Therapeutic Microbiology: Probiotics and Related Strategies

2.1 The Indigenous Microbiota

• Chapter 2 : Role of the Indigenous Microbiota in Health and Disease

  Author: Gerald W. Tannock
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    This chapter focuses on the indigenous microbiota of the human large bowel, arguably the best-known ecosystem of the body. The study of microbial communities falls within the domain of microbial ecology—the study of the interrelationships that occur between populations within a community and between the community and the environment in which it is located. Microbial ecology is about how ecosystems work and therefore details the functions of populations, individually and collectively, in nature. The indigenous microbiota is a potent source of opportunistic infections that arise when the mechanisms that normally confine the microbes to a particular site are disrupted. Anaerobic infections following bowel surgery, urinary tract infections, chronic respiratory tract infections, dental/gingival diseases, and annoying skin conditions come into this category. Medical knowledge focuses on the pathogenesis of diseases and the derivation of intervention strategies. To understand health, one must learn about the mechanisms that operate in the healthy body by which stable ecosystems are sustained and maintained. Then, health might be guarded by reason, perhaps by interventions that would produce predictable outcomes on the basis of knowledge of molecular networks. Fortunately, the technological approaches to achieve these goals are at the fingertips of microbiologists: metagenomics to access and assess community genetics, and metabolomics to analyze functional attributes of the indigenous microbiota in concert with that of the host.

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2.2 Biology of Effector Organisms for Probiotic and Replacement Therapy

• Chapter 3 : Lactobacilli

  Author: Covadonga Barbés
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    This chapter discusses biology of effector organism such as lactobacilli for probiotic and replacement therapy. It talks about metabolism, nutritional requirements, natural habitats, and taxonomy of lactobacilli. The genus Lactobacillus has been studied extensively and is now a well-characterized genus in the lactic acid bacteria (LAB) group, which is composed of more than 100 recognized species. The genus is of interest for a number of reasons: its long history of safe use in the fermentation and preservation of traditional foods (dairy, meat, and vegetable products) and more recently its incorporation in functional probiotic foods, as well as its ubiquitous presence in human and animal microbiotas, especially in the gastrointestinal and genitourinary tracts (where it dominates the vaginal microbiota). However, the main interest is undoubtedly its role as a probiotic and as a biotherapeutic agent in some clinical situations. Lactobacillus spp. are among the most frequent and better characterized microorganisms used as a probiotic. Important considerations in the choice of a probiotic include safety, functional aspects, and technological aspects. Probiotics are being commercially developed for both human and animal consumption, especially in the poultry and aquaculture industries. Their application constitutes alternatives to antibiotics, as well as acting as prophylactics, in particular in the prevention of gastrointestinal infections. Some commercially probiotic products containing lactobacilli are listed in the chapter. The chapter talks about the use of lactobacilli in food, industrial, and medical applications.

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• Chapter 4 : Bifidobacteria: the Model Human Gut Commensal

  Authors: Marco Ventura, Francesca Turroni, Angela Ribbera, Elena Foroni, Douwe van Sinderen
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    This chapter discusses biology of bifidobacteria for probiotic and replacement therapy. Bifidobacteria were originally isolated from a breast-fed infant. Since then several species have been identified in the gastrointestinal tract (GIT) of mammals and insects. The availability of whole-genome sequences from bifidobacteria is extremely informative for the understanding of the processes underlying speciation and evolution in this genus as well as the adaptation to its specific habitat (e.g., the human intestine). Since bifidobacteria encounter a vast array of substrates in the GIT, information regarding their metabolic properties is crucial to formulate an optimal growth medium. Prebiotics are food substances which resist digestion in the proximal GIT and reach intact the distal region of the gut, where, besides their direct physiological effect, they also affect the GIT ecosystem by specifically stimulating the growth and activity of the probiotic components of the GIT microbiota (e.g., bifidobacteria), thereby eliciting a beneficial effect on the host’s health. Prebiotics are typically oligosaccharides that consist of a mixture of hexose oligomers with a variable extent of polymerization. The transmission of novel genes through horizontal gene transfer (HGT) is generally supported by vectors such as bacteriophages or plasmids which may become integrated into the bacterial chromosome. Generally, plasmids are rarely found in bifidobacteria. So far the majority of bifidobacterial plasmids have been identified within different B. longum biotype longum strains. The chapter ends with a discussion on taxonomy of bifidobacteria.

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• Chapter 5 : Saccharomyces spp.

