{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,30]],"date-time":"2026-06-30T07:22:55Z","timestamp":1782804175652,"version":"3.54.5"},"reference-count":81,"publisher":"Elsevier BV","issue":"10","license":[{"start":{"date-parts":[[2023,10,1]],"date-time":"2023-10-01T00:00:00Z","timestamp":1696118400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2023,10,1]],"date-time":"2023-10-01T00:00:00Z","timestamp":1696118400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2023,9,1]],"date-time":"2023-09-01T00:00:00Z","timestamp":1693526400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000069","name":"National Institute of Arthritis and Musculoskeletal and Skin Diseases","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000069","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000051","name":"National Human Genome Research Institute","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000051","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006492","name":"National Institute of Allergy and Infectious Diseases Division of Intramural Research","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100006492","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000054","name":"National Cancer Institute","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["cell.com","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Cell Reports Medicine"],"published-print":{"date-parts":[[2023,10]]},"DOI":"10.1016\/j.xcrm.2023.101205","type":"journal-article","created":{"date-parts":[[2023,9,26]],"date-time":"2023-09-26T14:29:46Z","timestamp":1695738586000},"page":"101205","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":6,"title":["Expanded microbiome niches of RAG-deficient patients"],"prefix":"10.1016","volume":"4","author":[{"given":"Ryan A.","family":"Blaustein","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zeyang","family":"Shen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sara Saheb","family":"Kashaf","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"ShihQueen","family":"Lee-Lin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sean","family":"Conlan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jim","family":"Thomas","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James","family":"Mullikin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alice","family":"Young","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gerry","family":"Bouffard","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Betty","family":"Barnabas","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shelise","family":"Brooks","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chloe","family":"Buchter","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Juyun","family":"Crawford","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joel","family":"Han","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shi-ling","family":"Ho","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Richelle","family":"Legaspi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Quino","family":"Maduro","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Holly","family":"Marfani","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Casandra","family":"Montemayor","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Karen","family":"Schandler","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Brian","family":"Schmidt","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christina","family":"Sison","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mal","family":"Stantripop","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sean","family":"Black","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mila","family":"Dekhtyar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cathy","family":"Masiello","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jenny","family":"McDowell","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Morgan","family":"Park","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pam","family":"Thomas","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Meg","family":"Vemulapalli","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marita","family":"Bosticardo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ottavia