Bifidobacteria are important gastrointestinal commensals of a number of animals, including humans, and various beneficial effects on host health have been attributed to them. Here, we announce the noncontiguous finished genome sequence of Bifidobacterium longum E18, isolated from a healthy adult, which reveals traits involved in its interaction with the host

Breitinger, Katrin J.

Dudnik, Alexey

Grimm, Verena

Riedel, Christian U.

van Sinderen, Douwe

Waidmann, Mark S.

Westermann, Christina

Yuan, Jing

Zhurina, Daria

Genome Announcements

Cork Open Research Archive

Title High-quality draft genome sequence of Bifidobacterium longum E18,isolated from a healthy adultAuthor(s) Zhurina, Daria; Dudnik, Alexey; Waidmann, Mark S.; Grimm, Verena;Westermann, Christina; Breitinger, Katrin J.; Yuan, Jing; van Sinderen,Douwe; Riedel, Christian U.Publication date 2013-12Original citation Zhurina, D., Dudnik, A., Waidmann, M. S., Grimm, V., Westermann, C.,Breitinger, K. J., Yuan, J., van Sinderen, D. and Riedel, C. U. (2013)'High-Quality Draft Genome Sequence of Bifidobacterium longum E18,Isolated from a Healthy Adult', Genome Announcements, 1(6). doi:10.1128/genomeA.01084-13Type of publication Article (peer-reviewed)Link to publisher'sversionhttp://dx.doi.org/10.1128/genomeA.01084-13Access to the full text of the published version may require asubscription.Rights © 2013 Zhurina et al. This is an open-access article distributedunder the terms of the Creative Commons Attribution 3.0 Unportedlicense.https://creativecommons.org/licenses/by/3.0/Item downloadedfromhttp://hdl.handle.net/10468/3446Downloaded on 2018-08-23T18:10:52ZHigh-Quality Draft Genome Sequence of Bifidobacterium longum E18,Isolated from a Healthy AdultDaria Zhurina,a Alexey Dudnik,b Mark S. Waidmann,a Verena Grimm,a Christina Westermann,a Katrin J. Breitinger,a Jing Yuan,cDouwe van Sinderen,d Christian U. RiedelaInstitute of Microbiology and Biotechnology, University of Ulm, Ulm, Germanya; Institute of Plant Biology, University of Zurich, Zurich, Switzerlandb; Institute of DiseaseControl and Prevention, Academy of Military Medical Sciences, Beijing, Chinac; Alimentary Pharmabiotic Centre and Department of Microbiology, Biosciences Institute,University College Cork, Cork, IrelanddBifidobacteria are important gastrointestinal commensals of a number of animals, including humans, and various beneficialeffects on host health have been attributed to them. Here, we announce the noncontiguous finished genome sequence of Bifido-bacterium longum E18, isolated from a healthy adult, which reveals traits involved in its interaction with the host.Received 15 November 2013 Accepted 26 November 2013 Published 19 December 2013Citation Zhurina D, Dudnik A, Waidmann MS, Grimm V, Westermann C, Breitinger KJ, Yuan J, van Sinderen D, Riedel CU. 2013. High-quality draft genome sequence ofBifidobacterium longum E18, isolated from a healthy adult. Genome Announc. 1(6):e01084-13. doi:10.1128/genomeA.01084-13.Copyright © 2013 Zhurina et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license.Address correspondence to Christian U. Riedel, christian.riedel@uni-ulm.de.Bifidobacteria are considered to beGRAS (generally recognizedas safe) microorganisms that are widely used as probiotics.Probiotics are defined as live microbial food supplements thathave a beneficial effect on host health when administered in ade-quate amounts (1). The beneficial effects of bifidobacteria havebeen studiedmainly in animal models and include immunemod-ulation, pathogen inhibition, and the alleviation of intestinal in-flammation (2–7). Genome sequencing and analysis of membersof the genus Bifidobacterium are powerful approaches to identifythe genetic determinants involved in the interactionwith the host.To extend knowledge of this subject, we have sequenced the ge-nome of the commensal B. longum E18 strain, which was isolatedfrom the feces of a healthy adult.A 7.9-kb paired-end library was constructed and sequencedusing a Roche Genome Sequencer FLX Titanium platform by acommercial sequencing service provider, Eurofins MWGOperon(Ebersberg, Germany). A