  Authors: Xinhua Chen, Ciarán P. Kelly
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    This chapter focuses mostly on studies carried out using the commercial strain of Saccharomyces boulardii as effector organism for probiotic and replacement therapy. It first discusses history and taxonomy of Saccharomyces species. S. boulardii utilizes multiple mechanisms to exert its beneficial effects. The mechanisms of action of Saccharomyces spp. as probiotic agents discussed are interference with bacterial adhesion, inactivation of bacterial virulence factors, enhancement of the mucosal immune response, modulating host signaling pathways, strengthening of enterocyte tight junctions, and capacity to affect immune cell redistribution. A number of animal disease models have been used to study the mechanisms of action of S. boulardii organisms as well as their potential clinical applications. S. boulardii has been used for the treatment or prevention of a variety of diarrheal diseases, such as antibiotic-associated diarrhea (AAD), acute infectious diarrhea in adults and children, traveler’s diarrhea, diarrhea in human immunodeficiency virus-infected patients, C. difficile-associated disease, and inflammatory bowel diseases including both Crohn’s disease and ulcerative colitis. Next, the chapter presents a description of some clinical trials that have shown the efficacy of S. boulardii in different diseases. Finally, it talks about adverse effects of Saccharomyces probiotic use.

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• Chapter 6 : Streptococci as Effector Organisms for Probiotic and Replacement Therapy

  Authors: John R. Tagg, Jeremy P. Burton, Philip A. Wescombe, Chris N. Chilcott
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    This chapter examines the involvement of members of the genus Streptococcus as probiotics or as candidates for replacement therapy. Some researchers have turned to the development of replacement therapy strategies using relatively harmless indigenous streptococci as oral and nasopharyngeal probiotics, since (it is reasoned) these should have greater colonization potential than lactobacilli and bifidobacteria for these target tissues. The emphasis of the chapter is largely on current knowledge of the contribution of dedicated interbacterial inhibitors, the bacteriocins and bacteriocin-like inhibitory substances (BLIS), to the efficacy of streptococci as potential probiotics. It lists some of the practical factors such as safety, stability, formulation, colonization efficacy, and health benefits that may need to be taken into consideration when evaluating oral streptococcal probiotics. Acid resistance and adhesion to intestinal mucosa are desirable characteristics for traditional probiotics. For streptococcal probiotics targeting the oral cavity, acid tolerance is not a critical factor. Chronic multispecies bacterial infections of the oral cavity (e.g., dental caries, periodontal disease, and halitosis) are endemic, expensive to treat, and recalcitrant to conventional preventative protocols. These infections appear typically to be caused by the collective actions of more than one organism—the microbial community producing damage that individual microorganisms are probably incapable of inflicting. Intestinal probiotics are widely accepted for microbial population replacement and recolonization of the gastrointestinal tract, and a variety of beneficial strains are now inexpensively provided for the consumer.

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• Chapter 7 : Escherichia coli

  Author: Michael Schultz
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    This chapter on probiotic Escherichia coli focuses on the properties, underlying mechanisms, and clinical uses of Escherichia coli strain Nissle 1917 as this is the most widely used and studied strain. However, it also refers to important work that has been done using other E. coli strains. The enterobacterium E. coli can be extraintestinally pathogenic (e.g., uropathogenic), intestinally pathogenic (e.g., enteropathogenic or enterohemorrhagic), and nonpathogenic or commensal (e.g., probiotic). The probiotic E. coli strain Nissle 1917 was isolated in 1917 from a soldier who appeared to be protected from gastrointestinal infections causing severe diarrhea in many of his comrades. Since that time, EcN has been studied intensively, not only with a focus on its apparent clinical use but also with a view to understanding how it counteracts the pathogenic mechanisms underlying a number of diseases. Its uniqueness, not only among other E. coli strains but also among other probiotic microorganisms, is evident. While being the subject of research for many other indications, this strain seems to be particularly relevant as an alternative to mesalazine in the maintenance of remission of ulcerative colitis (UC) and has potential for the treatment of irritable bowel syndrome (IBS).

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• Chapter 8 : Formulation, Administration, and Delivery of Probiotics

  Author: Kasipathy Kailasapathy
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    The emergence of antibiotic-resistant bacteria and natural ways of suppressing the growth of pathogens has contributed to the growth of probiotic foods and nutraceuticals. Probiotic bacteria not only compete and suppress “unhealthy fermentation” in the human intestine but also produce a number of beneficial health effects of their own. The viability of probiotics has been both a marketing and a technological challenge for many processing industries. Viability during the shelf life of the product and survival in the gastrointestinal (GI) tract to populate the human gut are two important issues in health benefit provision by probiotics. Additionally, factors related to the technological and sensory aspects of probiotic food production are of importance since only by satisfying the demands of consumers can the food industry succeed in promoting the consumption of functional probiotic products in the future. In the past, microorganisms were immobilized or entrapped in polymer matrices for use in food and biotechnological applications. As the technique of immobilization or entrapment became refined, the immobilized cell technology has evolved into encapsulation of cells. Compared to immobilization/entrapment techniques, microencapsulation (ME) has many advantages. There are several methods of ME. However, technologies applied to probiotics are generally limited to gelling, spray-drying, spray-cooling, extrusion, and emulsions. Controlled release of bacteria is a critical benefit of ME. As clinical evidence of the beneficial effects of probiotics accumulates, the food, nutraceutical, and pharmaceutical industries will formulate new and innovative probiotic-based therapeutic products.

