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The genus Bifidobacterium constitutes one of the main groups of the human microbiota and some species have a long history of safe consumption supporting an excellent safety record. However, in the context of the increasing worldwide problems associate to the rise of pathogenic microorganisms with acquired resistance to antibiotics, the risk associated to the presence of antibiotic resistance determinants should always be a key starting point for the introduction of any microbial strain into the food chain. Carboplatin Bifidobacteria are not an exception and the presence of resistance to antibiotics is of interest since these microorganisms could potentially act as a reservoir of such resistances. In this context it is necessary to evaluate the presence of antibiotic resistance in any bifidobacterial strain to be included into the food chain. To this end, the first step is the determination of the antibiotic resistance pattern of the strain and the comparison with the susceptibility breakpoints for that species, allowing identifying the presence of atypical resistances in the strain. In this chapter we discuss the many efforts done to harmonize the methods used for the evaluation of antimicrobial susceptibility in the genus Bifidobacterium and the currently available guidelines. Moreover, we describe, in detail, the reference protocols used for evaluating the in vitro antimicrobial activity on bifidobacteria.Bifidobacteria represent highly prevalent and abundant members of the gut microbiota during mammalian infancy. In this context, bifidobacterial species have been shown to be correlated with many aspects of host health by means of direct interactions with the host and cohabiting microbes. Metagenomic sequencing of fecal DNA represents a valuable approach for taxonomic and functional profiling of bacterial populations, and has allowed us to appreciate the relevance of bifidobacterial taxa in such complex bacterial communities, especially during the first stages of life.Bifidobacteria represent an important group of (mostly) commensal microorganisms, which have enjoyed increasing scientific and industrial attention due to their purported health-promoting attributes. For the latter reason, several species have been granted "generally recognized as safe" (GRAS) and "qualified presumption of safety" (QPS) status by the Food and Drugs Administration (FDA) and European Food Safety Authority (EFSA) organizations. Increasing scientific evidence supports their potential as oral delivery vectors to produce bioactive and therapeutic molecules at intestinal level. In order to achieve an efficient utilization of bifidobacterial strains as health-promoting (food) ingredients, it is necessary to provide evidence on the molecular mechanisms behind their purported beneficial and probiotic traits, and precise mechanisms of interaction with their human (or other mammalian) host. In this context, developing appropriate molecular tools to generate and investigate recombinant strains is necessary. While bifidobacteria have long remained recalcitrant to genetic manipulation, a wide array of Bifidobacterium-specific replicating vectors and genetic modification procedures have been described in literature. The current chapter intends to provide an updated overview on the vectors used to genetically modify and manipulate bifidobacteria, including their general characteristics, reviewing examples of their use to successfully generate recombinant bifidobacterial strains for specific purposes, and providing a general workflow and cautions to design and conduct heterologous expression in bifidobacteria. Knowledge gaps and fields of research that may help to widen the molecular toolbox to improve the functional and technological potential of bifidobacteria are also discussed.Bile salt hydrolase (BSH) activity is a desirable trait in putative probiotic bacteria, such as those belonging to the Bifidobacterium genus. On the one hand, bile salt hydrolysis is considered to represent a bile detoxification mechanism for gut commensal bacteria and thus the presence of this activity was believed to be a predictor of bile tolerance of putative probiotic strains. On the other hand, it has recently been revealed that chemical modifications of the bile acid pool performed by the gut microbiota strongly impact on host health. This explains the increasing interest to investigate the role played by bile-modifying enzymes of gut commensals on lowering cholesterol levels, on modulating gut inflammation or on influencing the development of cancer or metabolic disorders. This chapter compiles qualitative and quantitative methods to analyse BSH activity in bifidobacteria, though they could be adapted to other bacterial groups of interest.Bifidobacteria are commensal bacteria, which naturally colonize the gastrointestinal tract of a large number of animals, including humans, contributing to their health and well-being. An important taxonomic marker for the identification of members of the bifidobacterial group is the presence of the fructose-6-phosphate phosphoketolase (F6PPK) activity. The F6PPK enzyme is involved in the bifidus shunt based on the ability of F6PPK to split fructose-6-phosphate into erythrose-4-phosphate and acetyl phosphate. Here, we describe the two main methods utilized to detect the presence of F6PPK activity, that is, the enzymatic assay and the presence of the D-xylulose-5-phosphate/fructose-6-phosphate phosphoketolase bifidobacterial gene.Members of the Bifidobacterium genus are some of the earliest and most important colonizers of the human neonatal gastrointestinal tract (GIT), exerting wide-ranging effects on early development of the host. However, human isolates of bifidobacteria are very inefficient colonizers of specific-pathogen-free (SPF) mice creating a technical barrier to discovery and applied research in this area. We have developed a reproducible model to facilitate transient colonization of SPF mice with human isolates of this genus through prior depletion of the gut resident microbiota with antibiotics. This chapter outlines the technical details for performing efficient microbiota depletion with antibiotics and subsequent administration of bifidobacteria for colonization.
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