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

Arboleya, Silvia; Bottacini, Francesca; O'Connell Motherway, Mary; Ryan, Anthony C.; Ross, R. Paul; van Sinderen, Douwe; Stanton, Catherine

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

dc.contributor.author	Arboleya, Silvia
dc.contributor.author	Bottacini, Francesca
dc.contributor.author	O'Connell Motherway, Mary
dc.contributor.author	Ryan, Anthony C.
dc.contributor.author	Ross, R. Paul
dc.contributor.author	van Sinderen, Douwe
dc.contributor.author	Stanton, Catherine
dc.contributor.funder	Science Foundation Ireland
dc.contributor.funder	Department of Agriculture, Food and the Marine
dc.date.accessioned	2018-02-20T13:24:12Z
dc.date.available	2018-02-20T13:24:12Z
dc.date.issued	2018
dc.description.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.	en
dc.description.sponsorship	Department of Agriculture Food and Marine (INFANTMET (Infant Nutrition for Programming the Gut Microbiota in Neonates) Project (Ref No. 10FDairy).	en
dc.description.status	Peer reviewed	en
dc.description.version	Published Version	en
dc.format.mimetype	application/pdf	en
dc.identifier.articleid	33
dc.identifier.citation	Arboleya, S., Bottacini, F., O’Connell-Motherway, M., Ryan, C. A., Ross, R. P., van Sinderen, D. and Stanton, C. (2018) 'Gene-trait matching across the Bifidobacterium longum pan-genome reveals considerable diversity in carbohydrate catabolism among human infant strains', BMC Genomics, 19(1), 33 (16pp). doi: 10.1186/s12864-017-4388-9	en
dc.identifier.doi	10.1186/s12864-017-4388-9
dc.identifier.endpage	16
dc.identifier.issn	1471-2164
dc.identifier.journaltitle	BMC Genomics	en
dc.identifier.startpage	1
dc.identifier.uri	https://hdl.handle.net/10468/5498
dc.identifier.volume	19
dc.language.iso	en	en
dc.publisher	BioMed Central	en
dc.relation.project	info:eu-repo/grantAgreement/SFI/SFI Research Centres/12/RC/2273/IE/Alimentary Pharmabiotic Centre (APC) - Interfacing Food & Medicine/
dc.relation.uri	https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-4388-9
dc.rights	© 2018, the Authors. Open Access. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.	en
dc.rights.uri	http://creativecommons.org/licenses/by/4.0/
dc.subject	Bifidobacterium longum	en
dc.subject	Pan-genome	en
dc.subject	Carbohydrates	en
dc.subject	Comparative genomes	en
dc.subject	Gene trait matching	en
dc.subject	Microbiota	en
dc.title	Gene-trait matching across the Bifidobacterium longum pan-genome reveals considerable diversity in carbohydrate catabolism among human infant strains	en
dc.type	Article (peer-reviewed)	en