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2.3 Prebiotics and Functional Carbohydrates

• Chapter 9 : Introduction to Prebiotics

  Authors: Helena M. R. T. Parracho, Delphine M. Saulnier, Anne L. McCartney, Glenn R. Gibson
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    Most of our understanding of the human colonic microbiota is derived from studying the microbial contents of fecal samples, because it is impractical to access the human large intestine during normal digestion, and as an alternative, bacteria detected in feces are most representative of populations present in distal region of the intestine. The colonic microbiota is suggested to play an important role in protection against pathogens and has important trophic effects on intestinal epithelia and immune structure and function. This chapter discusses methods for monitoring the intestinal microbiota, including culture techniques and molecular-based techniques. An alternative approach to probiotics for intestinal microbiota modulation is the use of prebiotics. The best currently recognized prebiotics in Europe are fructooligosaccharides (FOS), galactooligosaccharides (GOS), and lactulose, which (except for lactulose) are legally classified as food or food ingredients. The majority of clinical trials with humans have focused on demonstrating their efficacy in increasing intestinal levels of bifidobacteria and sometimes lactobacilli in fecal samples of healthy subjects. The most documented and recognized effect of prebiotics is the promotion of the growth of beneficial bacteria in the colon.

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• Chapter 10 : Human Milk Oligosaccharides as Prebiotics

  Authors: Giovanni V. Coppa, Orazio Gabrielli
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    The characteristic composition of the intestinal microbiota of breast-fed neonates is due to the presence of particular substances in human milk. This chapter aims to identify the components that are able to promote the prebiotic effect in human milk, and is oriented towards modifying the composition of infant formulas in order to obtain an intestinal microbiota similar to that of breast-fed babies. It discusses history, synthesis, structure, metabolism of human milk oligosaccharides (HMO). No natural substances have the same biochemical composition as that of HMO, nor can they be synthesized in large quantities at acceptable prices. To overcome these problems, the industry has focused on the production of several carbohydrates, so-called nondigestible oligosaccharides (NDO), which, although having compositions different from those of HMO, are able to selectively stimulate the growth of bifidobacteria and lactobacilli in the colon, reproducing the prebiotic effects of HMO. In conclusion, data related to the use of NDO in infant formulas clearly show the efficacy of galactooligosaccharides (GOS)/inulin mixtures, the capacity of GOS to induce a bifidogenic effect, even if in only a small number of studies, and the positive effects of FOS at a concentration of 4.0 g/liter on the intestinal microbiota. It has been demonstrated that, due to the presence of resistant bonds in their molecules, NDO are able to exert a prebiotic effect. This further confirms that, because of their peculiar structure, HMO have a very significant role in modulating the intestinal microbiota of neonates.

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• Chapter 11 : Inulin-Type Fructans

  Authors: Jan Van Loo, Douwina Bosscher
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    Inulin-type fructans are the most extensively studied pre-biotic compounds with proven efficacy. As research progressed, three criteria that a food ingredient should fulfill before it can be classified as a prebiotic were accepted: first, it should be nondigestible and resistant to gastric acidity, hydrolysis by intestinal (brush border/pancreatic) digestive enzymes, and gastrointestinal absorption; second, it should be fermentable; and third, it should, in a selective way, stimulate the growth and/or metabolic activity of intestinal bacteria that are associated with health and well-being. Given the increasing prevalence of osteoporosis, increasing calcium absorption from the diet by the addition of inulin-type fructans is an important strategy to improve bone metabolism at all ages. At present there are two approaches to prevent osteoporosis. The first is by optimizing bone mass acquisition in the skeleton during growth, and the second is by minimizing bone loss in later life. More recently it was demonstrated that the effects of inulin-type fructans on cholesterol and lipid metabolism have beneficial consequences in the process of atherosclerosis given that both are at the basis of disease development. The mechanisms responsible for the effects of inulin-type fructans on lipid and cholesterol metabolism in the human body are complex and include various interdependent biochemical pathways which take place in the liver, pancreas, intestine, and peripheral tissues. Research in this field has evolved, with the primary focus being on endocrine activity in the gut.