M.","family":"Delmonte","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cassandra J.","family":"Holmes","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Monica E.","family":"Taylor","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Glenna","family":"Banania","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Keisuke","family":"Nagao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dimana","family":"Dimitrova","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jennifer A.","family":"Kanakry","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Helen","family":"Su","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Steven M.","family":"Holland","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jenna R.E.","family":"Bergerson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexandra F.","family":"Freeman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luigi D.","family":"Notarangelo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Heidi H.","family":"Kong","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6860-348X","authenticated-orcid":false,"given":"Julia A.","family":"Segre","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.xcrm.2023.101205_bib1","doi-asserted-by":"crossref","first-page":"492","DOI":"10.1038\/s41422-020-0332-7","article-title":"Interaction between microbiota and immunity in health and disease","volume":"30","author":"Zheng","year":"2020","journal-title":"Cell Res."},{"key":"10.1016\/j.xcrm.2023.101205_bib2","first-page":"121","article-title":"Role of microbiota in immunity and inflammation","volume":"157","author":"Belkaid","year":"2014","journal-title":"Natl. Inst. Heal."},{"key":"10.1016\/j.xcrm.2023.101205_bib3","doi-asserted-by":"crossref","first-page":"2103","DOI":"10.1101\/gr.159467.113","article-title":"The altered landscape of the human skin microbiome in patients with primary immunodeficiencies","volume":"23","author":"Oh","year":"2013","journal-title":"Genome Res."},{"key":"10.1016\/j.xcrm.2023.101205_bib4","doi-asserted-by":"crossref","first-page":"1815","DOI":"10.1038\/s41591-018-0211-7","article-title":"Expanded skin virome in DOCK8-deficient patients","volume":"24","author":"Tirosh","year":"2018","journal-title":"Nat. Med."},{"key":"10.1016\/j.xcrm.2023.101205_bib5","doi-asserted-by":"crossref","first-page":"610","DOI":"10.1182\/blood.2019000923","article-title":"Immune dysregulation in patients with RAG deficiency and other forms of combined immune deficiency","volume":"135","author":"Delmonte","year":"2020","journal-title":"Blood"},{"key":"10.1016\/j.xcrm.2023.101205_bib6","series-title":"Physiol. Behav.","first-page":"646","article-title":"RAG Deficiency: Two Genes, Many Diseases","volume":"38","author":"Delmonte","year":"2019"},{"key":"10.1016\/j.xcrm.2023.101205_bib7","doi-asserted-by":"crossref","first-page":"234","DOI":"10.1038\/nri.2016.28","article-title":"Human RAG mutations: Biochemistry and clinical implications","volume":"16","author":"Notarangelo","year":"2016","journal-title":"Nat. Rev. Immunol."},{"key":"10.1016\/j.xcrm.2023.101205_bib8","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1186\/s13059-019-1891-0","article-title":"Improved metagenomic analysis with Kraken 2","volume":"20","author":"Wood","year":"2019","journal-title":"Genome Biol."},{"key":"10.1016\/j.xcrm.2023.101205_bib9","doi-asserted-by":"crossref","first-page":"902","DOI":"10.1038\/nmeth.3589","article-title":"MetaPhlAn2 for enhanced metagenomic taxonomic profiling","volume":"12","author":"Truong","year":"2015","journal-title":"Nat. Methods"},{"key":"10.1016\/j.xcrm.2023.101205_bib10","doi-asserted-by":"crossref","first-page":"169","DOI":"10.1038\/s41564-021-01011-w","article-title":"Integrating cultivation and metagenomics for a multi-kingdom view of skin microbiome diversity and functions","volume":"7","author":"Saheb Kashaf","year":"2022","journal-title":"Nat. Microbiol."},{"key":"10.1016\/j.xcrm.2023.101205_bib11","doi-asserted-by":"crossref","first-page":"1533","DOI":"10.1038\/s41564-017-0012-7","article-title":"Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life","volume":"2","author":"Parks","year":"2017","journal-title":"Nat. Microbiol."