Bifidobacteria: Genomics and Molecular Aspects
"essential reading for every bifidobacteria researcher" (Beneficial Microbes)
"covers the topic of Bifidobacterium extensively" (Doodys)
"essential reading" (BIOspektrum)
"well-written, informative and uses high-quality graphics" (Microbiology Today)
Caister Academic Press
and Douwe van Sinderen2
1Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias (CSIC), Villaviciosa, Asturias, Spain
2Dept of Microbiology, Alimentary Pharmabiotic Centre, University College Cork, Western Road, Cork, Ireland
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Bifidobacteria are Gram-positive anaerobic bacteria, found naturally in the gut of humans and other mammals. They are widely used as probiotic organisms in a vast array of formulations for the prevention, alleviation and treatment of many intestinal disorders. However bifidobacteria are fastidious microorganisms and difficult to study in the laboratory, so until recently, understanding of their genetics lagged behind that of other high GC content Gram-positive bacteria. The application of modern whole genome approaches to bifidobacteria research has changed all of this, permitting the accumulation of an impressive amount of data, something that could not have been foreseen a few years ago.
This book brings together the expertise and enthusiasm of the leading bifidobacteria experts from around the world to provide a state-of-the art overview of the molecular biology and genomics of this exciting and important microbial genus. Topics include: ecology, genomics, comparative genomics, metabolism, acid and bile resistance, stress response, probiotic properties, antimicrobial activity, interaction with the intestinal mucosa, safety assessment of bifidobacteria, synthesis and utilization of exopolysaccharides and prebiotics, antibiotic resistance/susceptibility profiles, viability and stability in commercial preparations, mobile genetic elements, cloning vectors and genetic manipulation of bifidobacteria. Essential reading for every bifidobacteria researcher, from the PhD student to the experienced scientist, and recommended reading for everyone with an interest in probiotics.
"I consider the book to be essential reading for every bifidobacteria researcher, from the PhD student to the experienced scientist, and also recommended reading for everyone with an interest in probiotics" from Beneficial Microbes (2010) 1: 455-461.
"This book would be useful to all scientists working on the benefits of intestinal Bifidobacteria. The review of topics will help promote additional research in academic settings as well as industrial development of products. The authors of each chapter are well-recognized scientists from many different settings such as government, academia and industry ... There are few books focused on the benefits of resident bacteria. This book covers the topic of Bifidobacterium extensively and will lead other scientists to move into this area, and their research can lead to products that enhance human health." from Doodys
"an overview of current knowledge" from SciTech Book News
"Leading scientists in the field present reviews that cover their specialist research topic. Well-written chapters ... the editors have done an excellent job in ensuring that the book is a good and enjoyable read ... essential reading for all specialists in the field of Bifidobacteria." from BIOspektrum
"... highly regarded authors ... an up-to-date analysis of various aspects of bifidobacterial biology that is well-written, informative and uses high-quality graphics ... aspects like probiotic traits, safety, physiology and ecology are covered ... the editors and authors should be congratulated on their approach and the finished work." from Microbiology Today
Table of contents
1 . Analysis of bifidobacterial populations in bowel ecology studies
Gerald W. Tannock
Members of the genus Bifidobacterium are fermentative bacteria that utilize a variety of carbohydrates, especially oligosaccharides, resulting in the formation of acetic and lactic acids. Hexoses are utilized by an unusual metabolic pathway known as the 'bifid shunt'. The ecology of bifidobacteria can be determined in the laboratory using culture-dependent and culture-independent methods. Nine bifidobacterial species that can be considered to be autochthonous to the bowel have been detected in human faeces. Bifidobacteria achieve large population sizes in the bowels of humans during the first few months after birth. Bifidobacterial populations are probably enriched in the bowel by some of a huge variety of oligosaccharides present in breast milk. The variety of oligosaccharides in milk may partially dictate the kinds of bifidobacteria that establish in the bowel of a given child. Naïve immune cells harvested from cord blood respond differentially to bifidobacterial species. Thus the occurrence of immunological diseases such as childhood allergies may be influenced by the kinds of bifidobacteria to which a child is exposed in early life. Therefore methods by which particular, immunologically potent bifidobacteria can be enriched in the infant bowel warrant intensive research.
