{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,18]],"date-time":"2026-08-18T01:33:38Z","timestamp":1787016818842,"version":"build-2736575974"},"reference-count":78,"publisher":"American Society for Microbiology","issue":"4","license":[{"start":{"date-parts":[[2025,4,9]],"date-time":"2025-04-09T00:00:00Z","timestamp":1744156800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2025,4,9]],"date-time":"2025-04-09T00:00:00Z","timestamp":1744156800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"name":"IBM | IBM Research","award":["AI Horizons Network"],"award-info":[{"award-number":["AI Horizons Network"]}]},{"name":"HHS | National Institutes of Health","award":["P01 HL131474"],"award-info":[{"award-number":["P01 HL131474"]}]},{"DOI":"10.13039\/501100009708","name":"Novo Nordisk Foundation","doi-asserted-by":"publisher","award":["NNF20SA0066621"],"award-info":[{"award-number":["NNF20SA0066621"]}],"id":[{"id":"10.13039\/501100009708","id-type":"DOI","asserted-by":"publisher"}]},{"name":"National Science Foundation","award":["2031989"],"award-info":[{"award-number":["2031989"]}]},{"DOI":"10.13039\/501100007469","name":"Alfred Benzon Foundation","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100007469","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100002341","name":"Academy of Finland","doi-asserted-by":"crossref","award":["321351 and 354447"],"award-info":[{"award-number":["321351 and 354447"]}],"id":[{"id":"10.13039\/501100002341","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100004756","name":"Emil Aaltosen S\u00e4\u00e4ti\u00f6","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100004756","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100005633","name":"Syd\u00e4ntutkimuss\u00e4\u00e4ti\u00f6","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100005633","id-type":"DOI","asserted-by":"crossref"}]},{"name":"HHS | National Institutes of Health","award":["R01ES027595"],"award-info":[{"award-number":["R01ES027595"]}]},{"name":"ANID Becas Chile Doctorado","award":["2018-72190270"],"award-info":[{"award-number":["2018-72190270"]}]},{"DOI":"10.13039\/501100002341","name":"Academy of Finland","doi-asserted-by":"crossref","award":["321356"],"award-info":[{"award-number":["321356"]}],"id":[{"id":"10.13039\/501100002341","id-type":"DOI","asserted-by":"crossref"}]},{"name":"UC San Diego Center for Microbiome Innovation","award":["N\/A"],"award-info":[{"award-number":["N\/A"]}]},{"DOI":"10.13039\/501100002341","name":"Academy of Finland","doi-asserted-by":"crossref","award":["335525"],"award-info":[{"award-number":["335525"]}],"id":[{"id":"10.13039\/501100002341","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Union's Horizon Europe Research and Innovation 459 Actions","award":["101046041"],"award-info":[{"award-number":["101046041"]}]},{"DOI":"10.13039\/501100001665","name":"French National Research Agency","doi-asserted-by":"crossref","award":["ANR-17-CE11-0014"],"award-info":[{"award-number":["ANR-17-CE11-0014"]}],"id":[{"id":"10.13039\/501100001665","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001665","name":"French National Research Agency","doi-asserted-by":"crossref","award":["ANR-20-CE44-0005"],"award-info":[{"award-number":["ANR-20-CE44-0005"]}],"id":[{"id":"10.13039\/501100001665","id-type":"DOI","asserted-by":"crossref"}]},{"name":"HHS | National Institutes of Health","award":["R01GM069811"],"award-info":[{"award-number":["R01GM069811"]}]},{"name":"Munz Chair of Cardiovascular Prediction and Prevention"},{"name":"NIHR | NIHR Cambridge Biomedical Research Centre"},{"DOI":"10.13039\/501100000274","name":"British Heart Foundation","doi-asserted-by":"crossref","award":["RG\/13\/13\/30194"],"award-info":[{"award-number":["RG\/13\/13\/30194"]}],"id":[{"id":"10.13039\/501100000274","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100000274","name":"British Heart Foundation","doi-asserted-by":"crossref","award":["RG\/18\/13\/33946"],"award-info":[{"award-number":["RG\/18\/13\/33946"]}],"id":[{"id":"10.13039\/501100000274","id-type":"DOI","asserted-by":"crossref"}]},{"name":"NIHR | NIHR Cambridge Biomedical Research Centre","award":["BRC-1215-20014"],"award-info":[{"award-number":["BRC-1215-20014"]}]},{"name":"HHS | National Institutes of Health","award":["1DP1AT010885"],"award-info":[{"award-number":["1DP1AT010885"]}]},{"DOI":"10.13039\/501100023699","name":"Health Data Research UK","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100023699","id-type":"DOI","asserted-by":"crossref"}]},{"name":"HHS | National Institutes of