},{"key":"10.1016\/j.xcrm.2023.101205_bib12","doi-asserted-by":"crossref","DOI":"10.1038\/nmicrobiol.2016.48","article-title":"A new view of the tree of life","volume":"1","author":"Hug","year":"2016","journal-title":"Nat. Microbiol."},{"key":"10.1016\/j.xcrm.2023.101205_bib13","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1038\/s41587-020-0603-3","article-title":"A unified catalog of 204,938 reference genomes from the human gut microbiome","volume":"39","author":"Almeida","year":"2021","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.xcrm.2023.101205_bib14","doi-asserted-by":"crossref","first-page":"298","DOI":"10.1016\/j.molmed.2021.01.003","article-title":"Breakthroughs and Bottlenecks in Microbiome Research","volume":"27","author":"Liwinski","year":"2021","journal-title":"Trends Mol. Med."},{"key":"10.1016\/j.xcrm.2023.101205_bib15","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1038\/s41590-017-0007-9","article-title":"Emerging viral diseases from a vaccinology perspective: Preparing for the next pandemic review-article","volume":"19","author":"Graham","year":"2018","journal-title":"Nat. Immunol."},{"key":"10.1016\/j.xcrm.2023.101205_bib16","doi-asserted-by":"crossref","first-page":"3348","DOI":"10.1172\/JCI139601","article-title":"Prototype pathogen approach for pandemic preparedness: World on fire","volume":"130","author":"Graham","year":"2020","journal-title":"J.\u00a0Clin. Invest."},{"key":"10.1016\/j.xcrm.2023.101205_bib17","doi-asserted-by":"crossref","first-page":"E6","DOI":"10.1038\/s41586-018-0310-0","article-title":"The evolutionary history of vertebrate RNA viruses","volume":"561","author":"Shi","year":"2018","journal-title":"Nature"},{"key":"10.1016\/j.xcrm.2023.101205_bib18","doi-asserted-by":"crossref","first-page":"539","DOI":"10.1016\/j.jaci.2022.10.022","article-title":"The diagnosis of severe combined immunodeficiency (SCID): The Primary Immune Deficiency Treatment Consortium (PIDTC) 2022 Definitions","volume":"151","author":"Dvorak","year":"2023","journal-title":"J.\u00a0Allergy Clin. Immunol."},{"key":"10.1016\/j.xcrm.2023.101205_bib19","doi-asserted-by":"crossref","first-page":"5139","DOI":"10.1038\/s41467-022-32805-z","article-title":"A compendium of 32,277 metagenome-assembled genomes and over 80 million genes from the early-life human gut microbiome","volume":"13","author":"Zeng","year":"2022","journal-title":"Nat. Commun."},{"key":"10.1016\/j.xcrm.2023.101205_bib20","doi-asserted-by":"crossref","first-page":"eabd8077","DOI":"10.1126\/scitranslmed.abd8077","article-title":"Alterations of human skin microbiome and expansion of antimicrobial resistance after systemic antibiotics","volume":"13","author":"Jo","year":"2021","journal-title":"Sci. Transl. Med."},{"key":"10.1016\/j.xcrm.2023.101205_bib21","doi-asserted-by":"crossref","first-page":"eaal4651","DOI":"10.1126\/scitranslmed.aal4651","article-title":"Staphylococcus aureus and staphylococcus epidermidis strain diversity underlying pediatric atopic dermatitis","volume":"9","author":"Byrd","year":"2017","journal-title":"Sci. Transl. Med."},{"key":"10.1016\/j.xcrm.2023.101205_bib22","doi-asserted-by":"crossref","first-page":"518","DOI":"10.1086\/505494","article-title":"Tigecycline : A Critical Analysis","volume":"43","author":"Stein","year":"2006","journal-title":"Clin. Infect. Dis."},{"key":"10.1016\/j.xcrm.2023.101205_bib23","doi-asserted-by":"crossref","first-page":"578","DOI":"10.1038\/s41587-020-00774-7","article-title":"CheckV assesses the quality and completeness of metagenome-assembled viral genomes","volume":"39","author":"Nayfach","year":"2021","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.xcrm.2023.101205_bib24","doi-asserted-by":"crossref","first-page":"1393","DOI":"10.1099\/jgv.0.001318","article-title":"Updated classification of norovirus genogroups and genotypes","volume":"100","author":"Chhabra","year":"2019","journal-title":"J.\u00a0Gen. Virol."