2 . Genomics of Bifidobacteria: Where we stand now and where we are going
Marco Ventura, Francesca Turroni, Francesca Bottacini and Douwe van Sinderen
During recent years microbiological research has been fundamentally changed by the ever increasing number of publicly available bacterial whole-genome sequences. This sequence information has largely affected our understanding of the metabolic capabilities, genetics and phylogeny of bacteria. Bifidobacteria constitute one of the key microbial groups of the human intestinal microbiota, due to their perceived positive contribution to maintain a balanced gut homeostasis. In recent years bifidobacteria have drawn much scientific attention because of their use as live bacteria in numerous food preparations with several health-related claims. For this reason these bifidobacteria represent a developing area of scientific interest with respect to genomics, molecular biology, genetics and physiology. Recent genome sequencing of different bifidobacterial species has provided the complete genetic make-up of these bacteria. In this chapter we will discuss how genomic data has provided insights into bifidobacterial evolution, while also revealing genetic functions that explain their presence in the particular ecological environment of the gastrointestinal tract.
3 . Bifidobacterial ecology and comparative genomics: Perspectives and prospects
Marco Ventura, Francesca Turroni, Francesca Bottacini, Vanessa Giubellini and Douwe van Sinderen
The gastrointestinal tract (GIT) of humans and other mammals are colonized by a vast number of bacterial cells, including microorganisms such as bifidobacteria, which have been attributed an important role in maintaining a healthy GIT. However, despite this generally accepted beneficial role of bifidobacteria, the underlying molecular mechanisms by which these commensal bacteria exert this health-promoting or probiotic activity is far from understood. Recent genome sequencing has provided detailed insights into the genetic make-up of some members of the genus Bifidobacterium, although it represents only the first step in moving towards a better understanding of the biology and metabolic capabilities of these bacteria. Furthermore, comparative analyses of these genomes may increase our understanding of the physiological and metabolic behavior of these microorganisms, in particular with regards to the way in which bifidobacteria have adapted to the intestinal environment.
4 . Metabolism of bifidobacteria
David A. Sela, Neil P. J Price and David A. Mills
The genus Bifidobacterium possesses a unique fructose-6-phosphate phosphoketolase pathway employed to ferment carbohydrates. Much metabolic research on bifidobacteria has focused on oligosaccharide metabolism as these carbohydrate polymers are available in their otherwise nutrient-limited habitats. Interestingly, infant-associated bifidobacterial phylotypes appear to have evolved the ability to ferment milk oligosaccharides, whereas adult-associated species utilize plant oligosaccharides, consistent with what they encounter in their respective environments. As breast-fed infants often harbor bifidobacteria dominated gut consortia, there have been numerous applications to mimic the bifidogenic properties of milk oligosaccharides. These are broadly classified as plant-derived fructo-oligosaccharides or dairy-derived galacto-oligosaccharides, which are differentially metabolized and distinct from milk oligosaccharide catabolism. In the following chapter we review bifidobacterial carbohydrate metabolism, as well as several other topics including nitrogen and iron metabolism.
5 . Acid and bile resistance and stress response in bifidobacteria
Borja Sánchez, Lorena Ruiz, Douwe van Sinderen, Abelardo Margolles and Aldert L. Zomer
Members of the genus Bifidobacterium are Gram-positive bacteria which are commonly found in the gastrointestinal tract (GIT) of mammals, including humans. Because of their probiotic properties they are frequently incorporated as functional ingredients in food products. From probiotic production to storage and GIT delivery, bifidobacteria encounter a plethora of stresses, which negatively affect their viability and consequently their probiotic activity. In order to cope with these environmental challenges they need to protect themselves through stress-induced adaptative responses. A range of publications have investigated stress response in bifidobacteria and, from these published results, it has emerged that these bacteria employ an interacting network to manage their response to various environmental stresses. This chapter summarizes the current knowledge on the molecular mechanisms used by bifidobacteria to tolerate the deleterious action of acid, heat and bile on their physiology.
6 . Probiotic properties of bifidobacteria
Maddalena Rossi, and Alberto Amaretti
Bifidobacteria are major components of the indigenous bacterial population present in the human gut and are arguably most relevant to the health-promoting properties that have been attributed to elements of this microbiota. They exert a range of beneficial health effects, including the regulation of intestinal microbial homeostasis, the inhibition of pathogens and harmful bacteria that colonize and/or infect the gut mucosa, the modulation of local and systemic immune responses, the repression of procarcinogenic enzymatic activities within the microbiota, the production of vitamins, and the bioconversion of a number of dietary compounds into bioactive molecules. This chapter summarizes the reported health-promoting properties of members of the genus Bifidobacterium and discusses what research is still necessary for an in depth understanding of the probiotic function. In fact, although experimental evidence of the probiotic effectiveness of bifidobacteria has a long history, little information is available on the molecular mechanisms underlying the health-promoting claims, especially on such complex phenomena as anticarcinogenic and anti-inflammatory effects.