Health","award":["U01-CA199277"],"award-info":[{"award-number":["U01-CA199277"]}]},{"name":"HHS | National Institutes of Health","award":["P30-CA033572"],"award-info":[{"award-number":["P30-CA033572"]}]},{"name":"HHS | National Institutes of Health","award":["P30-CA023100"],"award-info":[{"award-number":["P30-CA023100"]}]},{"name":"HHS | National Institutes of Health","award":["UM1-CA164917"],"award-info":[{"award-number":["UM1-CA164917"]}]},{"name":"HHS | National Institutes of Health","award":["R01-CA077398"],"award-info":[{"award-number":["R01-CA077398"]}]},{"name":"National Science Foundation","award":["2038509"],"award-info":[{"award-number":["2038509"]}]},{"name":"UC | University of California, San Diego","award":["R00RG2503"],"award-info":[{"award-number":["R00RG2503"]}]},{"DOI":"10.13039\/100014894","name":"Emerald Foundation","doi-asserted-by":"crossref","award":["3022"],"award-info":[{"award-number":["3022"]}],"id":[{"id":"10.13039\/100014894","id-type":"DOI","asserted-by":"crossref"}]},{"name":"HHS | National Institutes of Health","award":["1P30DK120515"],"award-info":[{"award-number":["1P30DK120515"]}]},{"name":"HHS | National Institutes of Health","award":["R35GM119850"],"award-info":[{"award-number":["R35GM119850"]}]},{"name":"HHS | National Institutes of Health","award":["UH2AI153029"],"award-info":[{"award-number":["UH2AI153029"]}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["mBio"],"published-print":{"date-parts":[[2025,4,9]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title\/>\n                    <jats:p>The gastrointestinal (GI) tract is a site of replication of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and GI symptoms are often reported by patients. SARS-CoV-2 cell entry depends upon heparan sulfate (HS) proteoglycans, which commensal bacteria that bathe the human mucosa are known to modify. To explore human gut HS-modifying bacterial abundances and how their presence may impact SARS-CoV-2 infection, we developed a task-based analysis of proteoglycan degradation on large-scale shotgun metagenomic data. We observed that gut bacteria with high predicted catabolic capacity for HS differ by age and sex, factors associated with coronavirus disease 2019 (COVID-19) severity, and directly by disease severity during\/after infection, but do not vary between subjects with COVID-19 comorbidities or by diet. Gut commensal bacterial HS-modifying enzymes reduce spike protein binding and infection of authentic SARS-CoV-2, suggesting that bacterial grooming of the GI mucosa may impact viral susceptibility.<\/jats:p>\n                    <jats:sec>\n                      <jats:title>IMPORTANCE<\/jats:title>\n                      <jats:p>\n                        Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for coronavirus disease 2019, can infect the gastrointestinal (GI) tract, and individuals who exhibit GI symptoms often have more severe disease. The GI tract\u2019s glycocalyx, a component of the mucosa covering the large intestine, plays a key role in viral entry by binding SARS-CoV-2\u2019s spike protein via heparan sulfate (HS). Here, using metabolic task analysis of multiple large microbiome sequencing data sets of the human gut microbiome, we identify a key commensal human intestinal bacteria capable of grooming glycocalyx HS and modulating SARS-CoV-2 infectivity\n                        <jats:italic>in vitro<\/jats:italic>\n                        . Moreover, we engineered the common probiotic\n                        <jats:italic>Escherichia coli<\/jats:italic>\n                        Nissle 1917 (EcN) to effectively block SARS-CoV-2 binding and infection of human cell cultures. Understanding these microbial interactions could lead to better risk assessments and novel therapies targeting viral entry mechanisms.\n                      <\/jats:p>\n                    <\/jats:sec>\n                  <\/jats:sec>","DOI":"10.1128\/mbio.04015-24","type":"journal-article","created":{"date-parts":[[2025,2,25]],"date-time":"2025-02-25T09:08:27Z","timestamp":1740474507000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":5,"title":["SARS-CoV-2 infectivity can be modulated through bacterial grooming of the glycocalyx"],"prefix":"10.1128","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9334-1258","authenticated-orcid":false,"given":"Cameron","family":"Martino","sequence":"first","affiliation":[{"name":"Department of Pediatrics, University of California San Diego School of Medicine","place":["La Jolla, USA"]},{"name":"Bioinformatics and Systems Biology