},{"key":"10.1016\/j.xcrm.2023.101205_bib25","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0036685","article-title":"Genetic diversity of the genus cosavirus in the family picornaviridae: A new species, recombination, and 26 new genotypes","volume":"7","author":"Kapusinszky","year":"2012","journal-title":"PLoS One"},{"key":"10.1016\/j.xcrm.2023.101205_bib26","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1038\/nature13786","article-title":"Biogeography and individuality shape function in the human skin metagenome","volume":"514","author":"Oh","year":"2014","journal-title":"Nature"},{"key":"10.1016\/j.xcrm.2023.101205_bib27","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1038\/nature11234","article-title":"Structure, function and diversity of the healthy human microbiome","volume":"486","author":"Gevers","year":"2012","journal-title":"Nature"},{"key":"10.1016\/j.xcrm.2023.101205_bib28","doi-asserted-by":"crossref","first-page":"854","DOI":"10.1016\/j.cell.2016.04.008","article-title":"Temporal Stability of the Human Skin Microbiome","volume":"165","author":"Oh","year":"2016","journal-title":"Cell"},{"key":"10.1016\/j.xcrm.2023.101205_bib29","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1038\/nrmicro.2017.157","article-title":"The human skin microbiome","volume":"16","author":"Byrd","year":"2018","journal-title":"Nat. Rev. Microbiol."},{"key":"10.1016\/j.xcrm.2023.101205_bib30","doi-asserted-by":"crossref","first-page":"1909","DOI":"10.1016\/j.immuni.2022.08.016","article-title":"The CD4+ T\u00a0cell response to a commensal-derived epitope transitions from a tolerant to an inflammatory state in Crohn\u2019s disease","volume":"55","author":"Pedersen","year":"2022","journal-title":"Immunity"},{"key":"10.1016\/j.xcrm.2023.101205_bib31","doi-asserted-by":"crossref","first-page":"210","DOI":"10.1016\/j.chom.2020.12.002","article-title":"Murine model of colonization with fungal pathogen Candida auris to explore skin tropism, host risk factors and therapeutic strategies","volume":"29","author":"Huang","year":"2021","journal-title":"Cell Host Microbe"},{"key":"10.1016\/j.xcrm.2023.101205_bib32","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1182\/blood-2017-12-820985","article-title":"Hypomorphic Rag1 mutations alter the preimmune repertoire at early stages of lymphoid development","volume":"132","author":"Ott de Bruin","year":"2018","journal-title":"Blood"},{"key":"10.1016\/j.xcrm.2023.101205_bib33","doi-asserted-by":"crossref","first-page":"1165","DOI":"10.1016\/j.jaci.2020.04.005","article-title":"Cutaneous barrier leakage and gut inflammation drive skin disease in Omenn syndrome","volume":"146","author":"Rigoni","year":"2020","journal-title":"J.\u00a0Allergy Clin. Immunol."},{"key":"10.1016\/j.xcrm.2023.101205_bib34","doi-asserted-by":"crossref","first-page":"515","DOI":"10.1111\/apt.13302","article-title":"Chemotherapy-driven dysbiosis in the intestinal microbiome","volume":"42","author":"Montassier","year":"2015","journal-title":"Aliment. Pharmacol. Ther."},{"key":"10.1016\/j.xcrm.2023.101205_bib35","doi-asserted-by":"crossref","first-page":"20140087","DOI":"10.1098\/rstb.2014.0087","article-title":"The human gut resistome","volume":"370","author":"van Schaik","year":"2015","journal-title":"Philos. Trans. R. Soc. Lond. B Biol. Sci."},{"key":"10.1016\/j.xcrm.2023.101205_bib36","doi-asserted-by":"crossref","DOI":"10.1016\/j.celrep.2022.110649","article-title":"Acute and persistent effects of commonly used antibiotics on the gut microbiome and resistome in healthy adults","volume":"39","author":"Anthony","year":"2022","journal-title":"Cell Rep."},{"key":"10.1016\/j.xcrm.2023.101205_bib37","doi-asserted-by":"crossref","first-page":"1255","DOI":"10.1038\/s41564-018-0257-9","article-title":"Recovery of gut microbiota of healthy adults following antibiotic exposure","volume":"3","author":"Palleja","year":"2018","journal-title":"Nat. Microbiol."},{"key":"10.1016\/j.xcrm.2023.101205_bib38","doi-asserted-by":"crossref","first-page":"2285","DOI":"10.1038\/s41564-019-0550-2","article-title":"Persistent metagenomic signatures of early-life hospitalization and antibiotic treatment in the infant gut microbiota and resistome","volume":"4","author":"Gasparrini","year":"2019","journal-title":"Nat. Microbiol."