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• Chapter 12 : Resistant Starch as a Prebiotic

  Authors: Anthony Bird, David L. Topping
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    Optimizing the large-bowel microbiota in terms of function and products has the potential to improve public and personal health. Prebiotics and probiotics have attracted considerable attention for their potential in this regard. This is despite the fact that there is abundant evidence that the composition of the gut microbiota and its metabolic activities are responsive to changes in diet. There are also technical difficulties of incorporating probiotic microorganisms into foods and maintaining their shelf stability. Recognition of these two obstacles has prompted interest in the concept of prebiotics, which recognizes that dietary factors, especially macronutrients, are prime determinants of the community structure and fermentation profile of the large bowel ecosystem. An understanding of the biology of dietary starches, their digestion in the upper gut, and their interaction with the microbiota of the large bowel is essential in ascertaining the full prebiotic potential of resistant starch (RS). The classification of RS into groups RS1 through RS5 and the widely diverse types that are consumed in foods show that it is very difficult to link consumption directly to prebiotic action. One of the obstacles to progress is the lack of an internationally accepted and validated analytical method for RS in human foods. The methodological limitations of culture techniques for enumerating bacteria are well documented. Quantitative molecular techniques (such as fluorescence in situ hybridization), being more specific, sensitive, and precise, allow more subtle changes in the microbiota to be detected.

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• Chapter 13 : Effects of Prebiotic Supplementation on Bone Mineral Metabolism and Weight in Humans

  Author: Steven A. Abrams
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    The ability of prebiotics to enhance calcium absorption and bone mineralization has become an important rationale for their use. This chapter reviews the key human studies related to this potential effect and considers the role prebiotics may play in bone health. In addition, it discusses recent evidence that prebiotics may be beneficial in weight management. Finally, it considers potential applications of prebiotics in nutritional planning, especially for children and adolescents.

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• Chapter 14 : Prebiotics and Lipid Metabolism

  Authors: Nathalie M. Delzenne, Patrice D. Cani, Audrey M. Neyrinck
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    Several oligosaccharides which strictly correspond to the definition of prebiotics exhibit interesting effects on lipid metabolism. The resulting changes in the intestinal microbiota composition or fermentation activity could be implicated in the modulation of fatty acid and cholesterol metabolism. There is not a single biochemical locus through which prebiotics modulate serum, hepatic, and whole-body lipid content in animals. The effects observed depend on the pathophysiological and nutritional conditions. This may help to explain why in humans, where such conditions cannot be so rigorously controlled (namely, in terms of nutrient intake), the reported effects of prebiotics on circulating blood lipids are much more variable. Most of the data described to date have been obtained in animal studies; the relevance of such observations on obesity and cardiovascular disease risk in humans remains a key question, which is also addressed in this chapter. Fundamental research devoted to understanding the biochemical and physiological events (on glucose and lipid homeostasis, on gut hormone secretion, on satiety), as well as clinical research focusing on the target population, is required to achieve progress in the new area of the nutritional management of metabolic syndromes, based on modulation of the gut microbiota and intestinal function by specific food components.

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2.4 Genomics of Lactic Acid Bacteria

• Chapter 15 : Functional Genomics of Lactic Acid Bacteria

  Authors: Tri Duong, Todd R. Klaenhammer
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    The lactic acid bacteria (LAB) are a diverse group of microorganisms related by their common metabolic and physiological characteristics and named for the major end product of their primary metabolism. Major advances have been made in the genomic characterization of the LAB. A number of LAB genomes have been sequenced and are publicly available, while more genomes are being sequenced. This chapter lists genome features of sequenced LAB. While genomic analyses of LAB have identified features important for the functionality of the organisms in bioprocessing and health, further characterization of genes and gene products remains important for understanding cell physiology, metabolic and signaling networks, and molecular interactions of LAB with their environments. This information is rapidly providing a mechanistic understanding of these microorganisms and identifying important gene sets critical to their functionality. An understanding of genes directing important metabolic pathways combined with the tools available for the inactivation of undesirable genes and overexpression of existing or novel genes will certainly aid in the production of important food ingredients or food products with improved flavor and nutritional properties. Because of their acid tolerance, record of safety, and ability to modulate the immune system, considerable interest has developed for using LAB as live vectors for the delivery of vaccines and other biotherapeutics to the intestinal mucosa.