Program, University of California San Diego","place":["La Jolla, USA"]},{"name":"Center for Microbiome Innovation, University of California San Diego","place":["La Jolla, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Benjamin P.","family":"Kellman","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, University of California San Diego School of Medicine","place":["La Jolla, USA"]},{"name":"Bioinformatics and Systems Biology Program, University of California San Diego","place":["La Jolla, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel R.","family":"Sandoval","sequence":"additional","affiliation":[{"name":"Department of Cellular and Molecular Medicine, University of California San Diego","place":["La Jolla, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thomas Mandel","family":"Clausen","sequence":"additional","affiliation":[{"name":"Department of Cellular and Molecular Medicine, University of California San Diego","place":["La Jolla, USA"]},{"name":"Copenhagen Center for Glycomics, Department of Molecular and Cellular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen","place":["Copenhagen, Denmark"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Robert","family":"Cooper","sequence":"additional","affiliation":[{"name":"Department of Bioengineering, University of California San Diego","place":["La Jolla, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alhosna","family":"Benjdia","sequence":"additional","affiliation":[{"name":"Universit\u00e9 Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, ChemSyBio","place":["78350, Jouy-en-Josas, France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Feryel","family":"Soualmia","sequence":"additional","affiliation":[{"name":"Universit\u00e9 Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, ChemSyBio","place":["78350, Jouy-en-Josas, France"]},{"name":"Sorbonne Universit\u00e9, Faculty of Sciences and Engineering, IBPS, UMR 8263 CNRS-SU, ERL INSERM U1345, Development, Adaptation and Ageing","place":["F-75252 Paris, France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alex E.","family":"Clark","sequence":"additional","affiliation":[{"name":"Department of Medicine, University of California San Diego","place":["La Jolla, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aaron F.","family":"Garretson","sequence":"additional","affiliation":[{"name":"Department of Medicine, University of California San Diego","place":["La Jolla, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Clarisse A.","family":"Marotz","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, University of California San Diego School of Medicine","place":["La Jolla, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Se Jin","family":"Song","sequence":"additional","affiliation":[{"name":"Center for Microbiome Innovation, University of California San Diego","place":["La Jolla, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephen","family":"Wandro","sequence":"additional","affiliation":[{"name":"Center for Microbiome Innovation, University of California San Diego","place":["La Jolla, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Livia S.","family":"Zaramela","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, University of California San Diego School of Medicine","place":["La Jolla, USA"]},{"name":"Department of Biochemistry, Ribeir\u00e3o Preto Medical School, University of S\u00e3o Paulo","place":["Ribeir\u00e3o Preto, Brazil"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0631-2817","authenticated-orcid":true,"given":"Rodolfo A.","family":"Salido","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, University of California San Diego School of Medicine","place":["La Jolla, USA"]},{"name":"Center for Microbiome Innovation, University of California San Diego","place":["La Jolla, USA"]},{"name":"Department of Bioengineering, University of California San Diego","place":["La Jolla, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qiyun","family":"Zhu","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, University of California San Diego School of Medicine","place":["La Jolla, USA"]},{"name":"School of Life Sciences, Arizona State University","place":["Tempe, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Erick","family":"Armingol","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, University of California San Diego School of Medicine","place":["La Jolla, USA"]},{"name":"Bioinformatics and Systems Biology Program, University of California San Diego","place":["La