{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T00:42:43Z","timestamp":1791333763146,"version":"4.3.1"},"reference-count":64,"publisher":"American Society for Microbiology","issue":"1","license":[{"start":{"date-parts":[[2017,2,28]],"date-time":"2017-02-28T00:00:00Z","timestamp":1488240000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2017,2,28]],"date-time":"2017-02-28T00:00:00Z","timestamp":1488240000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"crossref","award":["HHSN272201400008C"],"award-info":[{"award-number":["HHSN272201400008C"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"crossref","award":["HHSN266200700010C"],"award-info":[{"award-number":["HHSN266200700010C"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000879","name":"Alfred P. Sloan Foundation","doi-asserted-by":"publisher","award":["Microbiology of the Built Environment"],"award-info":[{"award-number":["Microbiology of the Built Environment"]}],"id":[{"id":"10.13039\/100000879","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007707","name":"UC | University of California, Davis","doi-asserted-by":"publisher","award":["UC Davis College of Biological Sciences New Biology Postdoctoral Fellowship"],"award-info":[{"award-number":["UC Davis College of Biological Sciences New Biology Postdoctoral Fellowship"]}],"id":[{"id":"10.13039\/100007707","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100005595","name":"University of California","doi-asserted-by":"publisher","award":["UC Davis Chancellor's Postdoctoral Fellowship"],"award-info":[{"award-number":["UC Davis Chancellor's Postdoctoral Fellowship"]}],"id":[{"id":"10.13039\/100005595","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["mSystems"],"published-print":{"date-parts":[[2017,2,28]]},"abstract":"<jats:p>Seasonal influenza causes 3 to 5 million severe illnesses and 250,000 to 500,000 human deaths each year. While pandemic influenza viruses emerge only periodically, they can be devastating\u2014for example, the 1918 H1N1 pandemic virus killed more than 20 million people. IAVs infect the respiratory tract and cause significant morbidity and mortality in humans. In contrast, IAVs infect the gastrointestinal tract of waterfowl, producing little pathology. Recent studies indicated that viruses can alter the microbiome at the respiratory and gastrointestinal mucosa, but there are no reports of how the microbiota of the natural host of influenza is affected by infection. Here we find that the mallard microbiome is altered during IAV infection. Our results suggest that detailed examination of humans and animals infected with IAVs may reveal individualized microbiome profiles that correspond to health and disease. Moreover, future studies should explore whether the altered microbiome facilitates maintenance and transmission of IAVs in waterfowl populations.<\/jats:p>","DOI":"10.1128\/msystems.00188-16","type":"journal-article","created":{"date-parts":[[2017,3,1]],"date-time":"2017-03-01T01:25:36Z","timestamp":1488331536000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":49,"title":["Community-Level Differences in the Microbiome of Healthy Wild Mallards and Those Infected by Influenza A Viruses"],"prefix":"10.1128","volume":"2","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4938-6226","authenticated-orcid":false,"given":"Holly H.","family":"Ganz","sequence":"first","affiliation":[{"name":"Genome Center, University of California, Davis, Davis, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ladan","family":"Doroud","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of California, Davis, Davis, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alana J.","family":"Firl","sequence":"additional","affiliation":[{"name":"Genome Center, University of California, Davis, Davis, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sarah M.","family":"Hird","sequence":"additional","affiliation":[{"name":"Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jonathan A.","family":"Eisen","sequence":"additional","affiliation":[{"name":"Genome Center, University of California, Davis, Davis, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Walter M.","family":"Boyce","sequence":"additional","affiliation":[{"name":"Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California, Davis, Davis, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_2_2_2","doi-asserted-by":"publisher","DOI":"10.1146\/annurev.pathmechdis.3.121806.154316"},{"key":"e_1_3_2_3_2","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1007\/978-3-642-77011-1_6","volume-title":"Genetic diversity of RNA viruses","author":"Gorman OT","year":"1992","unstructured":"Gorman OT Bean WJ Webster RG . 