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2.5 Proteomics of Lactic Acid Bacteria

• Chapter 16 : Proteomic Approaches To Study Lactic Acid Bacteria

  Authors: David P. A. Cohen, Elaine E. Vaughan, Willem M. de Vos, Erwin G. Zoetendal
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    Biology aims to describe, understand, and predict the functionality of living cells, tissues, organisms, and ecosystems. High-throughput approaches that allow simultaneous investigation of more than one parameter will ultimately lead to better understanding of the organism’s behavior. Examples of such high-throughput approaches are genomics, transcriptomics, proteomics, and metabolomics. This chapter focuses on the application of proteomics in microbiological research in which special attention is given to the lactic acid bacteria (LAB). Proteomics has been used to investigate the functionality of LAB during preparation or fermentation of foods or their responses towards certain stress conditions (e.g., bile salts and acid) that these organisms encounter during passage through the human gastrointestinal tract. Proteomic approaches make it possible to gain insights into the relative abundance of proteins under certain conditions, and this knowledge may help predict which proteins of LAB are involved in survival under harsh conditions. Following an introduction regarding recent developments in proteomics, the chapter describes major findings obtained by studying the proteomes of LAB, especially under physiological stress conditions. It highlights the major results that were obtained by studying the proteomes of LAB under various conditions. Two separate proteomic research strategies have been applied frequently to LAB. These approaches include the construction of protein reference maps, systematic indexing of proteins, and analyses of bacterial stress responses culminating in induced changes in different proteomes.

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3.1 Probiotics

• Chapter 17 : Probiotics in Human Medicine: Overview

  Authors: Jennifer K. Spinler, James Versalovic
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    The introduction of the core human microbiome concept initiates new ways of thinking about potential clinical applications of probiotics. While important characteristics of probiotics include their abilities to suppress the proliferation and virulence of pathogenic organisms, it is becoming quite clear that these organisms also have direct effects on human physiology and immunity. Studies are beginning to shed light on tangible effects of probiotics in allergic and autoimmune diseases, oral biology, diseases of the gastrointestinal and genitourinary tracts, and neurology and psychiatry. Advances in probiotics research are resulting in implementation of probiotics as treatment and prevention strategies for a multitude of human diseases.

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• Chapter 18 : Probiotics and Other Organisms in Allergy and Autoimmune Diseases

  Authors: G. A. W. Rook, N. Witt
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    The incidences of several chronic inflammatory disorders have been increasing strikingly in the developed countries. These include allergic disorders (asthma and hay fever) and some autoimmune diseases. The validity of the pathways is supported by clinical trials and experimental models in which microorganisms that are depleted from the environment in rich countries have been shown to treat allergy, autoimmunity, or intestinal inflammation. This chapter discusses current progress in this area. All of the classes of organisms discussed in the chapter have immunoregulatory potential, and workers studying probiotics might benefit from the experience of those working with killed mycobacteria or helminths, and vice versa. There have been extremely few studies of the actual effects on the human immune system of the probiotics and other microbes used in clinical trials. The chapter outlines a few studies that address the issue of immunoregulation. The reports of clinical trials involving helminths do not present any data on changes in parameters of immunoregulation.

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• Chapter 19 : Probiotics in Oral Biology and Dentistry

  Author: J. H. Meurman
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    This chapter discusses the characteristics of the oral microbiota, and examples of potential contributions of probiotics to oral health. Theoretically, probiotics could interfere in several steps of oral biofilm formation, the development and modification of oral microecology, and the proliferation of planktonic microorganisms in the saliva. Bacterial attachment to epithelial cells or dental surfaces is the first and most essential step in colonization and development of oral biofilms. Mechanisms of adhesion to oral surfaces have been studied using model systems that mimic biofilm formation. Studies on the effects of probiotics on periodontal disease are sparse. The severity of the disease ranges from asymptomatic and occasional gingival bleeding to abscesses caused by severe inflammation in the oral cavity. Periodontal disease in particular has been linked with systemic consequences such as the development of atherosclerosis and poor metabolic balance of diabetic patients. New strategies for controlling periodontal disease might benefit overall health status.

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• Chapter 20 : Probiotics in Gastrointestinal Diseases

  Author: Francisco Guarner
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    A large and diverse community of commensal bacteria is harbored in the human gut, in a symbiotic arrangement that influences both the physiology and pathology of the host. Microbial ecology in the gut can be modulated by pharmacological and nutritional interventions with probiotics and prebiotics, and a balanced microbial environment would likely promote symbiotic functions of bacteria and enhance human health. In controlled human studies, probiotics and prebiotics have been used for improving certain metabolic functions of the microbiota, for protection against infections, and for modulation of the immune system. This chapter summarizes the recommendation grades for the use of probiotics in gastroenterology according to the criteria of evidence-based medicine. Current clinical research is focused mainly at establishing the role and efficacy of probiotics and prebiotics in the prevention and control of inflammatory bowel disease (IBD) and colon cancer. Experimental studies have yielded convincing evidence of their potential utility for these indications. However, human studies have failed in some attempts to provide effective therapeutic strategies with probiotics and prebiotics. It is likely that the development of improved tools to investigate gut colonization will provide a more complete picture of the actual scenario in inflammatory disorders and colon cancer. As a consequence, new interventions will aim towards more robust modifications or remodeling of intestinal microbial populations with applications for improving gut health.