Jolla, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yoshiki","family":"V\u00e1zquez-Baeza","sequence":"additional","affiliation":[{"name":"Center for Microbiome Innovation, University of California San Diego","place":["La Jolla, USA"]},{"name":"Jacobs School of Engineering, University of California San Diego","place":["La Jolla, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel","family":"McDonald","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, University of California San Diego School of Medicine","place":["La Jolla, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James T.","family":"Sorrentino","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, University of California San Diego School of Medicine","place":["La Jolla, USA"]},{"name":"Bioinformatics and Systems Biology Program, University of California San Diego","place":["La Jolla, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4957-5417","authenticated-orcid":true,"given":"Bryn","family":"Taylor","sequence":"additional","affiliation":[{"name":"Biomedical Sciences Graduate Program, University of California San Diego","place":["La Jolla, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pedro","family":"Belda-Ferre","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, University of California San Diego School of Medicine","place":["La Jolla, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6733-2059","authenticated-orcid":true,"given":"Promi","family":"Das","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, University of California San Diego School of Medicine","place":["La Jolla, USA"]},{"name":"Scripps Institution of Oceanography, University of California San Diego","place":["La Jolla, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Farhana","family":"Ali","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, University of California San Diego School of Medicine","place":["La Jolla, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chenguang","family":"Liang","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, University of California San Diego School of Medicine","place":["La Jolla, USA"]},{"name":"Department of Bioengineering, University of California San Diego","place":["La Jolla, USA"]},{"name":"Merck & Co., Inc.","place":["Rahway, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yujie","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Bioengineering, University of California San Diego","place":["La Jolla, USA"]},{"name":"Department of Biological & Medical Informatics, University of California San Francisco, School of Pharmacy","place":["San Francisco, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luca","family":"Schifanella","sequence":"additional","affiliation":[{"name":"Department of Surgery, Division of Surgical Outcomes and Precision Medicine Research, Medical School, University of Minnesota","place":["Minneapolis, USA"]},{"name":"National Institutes of Health, National Cancer Institute, Center for Cancer Research, Animal Models and Retroviral Vaccine Section","place":["Bethesda, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alice","family":"Covizzi","sequence":"additional","affiliation":[{"name":"Department of Infectious diseases, Luigi Sacco Hospital, Milan and Department of Biomedical and Clinical Sciences (DIBIC), University of Milan","place":["Milan, Italy"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alessia","family":"Lai","sequence":"additional","affiliation":[{"name":"Department of Infectious diseases, Luigi Sacco Hospital, Milan and Department of Biomedical and Clinical Sciences (DIBIC), University of Milan","place":["Milan, Italy"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Agostino","family":"Riva","sequence":"additional","affiliation":[{"name":"Department of Infectious diseases, Luigi Sacco Hospital, Milan and Department of Biomedical and Clinical Sciences (DIBIC), University of Milan","place":["Milan, Italy"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christopher","family":"Basting","sequence":"additional","affiliation":[{"name":"Department of Surgery, Division of Surgical Outcomes and Precision Medicine Research, Medical School, University of Minnesota","place":["Minneapolis, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Courtney Ann","family":"Broedlow","sequence":"additional","affiliation":[{"name":"Department of Surgery, Division of Surgical Outcomes and Precision Medicine Research, Medical School, University of Minnesota","place":["Minneapolis, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aki S.","family":"Havulinna","sequence":"additional","affiliation":[{"name":"Department