7 . Antimicrobial activity of the genus Bifidobacterium
Ismail Fliss, Arthur C. Ouwehand, Ehab Kheadr, Sampo Lahtinen, and Stephen J. Davids
In view of their relative abundance in the large intestine, their totally inoffensive nature and their reputation as symbionts, bifidobacteria are viewed by many scientists as probable antagonists of many would-be colonizers of the large intestine. While science cannot at this point confirm that the beneficial effects of probiotics such as bifidobacteria necessarily include specific antimicrobial mechanisms that eliminate pathogens or prevent other intestinal bacteria from reaching numbers that lead to health problems, quite a few high-quality studies show how bifidobacteria might have such effects. Among the most likely antagonistic mechanisms, prodigious production of lactic and acetic acids, which in addition to lowering the ambient pH may act as metabolic inhibitors, should be considered the most significant. Another plausible mechanism is competition for adhesion sites on the intestinal epithelium. There is evidence that bifidobacteria secrete molecules of large molecular mass with the specific function of interfering with the attachment of other organisms. Other mechanisms, such as hydrogen peroxide or bacteriocin production are more speculative. The effectiveness of bifidobacteria as antagonists of pathogens or as competitors for epithelial adhesion sites varies considerably and appears to be strain-dependent.
8 . Interaction of bifidobacteria with the intestinal mucosa with a focus on immuno-modulating effects
Eiji Miyauchi, Jin-zhong Xiao, and Soichi Tanabe
Bifidobacteria predominate in the gastrointestinal tract (GIT) of mammals. They are thought to benefit the host in various ways through interaction with intestinal mucosal cells. The interaction is the initiating event in immuno-modulation and merits particular attention. Intestinal epithelial cells (IECs) help to maintain gut homeostasis physically and immunologically. Bifidobacteria communicate with IECs and can ameliorate their inflammation. In vitro studies show that bifidobacteria can induce maturation of dendritic cells as well as differentiation and maturation of naïve T cells. These bifidobacteria-host cell interactions are, at least in part, triggered by pattern-recognition receptors such as toll-like receptors. Bacterial cell wall constituents, such as peptidoglycans and lipoteichoic acids, and bacterial DNA are involved in modulation of immune responses. Many clinical trials have been conducted to clarify the effectiveness of bifidobacteria with regards to their ability to prevent and/or alleviate allergic disorders, inflammatory bowel diseases and irritable bowel syndrome.
9 . Safety assessment of bifidobacteria
Maria H. Saarela
Bifidobacteria can be considered to be very safe to humans since no cases where a probiotic bifidobacterial product has caused an infection have been reported. Also bifidobacteria belonging to the resident microbiota of the oro-gastrointestinal tract very rarely cause infections. Oral bifidobacterial species should, however, be avoided in probiotic products, since these are considered to be oral pathogens and they have also occasionally caused infections. Probiotic Bifidobacterium strains should be chosen among the species that either have previously been commonly used in probiotic human products or represent the commonly detected species in the human gastrointestinal tract (GIT). In addition, safety assessment of a Bifidobacterium strain should involve at least diverse phenotypic characterisation of the strain (to indicate whether it is a typical representative of the species), antibiotic resistance pattern assessment (some strains might carry acquired resistance genes and these should be avoided), and assessment of side effects during human studies. Finally, an epidemiological surveillance of adverse incidents in consumers (post-market) should be performed at a later stage. Qualified Presumption of Safety (QPS) and its four pillars of safety assessment should be the basis of the safety evaluation of probiotics, although QPS is currently applied only to bacteria added to feed and used as biocontrol agents in EU.
10 . Synthesis and utilization of exopolysaccharides and prebiotics
Sandra Macfarlane, Katie E. Blackett and George T. Macfarlane
Many bacteria and fungi secrete exopolysaccharides (EPS), which have been demonstrated to have significant ecological, physiological and pathological functions in the human body. These substances have also been harnessed for industrial purposes, and are widely used in the food industry. EPS formation has been studied extensively in various species of lactic bacteria, but relatively few investigations have been performed on these processes in bifidobacteria. However, although yields are generally low in comparison to other microorganisms, studies have shown that various bifidobacterial species secrete rhamnose-, glucose- and galactose-based EPS that have immunopotentiating activities, anti-mutagenic properties and the ability to promote or inhibit adhesion of other organisms to mucosal surfaces. Bifidobacteria have also been found to utilize the polymers they produce, as well as those formed by other microbial species, suggesting that these molecules may have prebiotic properties. Bifidobacterial communities in the large intestine are not only targets for prebiotics, but β-galactosidases produced by different species have been used to synthesise galacto-oligosaccharides with enhanced selectivity for the producing organisms.