total of 246,462 individual quality-filtered reads comprising 53,491,261 bp were obtained, resultingin a 26.7-fold average coverage. The read sequences were assem-bled using Newbler 2.3 and Staden package 2.0.0b9 into six con-tigs put together into one megascaffold. Initial tRNA, rRNA, andopen reading frame (ORF) prediction and functional annotationwere done using the RAST server (8). The translational start sitesof automatically annotated ORFs were manually corrected usingArtemis software (9) based on the positions of potential ribosomalbinding sites, the GC profile, and alignments with homologousORFs from other organisms.Manual corrections of automaticallyassigned functions were verified on an individual gene-by-genebasis using BLASTp (10) searches against the nonredundant pro-tein sequence database.The estimated genome size of strain E18 is 2,372,966 bp,with an average GC content of 59.96%. The genome contains1,862 protein-encoding genes, 4 rRNA operons, and an unusu-ally high number of tRNA genes (62 in total). Putative functionswere assigned to 1,299 genes (67%). The amino acid sequencesencoded by 99 genes contain putative signal peptide sequences,and thus, these proteins might be secreted via the classical secpathway.B. longumE18 harbors a complete tatABC secretion system(BLONG_0088-90) and at least 4 of the secreted proteins(BLONG_0091, BLONG_0223, BLONG_0425, and BLONG_1620)are predicted to be exported via this pathway. Approximately halfof all secreted proteins are predicted hydrolases, substrate bindingproteins, and components of transport systems with a putativerole in the acquisition of nutrients, which represents an adapta-tion of bifidobacteria to the gastrointestinal habitat (11–13). Fur-ther genes with a potential role in interaction with the host carriedin theB. longum E18 genome include two putative exopolysaccha-ride (EPS) biosynthesis gene clusters (BLONG_0398-0417 andBLONG_2008-2021) and a gene cluster encoding Tad pili(BLONG_0140-0145). Both traits were previously shown to beimportant for in vivo colonization andmodulation of the immunesystem by bifidobacteria (2, 14).Nucleotide sequence accession numbers. The genome se-quence of B. longum E18 has been deposited at DDBJ/EMBL/GenBank under the accession no. AUYD00000000. The versiondescribed in this paper is version AUYD01000000. The assignedNCBI taxonomy identification number is 1322347.ACKNOWLEDGMENTSC.U.R., D.Z., V.G., and J.Y. were funded by the German Academic Ex-change Service and FederalMinistry of Education andResearch (grant no.D/09/04778). D.Z. additionally received a Research Prize (Forschungsbo-nus) of the University of Ulm for this project. A.D. was supported by theSwiss National Science Foundation (grant no. 31003A-134936). D.V.S.was supported by the Science Foundation Ireland (SFI) under grant no.07/CE/B1368 and SFI/12/RC/2273. C.W. received an LGFG stipend (no.1215 LGFG-E).We are grateful to Aldert Zomer (Nijmegen Medical Centre, Nether-lands) for help with the initial steps of genome assembly.Genome AnnouncementsNovember/December 2013 Volume 1 Issue 6 e01084-13 genomea.asm.org 1 on December 14, 2016 by IRIShttp://genomea.asm.org/Downloaded from REFERENCES1. Food and Agricultural Organization of the United Nations/WorldHealth Organization. 2011. Guidelines for the evaluation of probiotics infood. Joint FAO/WHOWorking GroupMeet., London, LondonOntario,Canada, 30 April to 1 May 2002.2. Fanning S, Hall LJ, Cronin M, Zomer A, Macsharry J, Goulding D,O’Connell Motherway M, Shanahan F, Nally K, Dougan G, van Sin-deren D. 2012. Bifidobacterial surface-exopolysaccharide facilitatescommensal-host interaction through immune modulation and pathogenprotection. Proc. Natl. Acad. Sci. U. S. A. 109:2108–2113.3. 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High-quality draft genome sequence of Bifidobacterium longum E18, isolated from a healthy adult

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High-quality draft genome sequence of Bifidobacterium longum E18, isolated from a healthy adult

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