},{"key":"10.1016\/j.xcrm.2023.101205_bib39","article-title":"Epidemiology characteristics of human coronaviruses in patients with respiratory infection symptoms and phylogenetic analysis of HCoV-OC43 during 2010-2015 in Guangzhou","volume":"13","author":"Zhang","year":"2018","journal-title":"PLoS One"},{"key":"10.1016\/j.xcrm.2023.101205_bib40","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0217744","article-title":"Human coronavirus alone or in co-infection with rhinovirus C is a risk factor for severe respiratory disease and admission to the pediatric intensive care unit: A one-year study in Southeast Brazil","volume":"14","author":"Matsuno","year":"2019","journal-title":"PLoS One"},{"key":"10.1016\/j.xcrm.2023.101205_bib41","series-title":"Incidence and Outcome of Coinfections with SARS-CoV-2 and Rhinovirus","author":"Le Glass","year":"2021"},{"key":"10.1016\/j.xcrm.2023.101205_bib42","doi-asserted-by":"crossref","first-page":"1222","DOI":"10.3389\/fmicb.2018.01222","article-title":"Epidermodysplasia verruciformis: Inborn errors of immunity to human beta-papillomaviruses","volume":"9","author":"de Jong","year":"2018","journal-title":"Front. Microbiol."},{"key":"10.1016\/j.xcrm.2023.101205_bib43","doi-asserted-by":"crossref","first-page":"1118","DOI":"10.1093\/infdis\/jiab622","article-title":"Yearlong COVID-19 Infection Reveals Within-Host Evolution of SARS-CoV-2 in a Patient With B-Cell Depletion","volume":"225","author":"Nussenblatt","year":"2022","journal-title":"J.\u00a0Infect. Dis."},{"key":"10.1016\/j.xcrm.2023.101205_bib49","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1089\/cmb.2012.0021","article-title":"SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing","volume":"19","author":"Bankevich","year":"2012","journal-title":"J.\u00a0Comput. Biol."},{"key":"10.1016\/j.xcrm.2023.101205_bib50","doi-asserted-by":"crossref","first-page":"158","DOI":"10.1186\/s40168-018-0541-1","article-title":"MetaWRAP\u2014a flexible pipeline for genome-resolved metagenomic data analysis","volume":"6","author":"Uritskiy","year":"2018","journal-title":"Microbiome"},{"key":"10.1016\/j.xcrm.2023.101205_bib51","doi-asserted-by":"crossref","first-page":"178","DOI":"10.1186\/s13059-021-02393-0","article-title":"GUNC: detection of chimerism and contamination in prokaryotic genomes","volume":"22","author":"Orakov","year":"2021","journal-title":"Genome Biol."},{"key":"10.1016\/j.xcrm.2023.101205_bib52","doi-asserted-by":"crossref","first-page":"2864","DOI":"10.1038\/ismej.2017.126","article-title":"DRep: A tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication","volume":"11","author":"Olm","year":"2017","journal-title":"ISME J."},{"key":"10.1016\/j.xcrm.2023.101205_bib53","doi-asserted-by":"crossref","first-page":"1925","DOI":"10.1093\/bioinformatics\/btz848","article-title":"GTDB-Tk: A toolkit to classify genomes with the genome taxonomy database","volume":"36","author":"Chaumeil","year":"2020","journal-title":"Bioinformatics"},{"key":"10.1016\/j.xcrm.2023.101205_bib54","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0009490","article-title":"FastTree 2 - Approximately maximum-likelihood trees for large alignments","volume":"5","author":"Price","year":"2010","journal-title":"PLoS One"},{"key":"10.1016\/j.xcrm.2023.101205_bib55","doi-asserted-by":"crossref","first-page":"526","DOI":"10.1093\/bioinformatics\/bty633","article-title":"ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R","volume":"35","author":"Paradis","year":"2019","journal-title":"Bioinformatics"},{"key":"10.1016\/j.xcrm.2023.101205_bib56","doi-asserted-by":"crossref","first-page":"244","DOI":"10.1186\/s13059-020-02155-4","article-title":"Estimating the quality of eukaryotic genomes recovered from metagenomic analysis with EukCC","volume":"21","author":"Saary","year":"2020","journal-title":"Genome Biol."},{"key":"10.1016\/j.xcrm.2023.101205_bib57","doi-asserted-by":"crossref","first-page":"132","DOI":"10.1186\/s13059-016-0997-x","article-title":"Mash: Fast genome and metagenome distance estimation using MinHash","volume":"17","author":"Ondov","year":"2016","journal-title":"Genome Biol."},{"key":"10.1016\/j.xcrm.2023.101205_bib58","doi-asserted-by":"crossref","first-page":"R12","DOI":"10.1186\/gb-2004-5-2-r12","article-title":"Versatile and open software for comparing large genomes","volume":"5","author":"Kurtz","year":"2004","journal-title":"Genome Biol."