11 . Antibiotic resistance/susceptibility profiles of bifidobacteria and molecular analysis of atypical resistances
Baltasar Mayo, Sigrid Mayrhofer, Susana Delgado, and Konrad J. Domig
Antibiotics have greatly improved human life expectancy and quality, being undisputed winners in the fight against infectious diseases over the past 70 years. However, their continued success is severely threatened by the global spread of antibiotic resistance (AR). There is significant and wide-spread concern that commensal and beneficial bacterial populations, such as food-borne and gastrointestinal tract (GIT)-associated bacteria, will become a reservoir for AR-conferring genes, from which these could readily be transferred to opportunistic and pathogenic organisms. Bifidobacteria represent a ubiquitous commensal bacterial group in the GIT of humans and animals, where they are supposed to exert protective and beneficial effects on their host. This has led to the use of selected strains as probiotics. High numbers of bifidobacteria are deliberately brought into contact with a vast array of intestinal microorganisms during probiotic consumption, which means that AR spread is possible if probiotic strains carry transferable AR-conferring genes. Strains carrying such genes should be excluded from use as probiotics. This chapter addresses key topics on the methodology of surveying AR in bifidobacteria, their intrinsic resistance/susceptibility profiles, and summarises the molecular basis and genetic organisation of atypical resistances from bifidobacteria. Among these, AR encoded by acquired genes, particularly those harboured in mobile genetic elements, pose the greatest risk of transfer. Knowledge on AR-conferring genes and their transfer potential is critical in preventing dissemination of AR among intestinal bacteria through the use of probiotics.
12 . Viability and stability of bifidobacteria in commercial preparations
Kamila Goderska and Catherine Stanton
Probiotic bacteria, including species of Lactobacillus and Bifidobacterium, have been associated with numerous health benefits. As a result, the global market for probiotic products is continuously growing and food products enriched with probiotic bacteria are one of the most successful categories of functional foods. However, incorporating probiotic bacteria into food matrices poses significant technological challenges, and can be difficult due to the various stresses imposed on the probiotic strains during food processing. Bifidobacteria in particular are sensitive microorganisms with low survival upon exposure to stresses, e.g. acid and temperature stress and oxygen exposure, encountered during their production, storage and consumption. Furthermore, incompatibility of the probiotic culture with the starter culture(s) used for the probiotic food fermentation may be a cause of further problems. So far, the use of probiotic bacteria is largely restricted to refrigerated fermented dairy products, where consumer health concerns, the traditional healthy image of dairy foods and the positive taste perceptions associated with these products are key catalysts driving this sector. However, non-dairy based vehicles such as fruit juices and soy-based products are also gaining popularity for delivery of probiotic bacteria. This review focuses on the behaviour of bifidobacteria in food matrices of both dairy and non-dairy origin, and examines recent advances in strategies to enhance bifidobacterial viability and stability during the processing and storage of probiotic products.
13 . Mobile genetic elements, cloning vectors and genetic manipulation of bifidobacteria
Pablo Álvarez Martín, Simone Guglielmetti, and Baltasar Mayo
Growth difficulties, because of their fastidious nutritive nature and oxygen sensitivity, and a lack of efficient genetic tools have impeded until recently proper development of molecular studies in Bifidobacterium. These studies, however, are critical to uncover the cross-talk between bifidobacteria and their hosts' cells, and also to prove unequivocally the supposed beneficial activities supplied through the gastrointestinal tract of mammals either endogenously or after ingestion as probiotics. Analysis of gene sequences provided by whole genome sequencing projects has opened new avenues to decipher the genetic basis of bacteria-cell interactions and probiotic effects. However, the purposeful development of stable cloning and expression vectors based on robust replicons -either from temperate phages or resident plasmids- is additionally needed. This chapter addresses the current knowledge on the mobile genetic elements of bifidobacteria (phages, plasmids, and transposons) and reviews the different types of vectors already available for the Bifidobacterium species, together with the transformation procedures for introducing DNA into bifidobacterial cells. It also covers recent molecular studies performed with such vectors and incipient results on the genetic modification of these organisms, establishing the basis that would allow the use of bifidobacteria for many biotechnological applications. Pitfalls, drawbacks, and future needs in the field are also discussed.
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(EAN: 9781904455684 9781912530694 Subjects: [bacteriology] [microbiology] [medical microbiology] [molecular microbiology] [genomics] [probiotics] )