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

• Published in: Scientific data Vol. 9; no. 1; p. 219
• Main Authors: Yan, Jinyuan, Liao, Chen, Taylor, Bradford P., Fontana, Emily, Amoretti, Luigi A., Wright, Roberta J., Littmann, Eric R., Dai, Anqi, Waters, Nicholas, Peled, Jonathan U., Taur, Ying, Perales, Miguel-Angel, Siranosian, Benjamin A., Bhatt, Ami S., van den Brink, Marcel R. M., Pamer, Eric G., Schluter, Jonas, Xavier, Joao B.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 18.05.2022; Nature Publishing Group; Nature Portfolio
• Subjects: 631/114/2402; 692/308; Bone cancer; Bone marrow transplantation; Data Descriptor; DNA sequencing; Fecal microflora; Feces - microbiology; Genomes; Hematopoietic Stem Cell Transplantation; Humanities and Social Sciences; Humans; Intestinal microflora; Metadata; Metagenomics; Microbiomes; Microbiota; Microbiota - genetics; multidisciplinary; RNA, Ribosomal, 16S - genetics; rRNA 16S; Science; Science (multidisciplinary); Stem cell transplantation; Transplants & implants; Virulence factors
• ISSN: 2052-4463; 2052-4463
• DOI: 10.1038/s41597-022-01302-9

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. Measurement(s) Metagenomics Technology Type(s) next generation DNA sequencing Sample Characteristic - Organism Bacteria Sample Characteristic - Environment gut microbiome Sample Characteristic - Location New York City