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• Chapter 21 : Probiotics and Diseases of the Genitourinary Tract

  Author: Gregor Reid
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    Numerous diseases occur in the genitourinary tract of men, women, and children. These disorders cover the gamut of infection, incontinence, cancer, inflammatory problems, and anatomical malfunctions in the urethra, bladder, kidney, prostate, vulva, vagina, cervix, and uterus. The potential for probiotics to counter these ailments is not restricted to infection, but it is in this area that most of the research to date has been done. This chapter begins with conditions under which there is somewhat of a rationale for probiotics to affect the urogenital tract, but for which actual data are sparse. The main goal of probiotics applications is to prevent genitourinary tract infections by populating the vagina with lactobacilli after antifungal agents have reduced the yeast count. Probiotics repopulate the genitourinary tract, compete with other bacteria, and are flushed from the host, necessitating regular, repeated administration. A study was performed to examine the ability of probiotics to prevent bacterial vaginosis (BV) and yeast vaginitis in patients receiving antibiotic therapy. Widespread and growing interest in the use of probiotics for urogenital health has served as an impetus for numerous research studies.

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• Chapter 22 : Probiotics in Neurology and Psychiatry

  Authors: Paul Forsythe, John Bienestock
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    Probiotics are live nonpathogenic organisms that promote beneficial health effects when ingested. Increasing numbers of reports indicate that probiotics may have therapeutic potential in disorders ranging from atopic dermatitis to arthritis, highlighting the systemic impact of these organisms. While probiotics have been proposed as adjuvant therapy for depression, to date little is known of the ability of probiotic treatment to modulate brain function. The brain and the gut are engaged in constant bidirectional communication. Such communication becomes apparent when alterations in gastrointestinal (GI) function are communicated to the brain, bringing about the perception of visceral events such as nausea, satiety, and pain or when, in turn, stressful experiences lead to altered GI secretions and motility. This communication system involves neural pathways as well as immune and endocrine mechanisms. Consistent observations have suggested that patients with major depression who are otherwise healthy have activated inflammatory pathways, as indicated by increased proinflammatory cytokines, increased acute-phase proteins, and greater expression of chemokines and adhesion molecules. In addition to direct neural pathways, the gut also communicates to the brain utilizing hormonal signaling pathways that involve the release of gut peptides from enteroendocrine cells which can act directly on the brain at the area postrema, one of the circumventricular organs that lie outside the blood-brain barrier. Future research should be aimed at determining specific mechanisms involved in linking the human microbiota in general with central nervous system (CNS) homeostasis and function.

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3.2 Prebiotics

• Chapter 23 : Prebiotics in Human Medicine

  Author: Ian Rowland
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    The main areas that are reviewed in this chapter include constipation, diarrhea, irritable bowel syndrome, inflammatory bowel disease (ulcerative colitis and Crohn’s disease), and colorectal cancer. Constipation may also be a side effect of medication intake, in particular, antidepressants, antihistamines, opioids, and diuretics. Diarrhea can be acute (less than 14 days duration and usually caused by enteric infections), persistent (lasting more than 14 days), or chronic (lasting 30 days or more). Antibiotic-associated diarrhea (AAD) usually occurs 2 to 8 weeks after treatment with antibiotics, especially broad-spectrum antimicrobial agents. Only one study of the effect of prebiotics consumption on prevention of traveler’s diarrhea has been published. In this study, 244 healthy subjects who were traveling to destinations at high or medium risk for traveler’s diarrhea were randomized to groups receiving either fructo-oligosaccharides (FOS) (10 g/day) or a placebo orally for 2 weeks prior to and during a 2-week excursion. Irritable bowel syndrome (IBS) is a very common gastrointestinal disorder associated with a wide range of symptoms, including abdominal pain or discomfort, loose or hard stools, bloating, and flatulence. Generally, treatment of IBS is focused on medications rather than nutritional approaches. The decline in immune function is associated mainly with changes in T-cell populations, although other components of the immune system are also affected. Clinical studies of applications of prebiotics in human medicine are limited compared to the numbers of reports regarding probiotics.

