APC Microbiome Ireland - Journal Articles

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    Shaping the future of probiotics and prebiotics
    (Elsevier, 2021) Cunningham, Marla; Azcarate-Peril, M. Andrea; Barnard, Alan; Benoit, Valerie; Grimaldi, Roberta; Guyonnet, Denis; Holscher, Hannah D.; Hunter, Kirsty; Manurung, Sarmauli; Obis, David; Petrova, Mariya I.; Steinert, Robert E.; Swanson, Kelly S.; van Sinderen, Douwe; Vulevic, Jelena; Gibson, Glenn R.; Hass Avocado Board; Almond Board of California; National Honey Board; Kellogg's; PepsiCo; Nutricia North America; Tate & Lyle
    Recent and ongoing developments in microbiome science are enabling new frontiers of research for probiotics and prebiotics. Novel types, mechanisms, and applications currently under study have the potential to change scientific understanding as well as nutritional and healthcare applications of these interventions. The expansion of related fields of microbiome-targeted interventions, and an evolving landscape for implementation across regulatory, policy, prescriber, and consumer spheres, portends an era of significant change. In this review we examine recent, emerging, and anticipated trends in probiotic and prebiotic science, and create a vision for broad areas of developing influence in the field.
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    Bacteriophage-host interactions as a platform to establish the role of phages in modulating the microbial composition of fermented foods
    (OAE Publishing, 2022) White, Kelsey; Yu, Jun-Hyeok; Eraclio, Giovanni; Dal Bello, Fabio; Nauta, Arjen; Mahony, Jennifer; van Sinderen, Douwe; Science Foundation Ireland; Irish Research Council
    Food fermentation relies on the activity of robust starter cultures, which are commonly comprised of lactic acid bacteria such as Lactococcus and Streptococcus thermophilus. While bacteriophage infection represents a persistent threat that may cause slowed or failed fermentations, their beneficial role in fermentations is also being appreciated. In order to develop robust starter cultures, it is important to understand how phages interact with and modulate the compositional landscape of these complex microbial communities. Both culture-dependent and -independent methods have been instrumental in defining individual phage-host interactions of many lactic acid bacteria (LAB). This knowledge needs to be integrated and expanded to obtain a full understanding of the overall complexity of such interactions pertinent to fermented foods through a combination of culturomics, metagenomics, and phageomics. With such knowledge, it is believed that factory-specific detection and monitoring systems may be developed to ensure robust and reliable fermentation practices. In this review, we explore/discuss phage-host interactions of LAB, the role of both virulent and temperate phages on the microbial composition, and the current knowledge of phageomes of fermented foods.
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    Cell wall polysaccharides of Gram positive ovococcoid bacteria and their role as bacteriophage receptors
    (Elsevier, 2021) Lavelle, Katherine; van Sinderen, Douwe; Mahony, Jennifer; Science Foundation Ireland
    Gram-positive bacterial cell walls are characterised by the presence of a thick peptidoglycan layer which provides protection from extracellular stresses, maintains cell integrity and determines cell morphology, while it also serves as a foundation to anchor a number of crucial polymeric structures. For ovococcal species, including streptococci, enterococci and lactococci, such structures are represented by rhamnose-containing cell wall polysaccharides, which at least in some instances appear to serve as a functional replacement for wall teichoic acids. The biochemical composition of several streptococcal, lactococcal and enterococcal rhamnose-containing cell wall polysaccharides have been elucidated, while associated functional genomic analyses have facilitated the proposition of models for individual biosynthetic pathways. Here, we review the genomic loci which encode the enzymatic machinery to produce rhamnose-containing, cell wall-associated polysaccharide (Rha cwps) structures of the afore-mentioned ovococcal bacteria with particular emphasis on gene content, biochemical structure and common biosynthetic steps. Furthermore, we discuss the role played by these saccharidic polymers as receptors for bacteriophages and the important role phages play in driving Rha cwps diversification and evolution.
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    A dual-chain assembly pathway generates the high structural diversity of cell-wall polysaccharides in Lactococcus lactis
    (American Society for Biochemistry and Molecular Biology Inc., 2019) Theodorou, Ilias; Courtin, Pascal; Palussière, Simon; Kulakauskas, Saulius; Bidnenko, Elena; Péchoux, Christine; Fenaille, François; Penno, Christophe; Mahony, Jennifer; van Sinderen, Douwe; Chapot-Chartier, Marie-Pierre; Science Foundation Ireland
    In Lactococcus lactis, cell-wall polysaccharides (CWPSs) act as receptors for many bacteriophages, and their structural diversity among strains explains, at least partially, the narrow host range of these viral predators. Previous studies have reported that lactococcal CWPS consists of two distinct components, a variable chain exposed at the bacterial surface, named polysaccharide pellicle (PSP), and a more conserved rhamnan chain anchored to, and embedded inside, peptidoglycan. These two chains appear to be covalently linked to form a large heteropolysaccharide. The molecular machinery for biosynthesis of both components is encoded by a large gene cluster, named cwps. In this study, using a CRISPR/Cas-based method, we performed a mutational analysis of the cwps genes. MALDI-TOF MS-based structural analysis of the mutant CWPS combined with sequence homology, transmission EM, and phage sensitivity analyses enabled us to infer a role for each protein encoded by the cwps cluster. We propose a comprehensive CWPS biosynthesis scheme in which the rhamnan and PSP chains are independently synthesized from two distinct lipid-sugar precursors and are joined at the extracellular side of the cytoplasmic membrane by a mechanism involving a membrane-embedded glycosyltransferase with a GT-C fold. The proposed scheme encompasses a system that allows extracytoplasmic modification of rhamnan by complex substituting oligo-/polysaccharides. It accounts for the extensive diversity of CWPS structures observed among lactococci and may also have relevance to the biosynthesis of complex rhamnose-containing CWPSs in other Gram-positive bacteria.
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    Bifidobacterial biofilm formation is a multifactorial adaptive phenomenon in response to bile exposure
    (Springer Nature, 2020) Kelly, Sandra M.; Lanigan, Noreen; O’Neill, Ian J.; Bottacini, Francesca; Lugli, Gabriele A.; Viappiani, Alice; Turroni, Francesca; Ventura, Marco; van Sinderen, Douwe; Science Foundation Ireland; Università degli Studi di Parma
    In the current study, we show that biofilm formation by various strains and species belonging to Bifidobacterium, a genus that includes gut commensals with reported health-promoting activities, is induced by high concentrations of bile (0.5% (w/v) or higher) and individual bile salts (20 mM or higher), rather than by acid or osmotic stress. The transcriptomic response of a bifidobacterial prototype Bifidobacterium breve UCC2003 to such high bile concentrations was investigated and a random transposon bank of B. breve UCC2003 was screened for mutants that affect biofilm formation in order to identify genes involved in this adaptive process. Eleven mutants affected in their ability to form a biofilm were identified, while biofilm formation capacity of an insertional mutation in luxS and an exopolysaccharide (EPS) negative B. breve UCC2003 was also studied. Reduced capacity to form biofilm also caused reduced viability when exposed to porcine bile. We propose that bifidobacterial biofilm formation is an adaptive response to high concentrations of bile in order to avoid bactericidal effects of high bile concentrations in the gastrointestinal environment. Biofilm formation appears to be a multi-factorial process involving EPS production, proteins and extracellular DNA release, representing a crucial strategy in response to bile stress in order to enhance fitness in the gut environment.