of Public Health and Welfare, Finnish Institute for Health and Welfare","place":["Helsinki and Turku, Finland"]},{"name":"Institute for Molecular Medicine Finland, FIMM - HiLIFE","place":["Helsinki, Finland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pekka","family":"Jousilahti","sequence":"additional","affiliation":[{"name":"Department of Public Health and Welfare, Finnish Institute for Health and Welfare","place":["Helsinki and Turku, Finland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4556-8444","authenticated-orcid":true,"given":"Mehrbod","family":"Estaki","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, University of California San Diego School of Medicine","place":["La Jolla, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tomasz","family":"Kosciolek","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, University of California San Diego School of Medicine","place":["La Jolla, USA"]},{"name":"Sano Centre for Computational Medicine","place":["Krakow, Poland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rayus","family":"Kuplicki","sequence":"additional","affiliation":[{"name":"Laureate Institute for Brain Research","place":["Tulsa, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Teresa A.","family":"Victor","sequence":"additional","affiliation":[{"name":"Laureate Institute for Brain Research","place":["Tulsa, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Martin P.","family":"Paulus","sequence":"additional","affiliation":[{"name":"Laureate Institute for Brain Research","place":["Tulsa, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kristen E.","family":"Savage","sequence":"additional","affiliation":[{"name":"Division of Health Analytics, Department of Computational and Quantitative Medicine, City of Hope","place":["Duarte, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jennifer L.","family":"Benbow","sequence":"additional","affiliation":[{"name":"Division of Health Analytics, Department of Computational and Quantitative Medicine, City of Hope","place":["Duarte, USA"]},{"name":"UC Health Data Warehouse, University of California Irvine","place":["Irvine, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emma S.","family":"Spielfogel","sequence":"additional","affiliation":[{"name":"Division of Health Analytics, Department of Computational and Quantitative Medicine, City of Hope","place":["Duarte, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cheryl A. M.","family":"Anderson","sequence":"additional","affiliation":[{"name":"Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego","place":["La Jolla, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria Elena","family":"Martinez","sequence":"additional","affiliation":[{"name":"Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego","place":["La Jolla, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"suffix":"Jr","given":"James V.","family":"Lacey","sequence":"additional","affiliation":[{"name":"Division of Health Analytics, Department of Computational and Quantitative Medicine, City of Hope","place":["Duarte, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shi","family":"Huang","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, University of California San Diego School of Medicine","place":["La Jolla, USA"]},{"name":"Center for Microbiome Innovation, University of California San Diego","place":["La Jolla, USA"]},{"name":"Faculty of Dentistry, The University of Hong Kong","place":["Hong Kong, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8663-1019","authenticated-orcid":true,"given":"Niina","family":"Haiminen","sequence":"additional","affiliation":[{"name":"IBM T. J. Watson Research Center","place":["Yorktown Heights, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laxmi","family":"Parida","sequence":"additional","affiliation":[{"name":"IBM T. J. Watson Research Center","place":["Yorktown Heights, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ho-Cheol","family":"Kim","sequence":"additional","affiliation":[{"name":"AI and Cognitive Software, IBM Research-Almaden","place":["San Jose, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jack A.","family":"Gilbert","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, University of California San Diego School of Medicine","place":["La Jolla, USA"]},{"name":"Center for Microbiome Innovation, University of California San Diego","place":["La Jolla, USA"]},{"name":"Scripps Institution of Oceanography, University of California San Diego","place":["La Jolla, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel A.","family":"Sweeney","sequence":"additional","affiliation":[{"name":"Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of California San Diego","place":["La Jolla, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sarah M.","family":"Allard","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, University of California San Diego School of Medicine","place":["La Jolla, USA"]},{"name":"Scripps Institution of Oceanography, University of California San Diego","place":["La Jolla, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5655-8300","authenticated-orcid":false,"given":"Austin D.","family":"Swafford","sequence":"additional","affiliation":[{"name":"Center for Microbiome Innovation, University of California San Diego","place":["La Jolla, USA"]},{"name":"International Biomedical Research Alliance","place":["Bethesda, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Susan","family":"Cheng","sequence":"additional","affiliation":[{"name":"Division of Cardiology, Brigham and Women\u2019s Hospital","place":["Boston, USA"]},{"name":"Cedars-Sinai Medical Center","place":["Los Angeles, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael","family":"Inouye","sequence":"additional","affiliation":[{"name":"Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge","place":["Cambridge, United Kingdom"]},{"name":"Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute","place":["Melbourne, Australia"]},{"name":"Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge","place":["Cambridge, United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Teemu","family":"Niiranen","sequence":"additional","affiliation":[{"name":"Department of Public Health and Welfare, Finnish Institute for Health and Welfare","place":["Helsinki and Turku, Finland"]},{"name":"Division of Medicine, Turku University Hospital and University of Turku","place":["Turku, Finland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mohit","family":"Jain","sequence":"additional","affiliation":[{"name":"Department of Pharmacology, University of California, San Diego","place":["La Jolla, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Veikko","family":"Salomaa","sequence":"additional","affiliation":[{"name":"Department of Public Health and Welfare, Finnish Institute for Health and Welfare","place":["Helsinki and Turku, Finland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8062-3296","authenticated-orcid":true,"given":"Karsten","family":"Zengler","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, University of California San Diego School of Medicine","place":["La Jolla, USA"]},{"name":"Center for Microbiome Innovation, University of California San Diego","place":["La Jolla, USA"]},{"name":"Department of Bioengineering, University of California San Diego","place":["La Jolla, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2968-5480","authenticated-orcid":true,"given":"Nichole R.","family":"Klatt","sequence":"additional","affiliation":[{"name":"Department of Surgery, Division of Surgical Outcomes and Precision Medicine Research, Medical School, University of Minnesota","place":["Minneapolis, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jeff","family":"Hasty","sequence":"additional","affiliation":[{"name":"Department of Bioengineering, University of California San Diego","place":["La Jolla, USA"]},{"name":"Molecular Biology Section, Division of Biological Science, University of California San Diego","place":["La Jolla, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Olivier","family":"Berteau","sequence":"additional","affiliation":[{"name":"Universit\u00e9 Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, ChemSyBio","place":["78350, Jouy-en-Josas, France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aaron F.","family":"Carlin","sequence":"additional","affiliation":[{"name":"Department of Medicine, University of California San Diego","place":["La Jolla, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jeffrey D.","family":"Esko","sequence":"additional","affiliation":[{"name":"Department of Cellular and Molecular Medicine, University of California San Diego","place":["La Jolla, USA"]},{"name":"Glycobiology Research and Training Center, University of California San Diego","place":["La Jolla, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nathan E.","family":"Lewis","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, University of California San Diego School of Medicine","place":["La Jolla, USA"]},{"name":"Center for Microbiome Innovation, University of