecology of lactobacilli naturally present within the complex gastrointestinal microbiota of humans and animals has received much less attention but is a crucial aspect of probiotic research and development. Molecular technologies have facilitated detection and identification of lactobacilli and allowed insight into the occurrence, diversity and dynamics of intestinal Lactobacillus populations. Animal models in combination with biochemical and genetic approaches have been used to reveal the influence of lactobacilli on the host, on microbiota-associated characteristics and on other members of the gut microbiota as well as to identify some bacterial factors that contribute to the ecological performance of lactobacilli in the gut. Functional and comparative genomics have already been carried out for some Lactobacillus strains in order to identify features essential for gut colonization and hostmicrobe co-existence. Research to decipher these ecological interactions is rewarding because it not only increases fundamental knowledge about the gut ecosystem and bacterial physiology in relation to host welfare but also provides valuable information to select lactobacilli for probiotics and other pharmaceutical applications.
Chapter 4
Exopolysaccharide Production by Intestinal Lactobacilli
Michael G. Gänzle and Clarissa Schwab
Lactobacilli produce a broad range of homopolysaccharides through the activity of extracellular glycosyltransferases. Polymers from lactobacilli include levan- and inulin-type fructans and the a-glucans dextran, mutan and reuteran. Fructan and glucan production are generally associated with the formation of fructo-oligosaccharides (FOS) and glucose oligosaccharides respectively. In lactobacilli, homopolysaccharide and oligosaccharide production is most frequently found in those species that are associated with gastrointestinal ecosystems, for example Lactobacillus acidophilus, Lactobacillus johnsonii, Lactobacillus mucosae and Lactobacillus reuteri. In the past years, several glycosyltransferases of lactobacilli were characterized on the molecular and biochemical level. In this chapter, an overview is provided on the genetics and biochemistry of homopolysaccharide production by lactobacilli, and emerging concepts concerning the ecological significance of glucan and fructan production by intestinal lactobacilli are discussed.
Chapter 5
Beyond Genome Sequences: Approaches to Genome-wide Analysis of Gut Bacteria
Makda Fisseha and Fabrizio Arigoni
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 beneficialı 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.
Chapter 6
Molecular Interactions of Commensal Enteric Bacteria with the Intestinal Epithelium and the Mucosal Immune System: Implications for Chronic Intestinal Inflammation
Dirk Haller
No abstract provided by the author.
Chapter 7
Genetically Modified Probiotics
Lothar Steidler and Sabine Neirynck
The intestinal microbiota is a key component of both the metabolism and immunity of humans and animals. It is therefore not surprising that proficient use of selected strains isolated from this ecosystem has led to a variety of microbiological products. These can be helpful in healthcare, especially for the management of digestive diseases and food-borne illnesses. The knowledge boom both in immunity and in the mechanisms by which infectious agents are active has led to the identification of key regulatory molecules and circuits that can drive health or disease. Through genetic engineering it became possible to fully express biologically active copies of such powerful molecules from food and commensal bacteria. Many aspects of genetically modified (GM) probiotics now lead to the belief that these have the potential to fill the existing gap in the probiotic activity spectrum. If designed carefully, and with absolute attention for biological safety in its broadest sense, the development of GM probiotics has the potential to revolutionize medicine.
Chapter 8
Bacterial Therapeutics for the Treatment and Prevention of Urogenital Infections
Thomas P. Parks, Qiang Xu, Laurel A. Lagenaur and Peter P. Lee
The microbiota of the healthy human vagina is dominated by Lactobacillus species, which play an important role in protecting the host from urogenital infections. Disruption of the Lactobacillus-dominated microbiota can lead to abnormal vaginal microbial communities associated with bacterial vaginosis, and an increased incidence of urinary tract infection (UTI). In addition, epidemiological studies suggest that the normal vaginal microbial ecosystem may play a critical role in reducing the risk of sexually transmitted infections, including human immunodeficiency virus type 1 (HIV-1). This chapter will focus on the role of lactobacilli in the vaginal ecosystem and the rational use of these bacteria as therapeutic agents for the treatment and prevention of urogenital infections.
Chapter 9
Prebiotics and the Infant Microbiota
L.C. Roger and A.L. McCartney
It has long been established that there is a distinction between the gastrointestinal microbiota harboured by breast- and formula-fed infants. Although microbiological methodologies, infant formulae and the general health status of the community have all improved vastly over the last century, recent studies using modern molecular techniques have confirmed that there are differences in the faecal microbiota of exclusively milk-fed infants (depending on feeding regime). Molecular-based analysis has also highlighted the complexity of this bacterial ecosystem, with inter-individual and intra-individual variations observed, both within and across feeding groups. Coupled with the recognized health and well-being associated with breast-fed infants, the predominance of the bifidobacterial group has fuelled much interest in dietary interventions (or formulae fortifications) to modulate the composition of formula-fed infantsı faecal microbiota. The limited clinical data available to date are very promising, with clear evidence of the ability to use prebiotics in infant formulae to elicit a microbiota better resembling that seen in breast-fed infants. However, the long-term effects and health impact are yet to be elucidated.
Chapter 10
The Tangled Bank and Gut Microbial Ecology
Gerald W. Tannock
No abstract provided by the author.
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