},{"key":"10.1016\/j.xcrm.2023.101205_bib59","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1186\/s40168-017-0283-5","article-title":"VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data","volume":"5","author":"Ren","year":"2017","journal-title":"Microbiome"},{"key":"10.1016\/j.xcrm.2023.101205_bib60","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1186\/s40168-020-00990-y","article-title":"VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses","volume":"9","author":"Guo","year":"2021","journal-title":"Microbiome"},{"key":"10.1016\/j.xcrm.2023.101205_bib61","doi-asserted-by":"crossref","first-page":"3150","DOI":"10.1093\/bioinformatics\/bts565","article-title":"CD-HIT: Accelerated for clustering the next-generation sequencing data","volume":"28","author":"Fu","year":"2012","journal-title":"Bioinformatics"},{"key":"10.1016\/j.xcrm.2023.101205_bib63","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1186\/1471-2105-11-119","article-title":"Prodigal: Prokaryotic gene recognition and translation initiation site identification","volume":"11","author":"Hyatt","year":"2010","journal-title":"BMC Bioinf."},{"key":"10.1016\/j.xcrm.2023.101205_bib64","doi-asserted-by":"crossref","first-page":"W200","DOI":"10.1093\/nar\/gky448","article-title":"HMMER web server: 2018 update","volume":"46","author":"Potter","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.xcrm.2023.101205_bib65","doi-asserted-by":"crossref","first-page":"1792","DOI":"10.1093\/nar\/gkh340","article-title":"MUSCLE: Multiple sequence alignment with high accuracy and high throughput","volume":"32","author":"Edgar","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.xcrm.2023.101205_bib66","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows-Wheeler transform","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"10.1016\/j.xcrm.2023.101205_bib68","doi-asserted-by":"crossref","first-page":"1986","DOI":"10.1093\/bioinformatics\/bty037","article-title":"HPViewer: Sensitive and specific genotyping of human papillomavirus in metagenomic DNA","volume":"34","author":"Hao","year":"2018","journal-title":"Bioinformatics"},{"key":"10.1016\/j.xcrm.2023.101205_bib69","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1004557","article-title":"High-Specificity Targeted Functional Profiling in Microbial Communities with ShortBRED","volume":"11","author":"Kaminski","year":"2015","journal-title":"PLoS Comput. Biol."},{"key":"10.1016\/j.xcrm.2023.101205_bib47","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with Bowtie 2","volume":"9","author":"Langmead","year":"2012","journal-title":"Nat. Methods"},{"key":"10.1016\/j.xcrm.2023.101205_bib72","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J.\u00a0Mol. Biol."},{"key":"10.1016\/j.xcrm.2023.101205_bib73","article-title":"Automated assembly scaffolding elevates a new tomato system for high-throughput genome editing","author":"Alonge","year":"2021","journal-title":"bioRxiv"},{"key":"10.1016\/j.xcrm.2023.101205_bib74","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1016\/j.jcv.2011.03.006","article-title":"An automated genotyping tool for enteroviruses and noroviruses","volume":"51","author":"Kroneman","year":"2011","journal-title":"J.\u00a0Clin. Virol."},{"key":"10.1016\/j.xcrm.2023.101205_bib76","doi-asserted-by":"crossref","first-page":"28","DOI":"10.1111\/2041-210X.12628","article-title":"ggtree: an r package for visualization and annotation of phylogenetic trees with their covariates and other associated data","volume":"8","author":"Yu","year":"2017","journal-title":"Methods Ecol. Evol."},{"key":"10.1016\/j.xcrm.2023.101205_bib75","doi-asserted-by":"crossref","first-page":"W276","DOI":"10.1093\/nar\/gkac240","article-title":"Search and sequence analysis tools services from EMBL-EBI in 2022","volume":"50","author":"Madeira","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.xcrm.2023.101205_bib78","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","article-title":"STAR: ultrafast universal RNA-seq