{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T23:40:29Z","timestamp":1792798829357,"version":"4.5.0"},"reference-count":46,"publisher":"American Society for Microbiology","issue":"3","license":[{"start":{"date-parts":[[2017,6,20]],"date-time":"2017-06-20T00:00:00Z","timestamp":1497916800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2017,6,27]],"date-time":"2017-06-27T00:00:00Z","timestamp":1498521600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"name":"Clorox Corporation","id":[{"id":"https:\/\/ror.org\/02k4xm641","id-type":"ROR","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000002","name":"HHS | National Institutes of Health","doi-asserted-by":"publisher","award":["U01-HG004866-02"],"award-info":[{"award-number":["U01-HG004866-02"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007899","name":"University of Arizona","doi-asserted-by":"publisher","award":["Technology and Research Initiation Fund"],"award-info":[{"award-number":["Technology and Research Initiation Fund"]}],"id":[{"id":"10.13039\/100007899","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["mSystems"],"published-print":{"date-parts":[[2017,6,27]]},"abstract":"<jats:p>Periodontal disease affects the majority of adults worldwide and has been linked to numerous systemic diseases. Despite decades of research, the reasons for the substantial differences among periodontitis patients in disease incidence, progressivity, and response to treatment remain poorly understood. While deep sequencing of oral bacterial communities has greatly expanded our comprehension of the microbial diversity of periodontal disease and identified associations with healthy and disease states, predicting treatment outcomes remains elusive. Our results suggest that combining multiple omics approaches enhances the ability to differentiate among disease states and determine differential effects of treatment, particularly with the addition of metabolomic information. Furthermore, multi-omics analysis of biofilm community instability indicated that these approaches provide new tools for investigating the ecological dynamics underlying the progressive periodontal disease process.<\/jats:p>","DOI":"10.1128\/msystems.00016-17","type":"journal-article","created":{"date-parts":[[2017,6,20]],"date-time":"2017-06-20T20:40:26Z","timestamp":1497991226000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":63,"title":["Multi-omics Analysis of Periodontal Pocket Microbial Communities Pre- and Posttreatment"],"prefix":"10.1128","volume":"2","author":[{"given":"Katy J.","family":"Califf","sequence":"first","affiliation":[{"name":"Center for Microbial Genetics and Genomics and Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Karen","family":"Schwarzberg-Lipson","sequence":"additional","affiliation":[{"name":"Center for Microbial Genetics and Genomics and Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Neha","family":"Garg","sequence":"additional","affiliation":[{"name":"Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sean M.","family":"Gibbons","sequence":"additional","affiliation":[{"name":"Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8865-1670","authenticated-orcid":false,"given":"J. Gregory","family":"Caporaso","sequence":"additional","affiliation":[{"name":"Center for Microbial Genetics and Genomics and Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"J\u00f8rgen","family":"Slots","sequence":"additional","affiliation":[{"name":"Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chloe","family":"Cohen","sequence":"additional","affiliation":[{"name":"Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pieter C.","family":"Dorrestein","sequence":"additional","affiliation":[{"name":"Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California, USA"},{"name":"Department of Pediatrics, University of California, San Diego, San Diego, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9547-4169","authenticated-orcid":false,"given":"Scott T.","family":"Kelley","sequence":"additional","affiliation":[{"name":"Department of Biology, San Diego State University, San