{"doi":"10.1101/2021.08.23.457365","title":"A compilation of fecal microbiome shotgun metagenomics from hospitalized patients undergoing hematopoietic cell transplantation","abstract":"Abstract Hospitalized patients receiving hematopoietic cell transplants provide a unique opportunity to study how the human gut microbiome changes in response to perturbations, and how the resulting changes in the microbiome feedback on its living host. We previously compiled a large-scale longitudinal dataset of stool microbiome compositions from these patients and associated metadata 1 . In that dataset the microbiome analysis was limited to the taxonomic composition of the bacterial population obtained from 16S rRNA gene sequencing. Here, we augment those data with shotgun metagenomic sequences from a nested subset of 395 stool samples. 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 2 to be analyzed without the users having to download or transfer the files. We provide examples that show how shotgun sequencing enriches microbiome analyses beyond the taxonomic composition such as the analysis of gene functions including virulence factors and antibiotic resistances, and the assembly of genomes from metagenomic data.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2021,"id":216770,"datarank":0.2554436655193045,"base_score":1.6094379124341003,"endowment":1.6094379124341003,"self_citation_contribution":0.24141568686511508,"citation_network_contribution":0.01402797865418937,"self_endowment_contribution":0.24141568686511508,"citer_contribution":0.01402797865418937,"corpus_percentile":40.64361414094531,"corpus_rank":7670,"citation_count":4,"citer_count":2,"citers_with_citation_signal":1,"citers_with_endowment":1,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9287,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2021-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":303729,"name":"Chen Liao","orcid":"0000-0001-8474-1196","position":1,"is_corresponding":false},{"id":669759,"name":"Bradford P. Taylor","orcid":"0000-0001-7808-955X","position":2,"is_corresponding":false},{"id":108855,"name":"Emily Fontana","orcid":"0000-0002-9060-5382","position":3,"is_corresponding":false},{"id":108856,"name":"Luigi A. Amoretti","orcid":"0000-0002-4625-5119","position":4,"is_corresponding":false},{"id":108857,"name":"Roberta J. Wright","orcid":"0000-0001-5299-0024","position":5,"is_corresponding":false},{"id":298456,"name":"Anqi Dai","orcid":"0000-0003-3106-4624","position":6,"is_corresponding":false},{"id":813064,"name":"Nicholas R. Waters","orcid":"0000-0002-9035-2143","position":7,"is_corresponding":false},{"id":225648,"name":"Jonathan U. Peled","orcid":"0000-0002-4029-7625","position":8,"is_corresponding":false},{"id":108835,"name":"Ying Taur","orcid":"0000-0002-6601-8284","position":9,"is_corresponding":false},{"id":108873,"name":"Miguel‐Angel Perales","orcid":"0000-0002-5910-4571","position":10,"is_corresponding":false},{"id":282437,"name":"Benjamin A. Siranosian","orcid":"0000-0002-4935-8172","position":11,"is_corresponding":false},{"id":36377,"name":"Ami S. Bhatt","orcid":"0000-0001-8099-2975","position":12,"is_corresponding":false},{"id":108880,"name":"Marcel R.M. van den Brink","orcid":"0000-0003-0696-4401","position":13,"is_corresponding":false},{"id":108879,"name":"Eric G. Pamer","orcid":"0000-0002-6755-9904","position":14,"is_corresponding":false},{"id":804139,"name":"Jonas Schlüter","orcid":"0000-0002-6214-9367","position":15,"is_corresponding":false},{"id":108878,"name":"João B. Xavier","orcid":"0000-0003-3592-1689","position":16,"is_corresponding":false},{"id":567676,"name":"Jinyuan Yan","orcid":"0000-0003-2046-5625","position":0,"is_corresponding":true}],"reference_count":48,"raw_metadata":null,"created_at":"2026-07-18T23:53:15.868165Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}