{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,10]],"date-time":"2026-04-10T17:08:47Z","timestamp":1775840927031,"version":"3.50.1"},"reference-count":32,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2020,5,5]],"date-time":"2020-05-05T00:00:00Z","timestamp":1588636800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Cell. Infect. Microbiol."],"DOI":"10.3389\/fcimb.2020.00167","type":"journal-article","created":{"date-parts":[[2020,5,5]],"date-time":"2020-05-05T04:41:52Z","timestamp":1588653712000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":12,"title":["Significant Short-Term Shifts in the Microbiomes of Smokers With Periodontitis After Periodontal Therapy With Amoxicillin &amp; Metronidazole as Revealed by 16S rDNA Amplicon Next Generation Sequencing"],"prefix":"10.3389","volume":"10","author":[{"given":"Daniel","family":"Hagenfeld","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Johannes","family":"Matern","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Karola","family":"Prior","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Inga","family":"Harks","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Peter","family":"Eickholz","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Katrin","family":"Lorenz","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ti-Sun","family":"Kim","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Thomas","family":"Kocher","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"J\u00f6rg","family":"Meyle","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Do\u011fan","family":"Kaner","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ulrich","family":"Schlagenhauf","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dag","family":"Harmsen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Benjamin","family":"Ehmke","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1965","published-online":{"date-parts":[[2020,5,5]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"725","DOI":"10.1177\/0022034514538283","article-title":"Filifactor alocis: the newly discovered kid on the block with special talents","volume":"93","author":"Aruni","year":"2014","journal-title":"J. Dent. Res."},{"key":"B2","doi-asserted-by":"publisher","first-page":"483","DOI":"10.1111\/jcpe.12087","article-title":"Subgingival microbiome in smokers and non-smokers in periodontitis: an exploratory study using traditional targeted techniques and a next-generation sequencing","volume":"40","author":"Bizzarro","year":"2013","journal-title":"J. Clin. Periodontol."},{"key":"B3","doi-asserted-by":"publisher","first-page":"581","DOI":"10.1038\/nmeth.3869","article-title":"DADA2: high-resolution sample inference from Illumina amplicon data","volume":"13","author":"Callahan","year":"2016","journal-title":"Nat. Methods"},{"key":"B4","doi-asserted-by":"publisher","first-page":"200","DOI":"10.1111\/j.1600-051X.2005.00644.x","article-title":"Clinical and microbiological effect of scaling and root planing in smoker and non-smoker chronic and aggressive periodontitis patients","volume":"32","author":"Darby","year":"2005","journal-title":"J. Clin. Periodontol."},{"key":"B5","doi-asserted-by":"publisher","first-page":"226","DOI":"10.1186\/s40168-018-0605-2","article-title":"Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data","volume":"6","author":"Davis","year":"2018","journal-title":"Microbiome"},{"key":"B6","doi-asserted-by":"publisher","first-page":"581","DOI":"10.1902\/jop.2013.130278","article-title":"Clinical and microbiologic effects of adjunctive metronidazole plus amoxicillin in the treatment of generalized chronic periodontitis: smokers versus non-smokers","volume":"85","author":"Faveri","year":"2014","journal-title":"J. Periodontol."},{"key":"B7","doi-asserted-by":"publisher","first-page":"225","DOI":"10.1111\/adj.12225","article-title":"Subgingival bacterial recolonization after scaling and root planing in smokers with chronic periodontitis","volume":"60","author":"Feres","year":"2015","journal-title":"Aust. Dent. J."},{"key":"B8","doi-asserted-by":"publisher","first-page":"S94","DOI":"10.1111\/jcpe.12677","article-title":"Global epidemiology of dental caries and severe periodontitis - a comprehensive review","volume":"44","author":"Frencken","year":"2017","journal-title":"J. Clin. Periodontol."},{"key":"B9","doi-asserted-by":"publisher","first-page":"377","DOI":"10.1034\/j.1600-051x.2001.028005377.x","article-title":"Relationship of cigarette smoking to the subgingival microbiota","volume":"28","author":"Haffajee","year":"2001","journal-title":"J. Clin. Periodontol."},{"key":"B10","doi-asserted-by":"publisher","first-page":"e0195534","DOI":"10.1371\/journal.pone.0195534","article-title":"Do we treat our patients or rather periodontal microbes with adjunctive antibiotics in periodontal therapy? A 16S rDNA microbial community analysis","volume":"13","author":"Hagenfeld","year":"2018","journal-title":"PLoS ONE"},{"key":"B11","doi-asserted-by":"publisher","first-page":"435","DOI":"10.1111\/jre.12645","article-title":"No differences in microbiome changes between anti-adhesive and antibacterial ingredients in toothpastes during periodontal therapy","volume":"54","author":"Hagenfeld","year":"2019","journal-title":"J. Periodontal Res."},{"key":"B12","doi-asserted-by":"publisher","first-page":"832","DOI":"10.1111\/jcpe.12441","article-title":"Is progression of periodontitis relevantly influenced by systemic antibiotics? A clinical randomized trial","volume":"42","author":"Harks","year":"2015","journal-title":"J. Clin. Periodontol."},{"key":"B13","doi-asserted-by":"publisher","first-page":"1","DOI":"10.18637\/jss.v042.i08","article-title":"MatchIt: nonparametric preprocessing for parametric causal inference","volume":"42","author":"Ho","year":"2011","journal-title":"J. Stat. Softw."