aligner","volume":"29","author":"Dobin","year":"2013","journal-title":"Bioinformatics"},{"key":"10.1016\/j.xcrm.2023.101205_bib79","doi-asserted-by":"crossref","first-page":"576","DOI":"10.1016\/j.molcel.2010.05.004","article-title":"Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities","volume":"38","author":"Heinz","year":"2010","journal-title":"Mol. Cell"},{"key":"10.1016\/j.xcrm.2023.101205_bib44","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0125373","article-title":"Quantifying distribution of flow cytometric TCR-V\u03b2 usage with economic statistics","volume":"10","author":"Van Der Geest","year":"2015","journal-title":"PLoS One"},{"key":"10.1016\/j.xcrm.2023.101205_bib45","first-page":"1","article-title":"Cutadapt removes sequences from high-throughput sequencing reads","volume":"18","author":"Martin","year":"2013","journal-title":"EMBnet J"},{"key":"10.1016\/j.xcrm.2023.101205_bib46","doi-asserted-by":"crossref","first-page":"863","DOI":"10.1093\/bioinformatics\/btr026","article-title":"Quality control and preprocessing of metagenomic datasets","volume":"27","author":"Schmieder","year":"2011","journal-title":"Bioinformatics"},{"key":"10.1016\/j.xcrm.2023.101205_bib48","doi-asserted-by":"crossref","first-page":"2520","DOI":"10.1038\/s41596-021-00508-2","article-title":"Recovering prokaryotic genomes from host-associated, short-read shotgun metagenomic sequencing data","volume":"16","author":"Saheb Kashaf","year":"2021","journal-title":"Nat. Protoc."},{"key":"10.1016\/j.xcrm.2023.101205_bib62","doi-asserted-by":"crossref","first-page":"D499","DOI":"10.1093\/nar\/gkw879","article-title":"The Papillomavirus Episteme: A major update to the papillomavirus sequence database","volume":"45","author":"Van Doorslaer","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.xcrm.2023.101205_bib67","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The Sequence Alignment\/Map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"10.1016\/j.xcrm.2023.101205_bib70","first-page":"D517","article-title":"CARD 2020: Antibiotic resistome surveillance with the comprehensive antibiotic resistance database","volume":"48","author":"Alcock","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.xcrm.2023.101205_bib71","doi-asserted-by":"crossref","first-page":"926","DOI":"10.1093\/bioinformatics\/btu739","article-title":"UniRef clusters: A comprehensive and scalable alternative for improving sequence similarity searches","volume":"31","author":"Suzek","year":"2015","journal-title":"Bioinformatics"},{"key":"10.1016\/j.xcrm.2023.101205_bib77","article-title":"A Database Resource and Online Analysis Tools for Coronaviruses on a Historical and Global Scale","author":"Zhu","year":"2020","journal-title":"Database 00"},{"key":"10.1016\/j.xcrm.2023.101205_bib80","first-page":"2825","article-title":"Scikit-learn: Machine Learning in Python","volume":"12","author":"Pedregosa","year":"2011","journal-title":"J.\u00a0Mach. Learn. Res."},{"key":"10.1016\/j.xcrm.2023.101205_bib81","doi-asserted-by":"crossref","first-page":"1523","DOI":"10.1038\/s41467-019-09234-6","article-title":"Metascape provides a biologist-oriented resource for the analysis of systems-level datasets","volume":"10","author":"Zhou","year":"2019","journal-title":"Nat. Commun."}],"container-title":["Cell Reports Medicine"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2666379123003725?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2666379123003725?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2024,5,7]],"date-time":"2024-05-07T02:11:12Z","timestamp":1715047872000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S2666379123003725"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,10]]},"references-count":81,"journal-issue":{"issue":"10","published-print":{"date-parts":[[2023,10]]}},"alternative-id":["S2666379123003725"],"URL":"https:\/\/doi.org\/10.1016\/j.xcrm.2023.101205","relation":{},"ISSN":["2666-3791"],"issn-type":[{"value":"2666-3791","type":"print"}],"subject":[],"published":{"date-parts":[[2023,10]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Expanded microbiome niches of RAG-deficient patients","name":"articletitle","label":"Article Title"},{"value":"Cell Reports Medicine","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.xcrm.2023.101205","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"name":"copyright","label":"Copyright"}],"article-number":"101205"}}