دورية أكاديمية
أعرض في EDS

A compilation of fecal microbiome shotgun metagenomics from hematopoietic cell transplantation patients.

التفاصيل البيبلوغرافية
العنوان: A compilation of fecal microbiome shotgun metagenomics from hematopoietic cell transplantation patients.
المؤلفون: Yan J; Program for Computational and Systems Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA. yanj2@mskcc.org., Liao C; Program for Computational and Systems Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA., Taylor BP; Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA., Fontana E; Infectious Disease Service, Department of Medicine, and Immunology Program, Sloan Kettering Institute, New York, NY, USA., Amoretti LA; Infectious Disease Service, Department of Medicine, and Immunology Program, Sloan Kettering Institute, New York, NY, USA., Wright RJ; Infectious Disease Service, Department of Medicine, and Immunology Program, Sloan Kettering Institute, New York, NY, USA., Littmann ER; Duchossois Family Institute, University of Chicago, Chicago, IL, USA., Dai A; Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA., Waters N; Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA., Peled JU; Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.; Weill Cornell Medical College, New York, NY, USA., Taur Y; Infectious Disease Service, Department of Medicine, and Immunology Program, Sloan Kettering Institute, New York, NY, USA., Perales MA; Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.; Weill Cornell Medical College, New York, NY, USA., Siranosian BA; Department of Genetics, Stanford University, Stanford, CA, USA., Bhatt AS; Department of Genetics, Stanford University, Stanford, CA, USA.; Department of Medicine, Division of Hematology, Stanford University, Stanford, CA, USA.; Department of Medicine, Division of Blood and Marrow Transplantation and Cellular Therapy, Stanford University School of Medicine, Stanford, CA, USA., van den Brink MRM; Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.; Weill Cornell Medical College, New York, NY, USA., Pamer EG; Duchossois Family Institute, University of Chicago, Chicago, IL, USA., Schluter J; Institute for Computational Medicine, Department of Microbiology, New York University, New York, NY, USA., Xavier JB; Program for Computational and Systems Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA. xavierj@mskcc.org.
المصدر: Scientific data [Sci Data] 2022 May 18; Vol. 9 (1), pp. 219. Date of Electronic Publication: 2022 May 18.
نوع المنشور: Dataset; Journal Article
اللغة: English
بيانات الدورية: Publisher: Nature Publishing Group Country of Publication: England NLM ID: 101640192 Publication Model: Electronic Cited Medium: Internet ISSN: 2052-4463 (Electronic) Linking ISSN: 20524463 NLM ISO Abbreviation: Sci Data Subsets: MEDLINE
أسماء مطبوعة: Original Publication: London : Nature Publishing Group, 2014-
مواضيع طبية MeSH: Feces*/microbiology , Hematopoietic Stem Cell Transplantation* , Microbiota*/genetics, Humans ; Metagenomics ; RNA, Ribosomal, 16S/genetics
مستخلص: Hospitalized patients receiving hematopoietic cell transplants provide a unique opportunity to study the human gut microbiome. We previously compiled a large-scale longitudinal dataset of fecal microbiota and associated metadata, but we had limited that analysis to taxonomic composition of bacteria from 16S rRNA gene sequencing. Here we augment those data with shotgun metagenomics. The compilation amounts to a nested subset of 395 samples compiled from different studies at Memorial Sloan Kettering. Shotgun metagenomics describes the microbiome at the functional level, particularly in antimicrobial resistances and virulence factors. We provide accession numbers that link each sample to the paired-end sequencing files deposited in a public repository, which can be directly accessed by the online services of PATRIC to be analyzed without the users having to download or transfer the files. Then, we show how shotgun sequencing enables the assembly of genomes from metagenomic data. The new data, combined with the metadata published previously, enables new functional studies of the microbiomes of patients with cancer receiving bone marrow transplantation.
(© 2022. The Author(s).)
