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

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

Authors:	Yan, J.; Liao, C.; Taylor, B. P.; Fontana, E.; Amoretti, L. A.; Wright, R. J.; Littmann, E. R.; Dai, A.; Waters, N.; Peled, J. U.; Taur, Y.; Perales, M. A.; Siranosian, B. A.; Bhatt, A. S.; van den Brink, M. R. M.; Pamer, E. G.; Schluter, J.; Xavier, J. B.
Article Title:	A compilation of fecal microbiome shotgun metagenomics from hematopoietic cell transplantation patients
Abstract:	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.
Keywords:	bacteremia; vancomycin; recovery; intestinal microbiota; gut microbiota; domination
Journal Title:	Scientific Data
Volume:	9
ISSN:	2052-4463
Publisher:	Nature Publishing Group
Date Published:	2022-05-18
Start Page:	219
Language:	English
ACCESSION:	WOS:000797522700001
DOI:	10.1038/s41597-022-01302-9
PROVIDER:	wos
PMCID:	PMC9117330
PUBMED:	35585088
Notes:	Article; Data Paper -- 219 -- Source: Wos