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3.3 Synbiotics

• Chapter 24 : Synbiotics in Human Medicine

  Author: Stig Bengmark
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    Thirty years have passed since researchers reported that patients with inflammatory bowel disease (IBD) had a significantly different microbiota from that of healthy individuals. The strains with the greatest capacity to induce interleukin-12 (IL-12) seem to be the most effective probiotics to up-regulate major histocompatibility complex class II and B7-2 (CD86), indicative of immune cell maturation. The five most effective strains demonstrating potent inhibition against Clostridium difficile were Lactobacillus paracasei subsp. paracasei (two strains) and L. plantarum (three strains). Unfortunately, few studies have closely examined potentially synergistic effects of simultaneous administration of synbiotics containing lactic acid bacteria (LAB) (or other probiotics) and prebiotics. Several studies have been performed with probiotics including one trial with synbiotics. Alterations in microbial composition (increased amounts of anaerobic bacteria and suppression of pathogenic microbes) and increased fecal content of shortchain fatty acids (SCFAs) (from an average of 27.8 to 65.09 μmol/g of wet feces) were described in the synbiotics-treated group. Different species of LAB, doses of synbiotics, and combinations of antibiotics and synbiotics may yield a wider spectrum of beneficial effects in different disorders. A synbiotic formulation containing L. acidophilus ATCC 4962, FOS, inulin, and mannitol was administered to hypercholesterolemic pigs on high- and low-fat diets. The aims of this study included assessments of effects of synbiotics on plasma lipid profiles and erythrocyte membrane properties. Further scientific investigations are necessary in order to understand the unique interactions between the host-associated microbiota, diet, medical interventions with synbiotics, and aggregate effects on disease susceptibility, treatment, and prevention.

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• Chapter 25 : Strategies for Altering the Intestinal Microbiota of Animals

  Authors: Sergey R. Konstantinov, Jerry Wells
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    In this chapter the term probiotics is used in a broad sense to include the use of various different microbes in veterinary strategies aimed at manipulation or replacement of intestinal microbes. The reduction in the incidence of diarrhea by probiotics has frequently been studied because this problem is of the utmost importance for farm animals. Neonatal farmhouse animals including piglets often have an insufficiency of stomach acid, which is the first line of defense against bacterial invasion. Microbes of all types, including bacteria, viruses, archaea, fungi, and protozoans, colonize and persist in the intestinal tract of farm animals. Genomic analysis of differential gene expression in microbes and higher organisms has been greatly facilitated by the development of DNA microarrays. This technology has been exploited to monitor global intestinal transcriptional responses to the colonization of germ free mice with Bacteroides thetaiotaomicron, a prominent member of the normal murine and human intestinal microbiota. This study showed that this commensal was able to modulate expression of host genes participating in diverse and fundamental physiological functions, including nutrient absorption, mucosal barrier fortification, xenobiotic metabolism, angiogenesis, and postnatal intestinal maturation. Recent in vitro studies have suggested that probiotics can have protective effects on cytokine-induced apoptosis or permeability changes, attenuate epithelial inflammatory responses, and reduce invasion or adherence of pathogens.

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• Chapter 26 : Probiotics in Veterinary Medicine

  Authors: J. Scott Weese, Shayan Sharif, Alex Rodriguez-Palacios
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    Probiotic therapy is becoming increasingly popular in veterinary medicine, both for therapeutic uses and for growth promotion. Probiotics may be used in food animal species to prevent or treat disease, but this is typically focused on the herd, not individual animal, level. Other objectives include increasing growth rate, improving feed conversion, stimulating the immune system, and decreasing shedding of zoonotic pathogens. The two main areas of emphasis in poultry research include enteropathogen control and immune stimulation. Consistent with other probiotics, the two most commonly represented genera in poultry probiotics are Lactobacillus spp. and Bifidobacterium spp. Although undefined probiotics may be more efficacious than defined probiotics, their use is restricted in some countries because of the potential risks associated with the presence of pathogenic or antimicrobial-resistant bacteria. Importantly, Salmonella infection of chickens was associated with the production of proinflammatory and Th1 cytokines, such as IFN-γ. Probiotic therapy has received attention in cattle from many different perspectives, including increased production, decreased gastrointestinal disease, and decreased shedding of zoonotic enteropathogens. Probiotics are used in pigs for two main reasons: increased feed utilization efficiency with consequent weight gain and reduced frequency of diarrhea. Probiotics are becoming increasingly popular for treatment and prevention of diseases in companion animals, particularly horses, dogs, and cats. Probiotic therapy remains a promising option as parallel pressures to reduce antimicrobial use in animals, produce safe food cost-effectively, reduce environmental contamination with zoonotic pathogens, and maintain health in companion animals continue to be important priorities.

