Microbiology - Book Chapters

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    Determination of bifidobacterial carbohydrate utilization abilities and associated metabolic end products
    (Springer Science+Business Media, LLC, 03/03/2021) Solopova, Ana; van Sinderen, Douwe; van Sinderen, Douwe; Ventura, Marco
    Bifidobacteria are able to utilize a diverse range of host-derived and dietary carbohydrates, the latter of which include many plant-derived oligo- and polysaccharides. Different bifidobacterial strains may possess different carbohydrate utilization abilities. These metabolic abilities can be studied using classical bacterial growth assessment methods, such as measurement of changes in optical density or acidity of the culture in the presence of the particular carbohydrate to generate growth and acidification curves, respectively. Scientists may also be interested in the growth rate during the exponential growth phase, and the maximum OD that is reached on a particular sugar, or the length of the lag phase. Furthermore, high-performance liquid chromatography (HPLC) and high-performance anion exchange chromatography coupled to pulsed amperometric detection (HPAEC-PAD) are extensively used in carbohydrate and metabolic end-product analysis due to their versatility and separation capabilities.
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    Phageome analysis of bifidobacteria-rich samples
    (Springer Science+Business Media, LLC, 03/03/2021) McDonnell, Brian; Casey, Eoghan; Milani, Christian; Lugli, Gabriele Andrea; Viappiani, Alice; Mahony, Jennifer; Ventura, Marco; van Sinderen, Douwe; van Sinderen, Douwe; Ventura, Marco
    Bifidobacteria are important early colonizers of the human intestinal tract. The relative abundance of bifidobacterial species may be modulated, in part, by bacteriophage activity. Metagenomic studies of these populations is a crucial step in understanding this important interaction. This chapter outlines the technical instructions required to analyze the virome of a bifidobacteria-rich sample, for example, an infant fecal sample.
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    Bifidobacterium transformation
    (Springer Science+Business Media, LLC, 03/03/2021) Hoedt, Emily C.; Bongers, Roger S.; Bottacini, Francesca; Knol, Jan; MacSharry, John; van Sinderen, Douwe; van Sinderen, Douwe; Ventura, Marco; Nutricia Research Foundation; Science Foundation Ireland
    The protocol presented in this chapter describes a generic method for electrotransformation of Bifidobacterium spp., outlining a technique that is ideal for conferring selective properties onto strains as well as allowing the user to introduce or knock out/in selected genes for phenotypic characterization purposes. We have generalized on the plasmid chosen for transformation and antibiotic selection marker, but the protocol is versatile in this respect and we are able to achieve transformation efficiencies up to 107 transformants/μg of DNA.
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    Protocol to select bifidobacteria from fecal and environmental samples
    (Springer Science+Business Media, LLC, 03/03/2021) Alessandri, Giulia; Ossiprandi, Maria Cristina; Ventura, Marco; van Sinderen, Douwe; van Sinderen, Douwe; Ventura, Marco
    Bifidobacteria are commensal microorganisms able to colonize several ecological niches. Since their discovery, culture-dependent methods combined with the most modern next-generation sequencing techniques have contributed to shed light on the ecological, functional and genomic features of bifidobacteria, purporting them as microorganisms with probiotic traits. Thanks to their acclaimed health-promoting effects, several members of the Bifidobacterium genus have been included in a variety of functional foods and drugs. In this context, the functional relevance of bifidobacteria in the gut explains ongoing efforts to isolate novel and potentially beneficial strains. For this purpose, development of effective and selective isolation protocols in concert with knowledge on the physiological characteristics of bifidobacterial are fundamental requirements for their recovery and discovery from their natural environments, in particular from fecal samples.
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    Implementation of transposon mutagenesis in Bifidobacterium
    (Humana, New York, NY, 14/06/2019) Ruiz, Lorena; van Sinderen, Douwe; Ricke, Steven C.; Park, Si Hong; Davis, Morgan L.
    Random transposon mutagenesis allows for relatively rapid, genome-wide surveys to detect genes involved in functional traits, by performing screens of mutant libraries. This approach has been widely applied to identify genes responsible for activities of interest in multiple eukaryote and prokaryote organisms, although most studies on microorganisms have focused on pathogenic and clinically relevant bacteria. In this chapter we describe the implementation of an in vitro Tn5-based transposome strategy to generate a large collection of random mutants in the gut commensal Bifidobacterium breve UCC2003, and discuss considerations when applying this mutagenesis system to other Bifidobacterium species or strains of interest.