Diego, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_2_2_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1600-0757.2011.00397.x"},{"key":"e_1_3_2_3_2","doi-asserted-by":"publisher","DOI":"10.1034\/j.1600-0757.2001.22250102.x"},{"key":"e_1_3_2_4_2","doi-asserted-by":"publisher","DOI":"10.1111\/omi.12065"},{"key":"e_1_3_2_5_2","doi-asserted-by":"publisher","DOI":"10.1111\/jcpe.12077"},{"key":"e_1_3_2_6_2","doi-asserted-by":"publisher","DOI":"10.1038\/sj.bdj.2014.903"},{"key":"e_1_3_2_7_2","doi-asserted-by":"publisher","DOI":"10.1038\/nrendo.2011.106"},{"key":"e_1_3_2_8_2","doi-asserted-by":"publisher","DOI":"10.1155\/2015\/259074"},{"key":"e_1_3_2_9_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1601-5037.2006.00200.x"},{"key":"e_1_3_2_10_2","doi-asserted-by":"publisher","DOI":"10.1038\/nri3785"},{"key":"e_1_3_2_11_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.chom.2014.05.012"},{"key":"e_1_3_2_12_2","doi-asserted-by":"publisher","DOI":"10.1034\/j.1600-0765.2002.00004.x"},{"key":"e_1_3_2_13_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1600-0757.2011.00429.x"},{"key":"e_1_3_2_14_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1600-051X.1981.tb02024.x"},{"key":"e_1_3_2_15_2","doi-asserted-by":"publisher","DOI":"10.1902\/jop.1979.50.5.225"},{"key":"e_1_3_2_16_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0041606"},{"key":"e_1_3_2_17_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0086708"},{"key":"e_1_3_2_18_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1600-0757.2006.00174.x"},{"key":"e_1_3_2_19_2","doi-asserted-by":"publisher","DOI":"10.1177\/154405910808701104"},{"key":"e_1_3_2_20_2","doi-asserted-by":"publisher","DOI":"10.1186\/s12903-015-0006-x"},{"key":"e_1_3_2_21_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.00317-06"},{"key":"e_1_3_2_22_2","doi-asserted-by":"publisher","DOI":"10.1038\/ismej.2011.191"},{"key":"e_1_3_2_23_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1215210110"},{"key":"e_1_3_2_24_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0037919"},{"key":"e_1_3_2_25_2","doi-asserted-by":"publisher","DOI":"10.1038\/srep01843"},{"key":"e_1_3_2_26_2","doi-asserted-by":"publisher","DOI":"10.1111\/jre.12219"},{"key":"e_1_3_2_27_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1574-6976.2010.00251.x"},{"key":"e_1_3_2_28_2","doi-asserted-by":"publisher","DOI":"10.1093\/database\/baq013"},{"key":"e_1_3_2_29_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1516878112"},{"key":"e_1_3_2_30_2","doi-asserted-by":"publisher","DOI":"10.1128\/mSystems.00038-16"},{"key":"e_1_3_2_31_2","doi-asserted-by":"publisher","DOI":"10.1039\/c4np00044g"},{"key":"e_1_3_2_32_2","doi-asserted-by":"publisher","DOI":"10.1038\/nrmicro2337"},{"key":"e_1_3_2_33_2","doi-asserted-by":"publisher","DOI":"10.1111\/jre.12151"},{"key":"e_1_3_2_34_2","doi-asserted-by":"publisher","DOI":"10.1186\/s12915-014-0069-1"},{"key":"e_1_3_2_35_2","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.f.303"},{"key":"e_1_3_2_36_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.03006-05"},{"key":"e_1_3_2_37_2","doi-asserted-by":"publisher","DOI":"10.1038\/ismej.2011.139"},{"key":"e_1_3_2_38_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.00062-07"},{"key":"e_1_3_2_39_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp636"},{"key":"e_1_3_2_40_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0009490"},{"key":"e_1_3_2_41_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.01996-06"},{"key":"e_1_3_2_42_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1002358"},{"key":"e_1_3_2_43_2","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.3589"},{"key":"e_1_3_2_44_2","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.1923"},{"key":"e_1_3_2_45_2","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.3176"},{"key":"e_1_3_2_46_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btm098"},{"key":"e_1_3_2_47_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkm900"}],"container-title":["mSystems"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/mSystems.00016-17","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/mSystems.00016-17","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,3,8]],"date-time":"2022-03-08T00:01:07Z","timestamp":1646697667000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/mSystems.00016-17"}},"subtitle":[],"editor":[{"given":"Nicola","family":"Segata","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2017,6,27]]},"references-count":46,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2017,6,27]]}},"alternative-id":["10.1128\/mSystems.00016-17"],"URL":"https:\/\/doi.org\/10.1128\/msystems.00016-17","relation":{},"ISSN":["2379-5077"],"issn-type":[{"value":"2379-5077","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,6,27]]},"assertion":[{"value":"2017-02-28","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2017-03-20","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2017-06-20","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e00016-17"}}