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Analysis of 1321 Eubacterium rectale genomes from metagenomes uncovers complex phylogeographic population structure and subspecies functional adaptations

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dc.contributor.authorKarcher, Nicolai
dc.contributor.authorPasolli, Edoardo
dc.contributor.authorAsnicar, Francesco
dc.contributor.authorHuang, Kun D.
dc.contributor.authorTett, Adrian
dc.contributor.authorManara, Serena
dc.contributor.authorArmanini, Federica
dc.contributor.authorBain, Debbie
dc.contributor.authorDuncan, Sylvia H.
dc.contributor.authorLouis, Petra
dc.contributor.authorZolfo, Moreno
dc.contributor.authorManghi, Paolo
dc.contributor.authorValles-Colomer, Mireia
dc.contributor.authorRaffaetà, Roberta
dc.contributor.authorRota-Stabelli, Omar
dc.contributor.authorCollado, Maria Carmen
dc.contributor.authorZeller, Georg
dc.contributor.authorFalush, Daniel
dc.contributor.authorMaixner, Frank
dc.contributor.authorWalker, Alan W.
dc.contributor.authorHuttenhower, Curtis
dc.contributor.authorSegata, Nicola
dc.contributor.institutionUniversity of Aberdeen.Rowett Instituteen
dc.date.accessioned2020-06-10T11:05:01Z
dc.date.available2020-06-10T11:05:01Z
dc.date.issued2020-06-08
dc.descriptionFunding This work was supported by NIH NHGRI grant R01HG005220, NIDDK grant R24DK110499, NIDDK grant U54DE023798, and CMIT grant 6935956 to C.H., and by the European Research Council (ERC-STG project MetaPG-716575), MIUR “Futuro in Ricerca” RBFR13EWWI_001, the European Union (H2020-SFS-2018-1 project MASTER-818368 and H2020-SC1-BHC project ONCOBIOME-825410), and the National Cancer Institute of the National Institutes of Health (1U01CA230551) to N.S. Further support was provided by the Programma Ricerca Budget prestazioni Eurac 2017 of the Province of Bolzano, Italy to F.M., and by the EU-H2020 (DiMeTrack-707345) to E.P. and N.S. D.B., S.H.D., P.L., A.W.W. and The Rowett Institute received core funding support from the Scottish Government Rural and Environmental Sciences and Analytical Services (SG-RESAS). Availability of data and materials All datasets used in this study are publicly available and matched with their respective PMID (Additional file 5). The high-quality E. rectale MAGs in fasta format and a metadata file are available at http://segatalab.cibio.unitn.it/data/Erectale_Karcher_et_al.html and in the following Zenodo repository: https://doi.org/10.5281/zenodo.3763191 [80]. The two new isolate genomes L2–21 and T3BWe13 have been uploaded to NCBI and can be found in RefSeq under the accession numbers GCF_008122485.1 [81] and GCF_008123415.1 [82], respectively.en
dc.description.statusPeer revieweden
dc.format.extent27
dc.format.extent3880756
dc.identifier170815435
dc.identifier665d56e3-355f-44fe-9981-519e0cee3fb1
dc.identifier85086297066
dc.identifier32513234
dc.identifier000540840900002
dc.identifier.citationKarcher, N, Pasolli, E, Asnicar, F, Huang, K D, Tett, A, Manara, S, Armanini, F, Bain, D, Duncan, S H, Louis, P, Zolfo, M, Manghi, P, Valles-Colomer, M, Raffaetà, R, Rota-Stabelli, O, Collado, M C, Zeller, G, Falush, D, Maixner, F, Walker, A W, Huttenhower, C & Segata, N 2020, 'Analysis of 1321 Eubacterium rectale genomes from metagenomes uncovers complex phylogeographic population structure and subspecies functional adaptations', Genome Biology, vol. 21, 138. https://doi.org/10.1186/s13059-020-02042-yen
dc.identifier.doi10.1186/s13059-020-02042-y
dc.identifier.issn1474-760X
dc.identifier.otherORCID: /0000-0003-2115-2399/work/76973768
dc.identifier.otherORCID: /0000-0002-4903-0978/work/76975498
dc.identifier.otherORCID: /0000-0001-5099-8495/work/79062828
dc.identifier.urihttps://hdl.handle.net/2164/14478
dc.identifier.urlhttp://www.scopus.com/inward/record.url?scp=85086297066&partnerID=8YFLogxKen
dc.identifier.vol21en
dc.language.isoeng
dc.relation.ispartofGenome Biologyen
dc.subjectBUTYRATE-PRODUCING BACTERIAen
dc.subjectGUT MICROBIOMEen
dc.subjectALIGNMENTen
dc.subjectTRANSMISSIONen
dc.subjectCSRAen
dc.subjectTOOLen
dc.subjectQH426 Geneticsen
dc.subjectGeneticsen
dc.subjectEcology, Evolution, Behavior and Systematicsen
dc.subjectCell Biologyen
dc.subjectRural and Environmental Science and Analytical Services (RESAS)en
dc.subjectEuropean Research Councilen
dc.subjectMetaPG-716575en
dc.subjectEuropean Commissionen
dc.subjectMASTER-818368en
dc.subjectONCOBIOME-825410en
dc.subjectSupplementary Dataen
dc.subject.lccQH426en
dc.titleAnalysis of 1321 Eubacterium rectale genomes from metagenomes uncovers complex phylogeographic population structure and subspecies functional adaptationsen
dc.typeJournal articleen

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