California San Diego","place":["La Jolla, USA"]},{"name":"Department of Bioengineering, University of California San Diego","place":["La Jolla, USA"]},{"name":"Jacobs School of Engineering, University of California San Diego","place":["La Jolla, USA"]},{"name":"Center for Molecular Medicine, Complex Carbohydrate Research Center, and Dept of Biochemistry and Molecular Biology, University of Georgia","place":["Athens, USA"]},{"name":"Department of Biotechnology and Biomedicine, Technical University of Denmark","place":["Lyngby, Denmark"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0975-9019","authenticated-orcid":true,"given":"Rob","family":"Knight","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, University of California San Diego School of Medicine","place":["La Jolla, USA"]},{"name":"Center for Microbiome Innovation, University of California San Diego","place":["La Jolla, USA"]},{"name":"Department of Bioengineering, University of California San Diego","place":["La Jolla, USA"]},{"name":"Department of Computer Science and Engineering, University of California San Diego","place":["La Jolla, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_6_2_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-020-2901-9"},{"key":"e_1_3_6_3_2","doi-asserted-by":"publisher","DOI":"10.1002\/jmv.26836"},{"key":"e_1_3_6_4_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.tige.2021.01.006"},{"key":"e_1_3_6_5_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.trsl.2020.08.004"},{"key":"e_1_3_6_6_2","doi-asserted-by":"publisher","DOI":"10.14740\/gr1350"},{"key":"e_1_3_6_7_2","doi-asserted-by":"publisher","DOI":"10.1007\/s00535-021-01778-z"},{"key":"e_1_3_6_8_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41575-021-00416-6"},{"key":"e_1_3_6_9_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jcmgh.2020.09.017"},{"key":"e_1_3_6_10_2","doi-asserted-by":"publisher","DOI":"10.1136\/gutjnl-2021-324622"},{"key":"e_1_3_6_11_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0140-6736(20)30628-0"},{"key":"e_1_3_6_12_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.medj.2022.04.001"},{"key":"e_1_3_6_13_2","doi-asserted-by":"publisher","DOI":"10.1007\/s00401-023-02612-x"},{"key":"e_1_3_6_14_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41390-022-02266-7"},{"key":"e_1_3_6_15_2","doi-asserted-by":"publisher","DOI":"10.1136\/gutjnl-2021-324280"},{"key":"e_1_3_6_16_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2020.09.033"},{"key":"e_1_3_6_17_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.sbi.2022.102439"},{"key":"e_1_3_6_18_2","doi-asserted-by":"publisher","DOI":"10.1136\/gutjnl-2020-320953"},{"key":"e_1_3_6_19_2","doi-asserted-by":"publisher","DOI":"10.1146\/annurev.biochem.71.110601.135458"},{"key":"e_1_3_6_20_2","doi-asserted-by":"publisher","DOI":"10.3390\/v11070596"},{"key":"e_1_3_6_21_2","doi-asserted-by":"publisher","DOI":"10.1128\/mSystems.00031-18"},{"key":"e_1_3_6_22_2","doi-asserted-by":"publisher","DOI":"10.1038\/nature18847"},{"key":"e_1_3_6_23_2","doi-asserted-by":"publisher","DOI":"10.1038\/nature24485"},{"key":"e_1_3_6_24_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0803124105"},{"key":"e_1_3_6_25_2","doi-asserted-by":"publisher","DOI":"10.1007\/BF02798420"},{"key":"e_1_3_6_26_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.00860-16"},{"key":"e_1_3_6_27_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1704367114"},{"key":"e_1_3_6_28_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-14509-4"},{"key":"e_1_3_6_29_2","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.M114.573303"},{"key":"e_1_3_6_30_2","doi-asserted-by":"publisher","DOI":"10.1128\/aem.41.2.360-365.1981"},{"key":"e_1_3_6_31_2","doi-asserted-by":"publisher","DOI":"10.1039\/C7OB01058C"},{"key":"e_1_3_6_32_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.chom.2015.09.002"},{"key":"e_1_3_6_33_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.crmeth.2021.100040"},{"key":"e_1_3_6_34_2","doi-asserted-by":"publisher","DOI":"10.1093\/ije\/dyx239"},{"key":"e_1_3_6_35_2","doi-asserted-by":"publisher","DOI":"10.1101\/2019.12.30.19015842"},{"key":"e_1_3_6_36_2","doi-asserted-by":"publisher","DOI":"10.1053\/j.gastro.2020.04.045"},{"key":"e_1_3_6_37_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-020-2521-4"},{"key":"e_1_3_6_38_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-019-13443-4"},{"key":"e_1_3_6_39_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41564-019-0564-9"},{"key":"e_1_3_6_40_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2016.10.043"},{"