ArticleScientific data2022
A compilation of fecal microbiome shotgun metagenomics from hematopoietic cell transplantation patients.
Article in Scientific data, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Metabiosis underlies a microbiota permissive to Pseudomonadota and increases the risk of gut-borne bloodstream infection.bioRxiv : the preprint server for biology · 2026Article
- DynaBiome: interpretable unsupervised learning of gut microbiome dysbiosis via temporal deep models.BMC bioinformatics · 2026Article
- Multi-omics insights into gut microbiota-metabolite interactions under probiotic intervention in a developmental cafeteria diet model.BMC genomics · 2026Article
- Ecological management of the microbiota in patients with cancer.Nature reviews. Clinical oncology · 2025Review
- Gut microbiota and colorectal cancer: mechanistic insights, diagnostic advances, and microbiome-based therapeutic strategies.Frontiers in microbiology · 2025Review
- Oral bacteria relative abundance in faeces increases due to gut microbiota depletion and is linked with patient outcomes.Nature microbiology · 2024Article
- Microbiota and metabolic adaptation shapebioRxiv : the preprint server for biology · 2024Article
- Insights into gut microbiomes in stem cell transplantation by comprehensive shotgun long-read sequencing.Scientific reports · 2024Article
- Clinically relevant antibiotic resistance genes are linked to a limited set of taxa within gut microbiome worldwide.Nature communications · 2023Article
- The TaxUMAP atlas: Efficient display of large clinical microbiome data reveals ecological competition in protection against bacteremia.Cell host & microbe · 2023Article
- The association between altered intestinal microbiome, impaired systemic and ocular surface immunity, and impaired wound healing response after corneal alkaline-chemical injury in diabetic mice.Frontiers in immunology · 2023Article
- Virulence Factors in Colorectal Cancer Metagenomes and Association of Microbial Siderophores with Advanced Stages.Microorganisms · 2022Article
- A compilation of fecal microbiome shotgun metagenomics from hematopoietic cell transplantation patients.Scientific data · 2022Article
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Authors and funding
18 authors.
Funding
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.
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