},{"key":"B14","unstructured":"Understanding Illumina Quality Scores2012"},{"key":"B15","doi-asserted-by":"publisher","first-page":"1037","DOI":"10.1111\/jcpe.12300","article-title":"Smoking decreases structural and functional resilience in the subgingival ecosystem","volume":"41","author":"Joshi","year":"2014","journal-title":"J. Clin. Periodontol."},{"key":"B16","doi-asserted-by":"publisher","first-page":"e0218266","DOI":"10.1371\/journal.pone.0218266","article-title":"Fretibacterium sp. human oral taxon 360 is a novel biomarker for periodontitis screening in the Japanese population","volume":"14","author":"Khemwong","year":"2019","journal-title":"PLoS ONE"},{"key":"B17","doi-asserted-by":"publisher","first-page":"e1","DOI":"10.1093\/nar\/gks808","article-title":"Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies","volume":"41","author":"Klindworth","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"B18","doi-asserted-by":"publisher","first-page":"325","DOI":"10.1902\/jop.1984.55.6.325","article-title":"Metronidazole in periodontitis: I. clinical and bacteriological results after 15 to 30 Weeks","volume":"55","author":"Loesche","year":"1984","journal-title":"J. Periodontol."},{"key":"B19","doi-asserted-by":"publisher","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol."},{"key":"B20","doi-asserted-by":"publisher","first-page":"10","DOI":"10.14806\/ej.17.1.200","article-title":"Cutadapt removes adapter sequences from high-throughput sequencing reads","volume":"17","author":"Martin","year":"2011","journal-title":"EMBnet. J."},{"key":"B21","doi-asserted-by":"publisher","first-page":"885","DOI":"10.1111\/j.1600-051X.2008.01304.x","article-title":"Clinical and microbiological benefits of systemic metronidazole and amoxicillin in the treatment of smokers with chronic periodontitis: a randomized placebo-controlled study","volume":"35","author":"Matarazzo","year":"2008","journal-title":"J. Clin. Periodontol."},{"key":"B22","doi-asserted-by":"publisher","first-page":"e61217","DOI":"10.1371\/journal.pone.0061217","article-title":"phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data","volume":"8","author":"McMurdie","year":"2013","journal-title":"PLoS ONE"},{"key":"B23","doi-asserted-by":"publisher","first-page":"227","DOI":"10.1111\/omi.12086","article-title":"Subgingival microbiome in smokers and non-smokers in Korean chronic periodontitis patients","volume":"30","author":"Moon","year":"2015","journal-title":"Mol. Oral Microbiol."},{"key":"B24","doi-asserted-by":"publisher","first-page":"679","DOI":"10.1099\/00207713-50-2-679","article-title":"Description of Mogibacterium pumilum gen. nov., sp. nov. and Mogibacterium vescum gen. nov., sp. nov., and reclassification of Eubacterium timidum (Holdeman et al. 1980) as Mogibacterium timidum gen. nov., comb. nov","volume":"50","author":"Nakazawa","year":"2000","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"B25","doi-asserted-by":"publisher","first-page":"846","DOI":"10.1177\/0022034514542468","article-title":"Newly identified pathogens associated with periodontitis: a systematic review","volume":"93","author":"Perez-Chaparro","year":"2014","journal-title":"J. Dent. Res."},{"key":"B26","doi-asserted-by":"publisher","first-page":"7188","DOI":"10.1093\/nar\/gkm864","article-title":"SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB","volume":"35","author":"Pruesse","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"B27","unstructured":"30628467R: A Language and Environment for Statistical Computing2017"},{"key":"B28","doi-asserted-by":"publisher","first-page":"1247","DOI":"10.1177\/0022034510377203","article-title":"Subgingival microbial profiles of smokers with periodontitis","volume":"89","author":"Shchipkova","year":"2010","journal-title":"J. Dent. Res."},{"key":"B29","doi-asserted-by":"publisher","first-page":"134","DOI":"10.1111\/j.1600-051X.1998.tb02419.x","article-title":"Microbial complexes in subgingival plaque","volume":"25","author":"Socransky","year":"1998","journal-title":"J. Clin. Periodontol."},{"key":"B30","doi-asserted-by":"publisher","first-page":"S149","DOI":"10.1111\/jcpe.12945","article-title":"Staging and grading of periodontitis: framework and proposal of a new classification and case definition","volume":"45","author":"Tonetti","year":"2018","journal-title":"J. Clin. Periodontol."},{"key":"B31","doi-asserted-by":"publisher","first-page":"128","DOI":"10.1111\/j.1600-051X.1989.tb01626.x","article-title":"Metronidazole plus amoxycillin in the treatment of Actinobacillus actinomycetemcomitans associated periodontitis","volume":"16","author":"van Winkelhoff","year":"1989","journal-title":"J. Clin. Periodontol."},{"key":"B32","doi-asserted-by":"publisher","first-page":"666","DOI":"10.1902\/jop.2001.72.5.666","article-title":"Smoking affects the subgingival microflora in periodontitis","volume":"72","author":"Winkelhoff","year":"2001","journal-title":"J. Periodontol."}],"container-title":["Frontiers in Cellular and Infection Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/article\/10.3389\/fcimb.2020.00167\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,5,5]],"date-time":"2020-05-05T04:41:55Z","timestamp":1588653715000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/article\/10.3389\/fcimb.2020.00167\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,5,5]]},"references-count":32,"alternative-id":["10.3389\/fcimb.2020.00167"],"URL":"https:\/\/doi.org\/10.3389\/fcimb.2020.00167","relation":{},"ISSN":["2235-2988"],"issn-type":[{"value":"2235-2988","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,5,5]]},"article-number":"167"}}