key":"e_1_3_6_41_2","doi-asserted-by":"publisher","DOI":"10.1128\/mSystems.00261-19"},{"key":"e_1_3_6_42_2","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-021-01083-0"},{"key":"e_1_3_6_43_2","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.M111.228841"},{"key":"e_1_3_6_44_2","doi-asserted-by":"publisher","DOI":"10.1017\/S0007114508143549"},{"key":"e_1_3_6_45_2","doi-asserted-by":"publisher","DOI":"10.1079\/pns2003206"},{"key":"e_1_3_6_46_2","doi-asserted-by":"publisher","DOI":"10.3389\/fnut.2022.934568"},{"key":"e_1_3_6_47_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41575-018-0061-2"},{"key":"e_1_3_6_48_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41579-022-00768-z"},{"key":"e_1_3_6_49_2","doi-asserted-by":"publisher","DOI":"10.1038\/nature11234"},{"key":"e_1_3_6_50_2","doi-asserted-by":"publisher","DOI":"10.1164\/rccm.201501-0128OC"},{"key":"e_1_3_6_51_2","doi-asserted-by":"publisher","DOI":"10.1164\/rccm.202008-3146ED"},{"key":"e_1_3_6_52_2","doi-asserted-by":"publisher","DOI":"10.1038\/nrmicro.2016.142"},{"key":"e_1_3_6_53_2","doi-asserted-by":"publisher","DOI":"10.1038\/nrg1769"},{"key":"e_1_3_6_54_2","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.3703"},{"key":"e_1_3_6_55_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gky537"},{"key":"e_1_3_6_56_2","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.01526-14"},{"key":"e_1_3_6_57_2","doi-asserted-by":"publisher","DOI":"10.1038\/nrmicro2746"},{"key":"e_1_3_6_58_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkw1092"},{"key":"e_1_3_6_59_2","doi-asserted-by":"publisher","DOI":"10.1002\/1873-3468.13045"},{"key":"e_1_3_6_60_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1006090"},{"key":"e_1_3_6_61_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkt1178"},{"key":"e_1_3_6_62_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gks479"},{"key":"e_1_3_6_63_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gky418"},{"key":"e_1_3_6_64_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1007185"},{"key":"e_1_3_6_65_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1006867"},{"key":"e_1_3_6_66_2","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.3720"},{"key":"e_1_3_6_67_2","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.1923"},{"key":"e_1_3_6_68_2","doi-asserted-by":"publisher","DOI":"10.1128\/mSystems.00069-18"},{"key":"e_1_3_6_69_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkl842"},{"key":"e_1_3_6_70_2","volume-title":"Numerical python: scientific computing and data science applications with Numpy, SciPy and Matplotlib","author":"Johansson R","year":"2018","unstructured":"Johansson R. 2018. Numerical python: scientific computing and data science applications with Numpy, SciPy and Matplotlib. Apress."},{"key":"e_1_3_6_71_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkm160"},{"key":"e_1_3_6_72_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0022-2836(05)80360-2"},{"key":"e_1_3_6_73_2","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-019-1834-9"},{"key":"e_1_3_6_74_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu170"},{"key":"e_1_3_6_75_2","doi-asserted-by":"publisher","DOI":"10.1186\/s13040-014-0034-0"},{"key":"e_1_3_6_76_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btr507"},{"key":"e_1_3_6_77_2","doi-asserted-by":"publisher","DOI":"10.1089\/cmb.2012.0021"},{"key":"e_1_3_6_78_2","doi-asserted-by":"publisher","DOI":"10.1099\/ijsem.0.000760"},{"key":"e_1_3_6_79_2","doi-asserted-by":"publisher","DOI":"10.1021\/ja901571p"}],"container-title":["mBio"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/mbio.04015-24","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/mbio.04015-24","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,4,9]],"date-time":"2025-04-09T09:06:35Z","timestamp":1744189595000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/mbio.04015-24"}},"subtitle":[],"editor":[{"given":"Samuel I.","family":"Miller","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2025,4,9]]},"references-count":78,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2025,4,9]]}},"alternative-id":["10.1128\/mbio.04015-24"],"URL":"https:\/\/doi.org\/10.1128\/mbio.04015-24","relation":{},"ISSN":["2150-7511"],"issn-type":[{"value":"2150-7511","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,4,9]]},"assertion":[{"value":"2024-12-23","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2025-01-30","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2025-02-25","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e04015-24"}}