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• Chapter 27 : Prebiotics and Synbiotics in Companion Animal Science

  Authors: David Hernot, Eva Ogué, George Fahey, Robert A. Rastall
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    There is now considerable evidence to suggest that the colonic microbiota is susceptible to manipulation through diet. Certain foods, recognized as colonic functional foods, confer additional health benefits by improving the composition and activities of the gastrointestinal microbiota. Dietary components used for this purpose include probiotics, prebiotics, and synbiotics. Infections of the gastrointestinal tract (GIT) have an impact on the entire organism and are a major health problem that accounts for a large percentage of veterinary admissions. Vickers et al. used an in vitro fermentation system to test prebiotic fermentability. In this study, yeast cell wall (YCW) containing mannanoligosaccharides (MOS), short-chain fructo-oligosaccharides (scFOS), and four inulin sources were compared to beet pulp, cellulose, and soy fiber, which are common fiber sources used in pet diets. Primary outcomes included bacterial growth as measured by fluorescence in situ hybridization (FISH) and short-chain fatty acids (SCFA) production after 10 and 24 h of fermentation. The probes used in this study were Bif164, Bac303, Lab158, His150, Ec1531, and Erec482, specific for Bifidobacterium spp., Bacteroides/Prevotella group, Lactobacillus/Enterococcus group, Clostridium clusters I and II (including C. perfringens/Clostridium histolyticum), E. coli, and Clostridium coccoides/Eubacterium rectale group, respectively. Although the canine and feline prebiotic literature is not as robust as that of humans, their use has gained steady support over the past decade. Recently research has focused upon the efficacy of various fibers as prebiotics in the canine and feline GIT.

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• Chapter 28 : Phage Therapy

  Authors: Mikael Skurnik, Saija Kiljunen, Maria Pajunen
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    Bacteriophages (phages) are viruses that infect bacterial hosts and depend on bacterial processes to produce viral proteins and viral particles. This chapter first discusses the phage life cycles, phage receptors, taxonomy, and its genomes. Next, it talks about the impact of phages on bacterial evolution. Early bacteriophage research was largely driven by the desire to use phages to combat bacterial diseases—phage therapy. Early phage therapy researchers used phages to cure shigellosis, cholera, and staphylococcal infections. The chapter presents the major concerns of phage therapy include efficacy, pharmacokinetics, and safety issues. Due to the explosive increase of antibiotic-resistant bacteria and the urgent need for new antimicrobial strategies, phage therapy research has experienced a renaissance. During the last decade, several ambitious in vivo phage therapy studies have been published, some of which are discussed in the chapter. The study of a Listeria monocytogenes phage P100 was conducted according to current guidelines that should accompany the application of phages in therapy. Based on the examples presented in the chapter, the use of bacteriophages to control bacterial infections is promising. The global increase of antibiotic-resistant organisms warrants the exploitation of alternative strategies to manage infectious diseases. The therapeutic use of bacteriophages, perhaps in combination with antibiotics or other treatments, may work. Clear-cut instructions and quality requirements for phage products should be made available.

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• Chapter 29 : The Road Ahead: a Look at the Future

  Authors: James Versalovic, Michael Wilson
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    Probiotics may be useful as part of a multipronged strategy to confront malnutrition in the developing world and may be combined with prebiotics, micronutrients, and other foods in global health programs. Future descriptions of probiotics are likely to describe entirely novel classes of microbes as fundamental discoveries are made in the international microbiome project. Beneficial effects of probiotics include the provision of key nutrients for the intestinal mucosa, regulation of cell proliferation and differentiation, and immunomodulation. While probiotics have been studied for the prevention of infections and the suppression of inflammation, new applications and refinements of existing strategies will be based on the science of systems biology. Next-generation probiotics may be selected or engineered to contain such bioconversion features as part of solutions in preventative medicine and therapeutics. Exciting new developments in the understanding of probiotics and the regulation of mucosal immunity are pointing to new directions with respect to selection and engineering of beneficial microbes. Probiotics may also suppress immunity in disorders of chronic inflammation, and such effects may reflect the activation of different immune signaling pathways requiring different types of probiotics for disease amelioration. Advances in comparative and functional genomics are creating new opportunities for rational engineering of different probiotic species. A more detailed understanding is emerging regarding the respective roles of different indigenous and symbiotic microbes in the gastrointestinal tract. Comparative genomics of symbiotic bacterial species has highlighted molecular evolution and its role in niche and habitat adaptation of Bacteroidetes in the distal human intestine.

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