dc.contributor.author	Bottacini, Francesca
dc.contributor.author	Zomer, Aldert
dc.contributor.author	Milani, Christian
dc.contributor.author	Ferrario, Chiara
dc.contributor.author	Lugli, Gabriele A.
dc.contributor.author	Egan, Muireann
dc.contributor.author	Ventura, Marco
dc.contributor.author	van Sinderen, Douwe
dc.contributor.funder	European Society of Clinical Microbiology and Infectious Diseases
dc.contributor.funder	Federation of European Microbiological Societies
dc.contributor.funder	Ministero dell’Istruzione, dell’Università e della Ricerca
dc.contributor.funder	European Commission
dc.contributor.funder	Science Foundation Ireland
dc.date.accessioned	2018-02-06T13:36:29Z
dc.date.available	2018-02-06T13:36:29Z
dc.date.issued	2017
dc.description.abstract	Background: Bifidobacterium breve represents a common member of the infant gut microbiota and its presence in the gut has been associated with host well being. For this reason it is relevant to investigate and understand the molecular mechanisms underlying the establishment, persistence and activities of this gut commensal in the host environment. Results: The assessment of vegetative promoters in the bifidobacterial prototype Bifidobacterium breve UCC2003 was performed employing a combination of RNA tiling array analysis and cDNA sequencing. Canonical −10 (TATAAT) and −35 (TTGACA) sequences were identified upstream of transcribed genes or operons, where deviations from this consensus correspond to transcription level variations. A Random Forest analysis assigned the −10 region of B. breve promoters as the element most impacting on the level of transcription, followed by the spacer length and the 5’-UTR length of transcripts. Furthermore, our transcriptome study also identified rho-independent termination as the most common and effective termination signal of highly and moderately transcribed operons in B. breve. Conclusion: The present study allowed us to identify genes and operons that are actively transcribed in this organism during logarithmic growth, and link promoter elements with levels of transcription of essential genes in this organism. As homologs of many of our identified genes are present across the whole genus Bifidobacterium, our dataset constitutes a transcriptomic reference to be used for future investigations of gene expression in members of this genus.	en
dc.description.sponsorship	Federation of European Microbiological Societies (FEMS-RG-2016-0103)	en
dc.description.status	Peer reviewed	en
dc.description.version	Published Version	en
dc.format.mimetype	application/pdf	en
dc.identifier.articleid	991
dc.identifier.citation	Bottacini, F., Zomer, A., Milani, C., Ferrario, C., Lugli, G. A., Egan, M., Ventura, M. and van Sinderen, D. (2017) 'Global transcriptional landscape and promoter mapping of the gut commensal Bifidobacterium breve UCC2003', BMC Genomics, 18(1), 991 (14pp). doi: 10.1186/s12864-017-4387-x	en
dc.identifier.doi	10.1186/s12864-017-4387-x
dc.identifier.endpage	14
dc.identifier.journaltitle	BMC Genomics	en
dc.identifier.startpage	1
dc.identifier.uri	https://hdl.handle.net/10468/5401
dc.identifier.volume	18
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.project	info:eu-repo/grantAgreement/SFI/SFI Strategic Research Cluster/08/SRC/B1393/IE/SRC AGRC: Glycoscience Research Cluster/
dc.relation.project	info:eu-repo/grantAgreement/EC/H2020::CSA/696300/EU/The second coordination and support action for the JPI Healthy Diet for a Healthy Life/CSA JPI HDHL 2.0
dc.relation.project	info:eu-repo/grantAgreement/SFI/SFI Technology and Innovation Development Award (TIDA) - Training Award/07/CE/B1368 TIDA Training 11/IE/Alimentary Pharmabiotic Centre - Second Term Funding/
dc.relation.uri	https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-4387-x
dc.rights	© 2017, 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	Gene expression	en
dc.subject	Bifidobacteria	en
dc.subject	Probiotics	en
dc.subject	Transcription	en
dc.title	Global transcriptional landscape and promoter mapping of the gut commensal Bifidobacterium breve UCC2003	en
dc.type	Article (peer-reviewed)	en

Global transcriptional landscape and promoter mapping of the gut commensal Bifidobacterium breve UCC2003

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