1992. Evolutionary processes in influenza viruses: divergence, rapid evolution, and stasis, p 75\u201397. InGenetic diversity of RNA viruses. Springer, New York, NY."},{"key":"e_1_3_2_4_2","doi-asserted-by":"publisher","DOI":"10.1038\/nrmicro2613"},{"key":"e_1_3_2_5_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.meegid.2013.02.020"},{"key":"e_1_3_2_6_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0008935"},{"key":"e_1_3_2_7_2","doi-asserted-by":"publisher","DOI":"10.1128\/mr.56.1.152-179.1992"},{"key":"e_1_3_2_8_2","first-page":"161","volume-title":"Fungi in biological control systems","author":"Whipps J","year":"1988","unstructured":"Whipps J Lewis K Cooke R . 1988, Mycoparasitism and plant disease control, p 161\u2013187. InFungi in biological control systems. Manchester University Press, Manchester, United Kingdom."},{"key":"e_1_3_2_9_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1002808"},{"key":"e_1_3_2_10_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1003829"},{"key":"e_1_3_2_11_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmed.2015.00030"},{"key":"e_1_3_2_12_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.immuni.2012.04.011"},{"key":"e_1_3_2_13_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1310750111"},{"key":"e_1_3_2_14_2","doi-asserted-by":"publisher","DOI":"10.1038\/nri2653"},{"key":"e_1_3_2_15_2","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2012.00015"},{"key":"e_1_3_2_16_2","doi-asserted-by":"publisher","DOI":"10.1038\/mi.2008.5"},{"key":"e_1_3_2_17_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.1257147"},{"key":"e_1_3_2_18_2","doi-asserted-by":"publisher","DOI":"10.1098\/rspb.2008.1501"},{"key":"e_1_3_2_19_2","doi-asserted-by":"publisher","DOI":"10.1038\/ismej.2011.119"},{"key":"e_1_3_2_20_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.74.19.9300-9305.2000"},{"key":"e_1_3_2_21_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1019378108"},{"key":"e_1_3_2_22_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0045371"},{"key":"e_1_3_2_23_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0069559"},{"key":"e_1_3_2_24_2","doi-asserted-by":"publisher","DOI":"10.1111\/1469-0691.12054"},{"key":"e_1_3_2_25_2","doi-asserted-by":"crossref","first-page":"142.7","DOI":"10.4049\/jimmunol.192.Supp.142.7","article-title":"Intranasal vaccination with live attenuated influenza vaccine increases diversity of the human nasal microbiome","volume":"192","author":"Lambert N","year":"2014","unstructured":"Lambert N Salk H Kennedy R Chia N Grill D Jacobson R Poland G . 2014. Intranasal vaccination with live attenuated influenza vaccine increases diversity of the human nasal microbiome (VAC8P. 1001). J Immunol192:142.7.","journal-title":"J Immunol"},{"key":"e_1_3_2_26_2","first-page":"A1315","volume-title":"A32 Microbial Interactions And Host Defense","author":"Oh Y","year":"2015","unstructured":"Oh Y Yang S-WJ Ngan DA Hirota JA Niikura M Tam S Knight DA Hackett T-L Dorscheid D Man S . 2015. The bacterial microbiome of gut, lung, and blood after H1N1 influenza virus infection in mice with and without house dust mite exposure, p A1315\u2013A1315. InA32 Microbial Interactions And Host Defense. American Thoracic Society, New York, NY."},{"key":"e_1_3_2_27_2","doi-asserted-by":"publisher","DOI":"10.1088\/1742-5468\/2008\/10\/P10008"},{"key":"e_1_3_2_28_2","doi-asserted-by":"crossref","unstructured":"Biemann C . 2006. Chinese whispers: an efficient graph clustering algorithm and its application to natural language processing problems p 73\u201380. In Proceedings of the First Workshop on Graph Based Methods for Natural Language Processing. Association for Computational Linguistics Stroudsburg PA.","DOI":"10.3115\/1654758.1654774"},{"key":"e_1_3_2_30_2","first-page":"2825","article-title":"Scikit-learn: machine learning in Python","volume":"12","author":"Pedregosa F","year":"2011","unstructured":"Pedregosa F Varoquaux G Gramfort A Michel V Thirion B Grisel O Blondel M Prettenhofer P Weiss R Dubourg V . 