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Individual samples were submitted to <jats:italic>16S rDNA<\/jats:italic> high\u2010 throughput sequencing and the analysis was made using mothur and R packages.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>Nine subjects with ChP and seven with <jats:styled-content style=\"fixed-case\">PH<\/jats:styled-content> were included and 101 samples were evaluated. Thirteen phyla, 118 genera and 211 <jats:styled-content style=\"fixed-case\">OTU<\/jats:styled-content>s were detected. Taxa from <jats:italic>Chloroflexi<\/jats:italic> and <jats:italic>Spirochaetes<\/jats:italic> phyla were associated with initial stages of disease. <jats:italic>Fretibacterium, Eubacterium[<jats:styled-content style=\"fixed-case\">XI<\/jats:styled-content>][G\u20106], Desulfobulbus, Peptostreptococcaceae[<jats:styled-content style=\"fixed-case\">XI<\/jats:styled-content>][G\u20101] and [G\u20103], Bacteroidetes[G\u20103], Bacteroidaceae[G\u20101]<\/jats:italic> genera and <jats:italic>Filifactor alocis<\/jats:italic>,<jats:italic> Fretibacterium fastidiosum<\/jats:italic>,<jats:italic> Johnsonella sp<\/jats:italic><jats:styled-content style=\"fixed-case\">HOT<\/jats:styled-content>166, <jats:italic>Peptostreptococcaceae[<jats:styled-content style=\"fixed-case\">XIII<\/jats:styled-content>][G\u20101]<\/jats:italic><jats:styled-content style=\"fixed-case\">HOT<\/jats:styled-content>113, <jats:italic>Porphyromonas endodontalis<\/jats:italic> and <jats:italic>Treponema sp<\/jats:italic>. <jats:styled-content style=\"fixed-case\">HOT<\/jats:styled-content>258, which are not conventionally associated with disease, increased with the deepening of the pockets and\/or were elevated in ChP; while <jats:italic>Streptococcus<\/jats:italic>,<jats:italic> Corynebacterium<\/jats:italic> and <jats:italic>Bergeyella<\/jats:italic> genera were associated with <jats:styled-content style=\"fixed-case\">PH<\/jats:styled-content> (<jats:italic>p<\/jats:italic>\u00a0&lt;\u00a0.05).<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>Striking differences were observed between the microbiota of shallow and moderate\/deep sites, but not between moderate and deep sites in ChP subjects. Differences between shallow sites in <jats:styled-content style=\"fixed-case\">PH<\/jats:styled-content> and ChP were also observed. The characterized microbiota included known oral microorganisms and newly identified periodontal taxa, some of them not\u2010yet\u2010cultured.<\/jats:p><\/jats:sec>","DOI":"10.1111\/jcpe.12811","type":"journal-article","created":{"date-parts":[[2017,9,5]],"date-time":"2017-09-05T00:02:54Z","timestamp":1504569774000},"page":"26-37","source":"Crossref","is-referenced-by-count":65,"title":["Do different probing depths exhibit striking differences in microbial profiles?"],"prefix":"10.1111","volume":"45","author":[{"given":"Paula Juliana","family":"P\u00e9rez\u2010Chaparro","sequence":"first","affiliation":[{"name":"Dental Research Division Department of Periodontology Guarulhos University  Guarulhos Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John Anthony","family":"McCulloch","sequence":"additional","affiliation":[{"name":"Department of Clinical and Toxicological Analyses Faculty of Pharmaceutical Sciences University of S\u00e3o Paulo  S\u00e3o Paulo Brazil"},{"name":"Trinchieri Lab Cancer and Inflammation Program National Cancer Institute National Institutes of Health  Bethesda MD USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elsa Masae","family":"Mamizuka","sequence":"additional","affiliation":[{"name":"Department of Clinical and Toxicological Analyses Faculty of Pharmaceutical Sciences University of S\u00e3o Paulo  S\u00e3o Paulo Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aline da Costa Lima","family":"Moraes","sequence":"additional","affiliation":[{"name":"Department of Plant Biology Biology Institute State University of Campinas  Campinas S\u00e3o Paulo Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marcelo","family":"Faveri","sequence":"additional","affiliation":[{"name":"Dental Research Division Department of Periodontology Guarulhos University  Guarulhos Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luciene Cristina","family":"Figueiredo","sequence":"additional","affiliation":[{"name":"Dental Research Division Department of Periodontology Guarulhos University  Guarulhos Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Poliana Mendes","family":"Duarte","sequence":"additional","affiliation":[{"name":"Dental Research Division Department of Periodontology Guarulhos University  Guarulhos Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2293-3392","authenticated-orcid":false,"given":"Magda","family":"Feres","sequence":"additional","affiliation":[{"name":"Dental Research Division Department of Periodontology Guarulhos University  Guarulhos Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2017,12]]},"reference":[{"key":"e_1_2_8_2_1","doi-asserted-by":"publisher","DOI":"10.1038\/ismej.2012.174"},{"key":"e_1_2_8_3_1","doi-asserted-by":"publisher","DOI":"10.1902\/annals.1999.4.1.1"},{"key":"e_1_2_8_4_1","doi-asserted-by":"publisher","DOI":"10.1177\/0022034514538283"},{"key":"e_1_2_8_5_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.micinf.2015.03.011"},{"key":"e_1_2_8_6_1","doi-asserted-by":"crossref","first-page":"3872","DOI":"10.1128\/IAI.05631-11","article-title":"Filifactor alocis has virulence attributes that can enhance its persistence under oxidative stress conditions and mediate invasion of epithelial cells by Porphyromonas gingivalis","volume":"19","author":"Aruni A. 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