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    Gene-trait matching across the Bifidobacterium longum pan-genome reveals considerable diversity in carbohydrate catabolism among human infant strains

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    Author
    Arboleya, Silvia
    Bottacini, Francesca
    O'Connell-Motherway, Mary
    Ryan, C. Anthony
    Ross, R Paul
    van Sinderen, Douwe
    STANTON, CATHERINE cc
    Keyword
    Bifidobacterium longum
    an-genome
    Carbohydrates
    Comparative genomes
    Gene-trait-matching
    Microbiota
    Date
    08/01/2018
    
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    URI
    http://hdl.handle.net/11019/1540
    Citation
    Arboleya S, Bottacini F, O’Connell-Motherway M, Ryan CA, Ross RP, van Sinderen D, Stanton C. Gene-trait matching across the Bifidobacterium longum pan-genome reveals considerable diversity in carbohydrate catabolism among human infant strains. BMC Genomics 2018;19(1):33; doi http://dx.doi.org/10.1186/s12864-017-4388-9.
    Abstract
    Background Bifidobacterium longum is a common member of the human gut microbiota and is frequently present at high numbers in the gut microbiota of humans throughout life, thus indicative of a close symbiotic host-microbe relationship. Different mechanisms may be responsible for the high competitiveness of this taxon in its human host to allow stable establishment in the complex and dynamic intestinal microbiota environment. The objective of this study was to assess the genetic and metabolic diversity in a set of 20 B. longum strains, most of which had previously been isolated from infants, by performing whole genome sequencing and comparative analysis, and to analyse their carbohydrate utilization abilities using a gene-trait matching approach. Results We analysed their pan-genome and their phylogenetic relatedness. All strains clustered in the B. longum ssp. longum phylogenetic subgroup, except for one individual strain which was found to cluster in the B. longum ssp. suis phylogenetic group. The examined strains exhibit genomic diversity, while they also varied in their sugar utilization profiles. This allowed us to perform a gene-trait matching exercise enabling the identification of five gene clusters involved in the utilization of xylo-oligosaccharides, arabinan, arabinoxylan, galactan and fucosyllactose, the latter of which is an abundant human milk oligosaccharide (HMO). Conclusions The results showed high diversity in terms of genes and predicted glycosyl-hydrolases, as well as the ability to metabolize a large range of sugars. Moreover, we corroborate the capability of B. longum ssp. longum to metabolise HMOs. Ultimately, their intraspecific genomic diversity and the ability to consume a wide assortment of carbohydrates, ranging from plant-derived carbohydrates to HMOs, may provide an explanation for the competitive advantage and persistence of B. longum in the human gut microbiome.
    Funder
    Science Foundation Ireland; Department of Agriculture, Food and the Marine, Ireland
    Grant Number
    SFI/12/RC/2273; 10FDairy
    ae974a485f413a2113503eed53cd6c53
    http://dx.doi.org/10.1186/s12864-017-4388-9
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    Teagasc publications in Biomed Central
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