2011. Scikit-learn: machine learning in Python. J Mach Learn Res12:2825\u20132830.","journal-title":"J Mach Learn Res"},{"key":"e_1_3_2_31_2","doi-asserted-by":"publisher","DOI":"10.1186\/1743-422X-8-21"},{"key":"e_1_3_2_32_2","doi-asserted-by":"publisher","DOI":"10.1186\/1472-6785-13-11"},{"key":"e_1_3_2_33_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0137401"},{"key":"e_1_3_2_34_2","doi-asserted-by":"publisher","DOI":"10.1098\/rspb.2013.0990"},{"key":"e_1_3_2_35_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.1133258"},{"key":"e_1_3_2_36_2","doi-asserted-by":"publisher","DOI":"10.1007\/s004420000549"},{"key":"e_1_3_2_37_2","doi-asserted-by":"publisher","DOI":"10.1890\/0012-9658(2002)083[2575:BIRAME]2.0.CO;2"},{"key":"e_1_3_2_38_2","doi-asserted-by":"publisher","DOI":"10.1890\/09-1243.1"},{"key":"e_1_3_2_39_2","doi-asserted-by":"publisher","DOI":"10.1146\/annurev-ecolsys-110411-160307"},{"key":"e_1_3_2_40_2","doi-asserted-by":"publisher","DOI":"10.1099\/mic.0.2006\/004077-0"},{"key":"e_1_3_2_41_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1471-0528.2010.02840.x"},{"key":"e_1_3_2_42_2","doi-asserted-by":"publisher","DOI":"10.1136\/gut.2005.073817"},{"key":"e_1_3_2_43_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0706625104"},{"key":"e_1_3_2_44_2","doi-asserted-by":"publisher","DOI":"10.5009\/gnl14344"},{"key":"e_1_3_2_45_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2015.01266"},{"key":"e_1_3_2_46_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1522149113"},{"key":"e_1_3_2_47_2","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.f.303"},{"key":"e_1_3_2_48_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.02272-07"},{"key":"e_1_3_2_49_2","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.659"},{"key":"e_1_3_2_50_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btr507"},{"key":"e_1_3_2_51_2","author":"Oksanen J","year":"2016","unstructured":"Oksanen J Blanchet FG Kindt R Legendre P Minchin PR O\u2019Hara RB Simpson GL Solymos P Stevens MHH Wagner H . 2016. vegan: community ecology package. R package version 2.3-5. https:\/\/cran.r-project.org\/package=vegan .","journal-title":"vegan: community ecology package. R package version 2.3-5"},{"key":"e_1_3_2_52_2","volume-title":"R: a language and environment for statistical computing","author":"Team RC","year":"2016","unstructured":"Team RC. 2016. R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. https:\/\/www.r-project.org\/ ."},{"key":"e_1_3_2_53_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btq166"},{"key":"e_1_3_2_54_2","unstructured":"Oliveros JC . 2007\u20132015. Venny. An interactive tool for comparing lists with Venn\u2019s diagrams. http:\/\/bioinfogp.cnb.csic.es\/tools\/venny\/index.html ."},{"key":"e_1_3_2_55_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2015.01200"},{"key":"e_1_3_2_56_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1002606"},{"key":"e_1_3_2_57_2","doi-asserted-by":"crossref","unstructured":"Bastian M Heymann S Jacomy M . 2009. Gephi: an open source software for exploring and manipulating networks p 361\u2013362. In . Proceedings of the Third International Conference on Weblogs and Social Media. The AAAI Press Menlo Park CA.","DOI":"10.1609\/icwsm.v3i1.13937"},{"key":"e_1_3_2_58_2","doi-asserted-by":"crossref","unstructured":"Schult DA Swart P . 2008. Exploring network structure dynamics and function using NetworkX p 11\u201316. In Proceedings of the 7th Python in Science Conferences (SciPy 2008).","DOI":"10.25080\/TCWV9851"},{"key":"e_1_3_2_59_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cimid.2008.01.002"},{"key":"e_1_3_2_60_2","doi-asserted-by":"publisher","DOI":"10.1637\/8462-082908-Reg.1"},{"key":"e_1_3_2_61_2","doi-asserted-by":"publisher","DOI":"10.1007\/s11262-011-0706-5"},{"key":"e_1_3_2_62_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0090826"},{"key":"e_1_3_2_63_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0061201"},{"key":"e_1_3_2_64_2","doi-asserted-by":"publisher","DOI":"10.1111\/imr.12097"},{"key":"e_1_3_2_65_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2014.00223"},{"key":"e_1_3_2_66_2","doi-asserted-by":"publisher","DOI":"10.3390\/v5081964"}],"container-title":["mSystems"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/mSystems.00188-16","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/mSystems.00188-16","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,6,15]],"date-time":"2025-06-15T21:47:15Z","timestamp":1750024035000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/mSystems.00188-16"}},"subtitle":[],"editor":[{"given":"Peter J.","family":"Turnbaugh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2017,2,28]]},"references-count":64,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2017,2,28]]}},"alternative-id":["10.1128\/mSystems.00188-16"],"URL":"https:\/\/doi.org\/10.1128\/msystems.00188-16","relation":{},"ISSN":["2379-5077"],"issn-type":[{"value":"2379-5077","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,2,28]]},"assertion":[{"value":"2016-12-06","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2016-12-14","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2017-02-28","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e00188-16"}}