References: J Clin Oncol. 2017 May 20;35(15):1650-1659. (PMID: 28296584)
Sci Data. 2019 Jul 22;6(1):129. (PMID: 31332186)
Nat Commun. 2017 Dec 22;8(1):2260. (PMID: 29273717)
Nat Biotechnol. 2021 Jun;39(6):727-736. (PMID: 33462508)
Genome Biol. 2019 Nov 28;20(1):257. (PMID: 31779668)
Front Cell Infect Microbiol. 2021 Jul 20;11:639667. (PMID: 34458156)
Sci Transl Med. 2018 Sep 26;10(460):. (PMID: 30257956)
Blood. 2018 Jun 28;131(26):2978-2986. (PMID: 29674425)
PLoS Comput Biol. 2012;8(6):e1002358. (PMID: 22719234)
Nature. 2020 Dec;588(7837):303-307. (PMID: 33239790)
PeerJ. 2019 Jul 26;7:e7359. (PMID: 31388474)
Nat Med. 2020 Jan;26(1):59-64. (PMID: 31907459)
Sci Data. 2022 May 18;9(1):219. (PMID: 35585088)
PLoS One. 2013;8(2):e57923. (PMID: 23460914)
Nature. 2019 May;569(7758):641-648. (PMID: 31142853)
Nat Microbiol. 2018 Jul;3(7):836-843. (PMID: 29807988)
J Clin Invest. 2010 Dec;120(12):4332-41. (PMID: 21099116)
Proc Natl Acad Sci U S A. 2011 Mar 15;108 Suppl 1:4554-61. (PMID: 20847294)
mSystems. 2018 Nov 13;3(6):. (PMID: 30443602)
Blood. 2020 Jul 2;136(1):130-136. (PMID: 32430495)
Sci Data. 2021 Mar 2;8(1):71. (PMID: 33654104)
Infect Immun. 2019 Jun 20;87(7):. (PMID: 31010813)
Bioinformatics. 2016 Feb 15;32(4):605-7. (PMID: 26515820)
Nucleic Acids Res. 2020 Jan 8;48(D1):D517-D525. (PMID: 31665441)
Nat Rev Microbiol. 2011 Apr;9(4):233-43. (PMID: 21358670)
Biochem Pharmacol. 2017 Jun 15;134:114-126. (PMID: 27641814)
Nat Methods. 2014 Nov;11(11):1144-6. (PMID: 25218180)
Infect Immun. 2019 Aug 21;87(9):. (PMID: 31262981)
Nature. 2010 Mar 4;464(7285):59-65. (PMID: 20203603)
Nucleic Acids Res. 2020 Jan 8;48(D1):D606-D612. (PMID: 31667520)
Biol Blood Marrow Transplant. 2015 Aug;21(8):1373-83. (PMID: 25977230)
Nucleic Acids Res. 2021 Jul 2;49(W1):W263-W270. (PMID: 34019648)
Nature. 2014 Jan 23;505(7484):559-63. (PMID: 24336217)
Nat Commun. 2022 Jan 31;13(1):586. (PMID: 35102136)
Genome Med. 2011 Mar 04;3(3):14. (PMID: 21392406)
Gut. 2016 Jan;65(1):57-62. (PMID: 26069274)
Clin Infect Dis. 2012 Oct;55(7):905-14. (PMID: 22718773)
Clin Infect Dis. 2021 Dec 6;73(11):e4627-e4635. (PMID: 31976518)
N Engl J Med. 2020 Feb 27;382(9):822-834. (PMID: 32101664)
Genome Res. 2017 May;27(5):824-834. (PMID: 28298430)
Elife. 2020 Dec 29;9:. (PMID: 33372654)
Sci Transl Med. 2016 May 18;8(339):339ra71. (PMID: 27194729)
BMC Cancer. 2021 May 22;21(1):591. (PMID: 34022842)
BMC Bioinformatics. 2018 Aug 29;19(1):307. (PMID: 30157759)
Science. 2019 Nov 29;366(6469):1143-1149. (PMID: 31780560)
Nucleic Acids Res. 2019 Jan 8;47(D1):D687-D692. (PMID: 30395255)
J Infect. 2014 Oct;69(4):341-351. (PMID: 24931578)
Cell Host Microbe. 2015 May 13;17(5):577-91. (PMID: 25974300)
Nat Rev Microbiol. 2018 Jul;16(7):410-422. (PMID: 29795328)
Clin Infect Dis. 2017 Nov 29;65(12):1984-1991. (PMID: 29020185)
معلومات مُعتمدة: U01 AI124275 United States AI NIAID NIH HHS; P30 CA008748 United States CA NCI NIH HHS; R56 AI137269 United States AI NIAID NIH HHS; K08 HL143189 United States HL NHLBI NIH HHS; R01 AI137269 United States AI NIAID NIH HHS
المشرفين على المادة: 0 (RNA, Ribosomal, 16S)
تواريخ الأحداث: Date Created: 20220518 Date Completed: 20220520 Latest Revision: 20240514
رمز التحديث: 20240514
مُعرف محوري في PubMed: PMC9117330
DOI: 10.1038/s41597-022-01302-9
PMID: 35585088
قاعدة البيانات: MEDLINE
الوصف
تدمد:2052-4463
DOI:10.1038/s41597-022-01302-9