{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,12]],"date-time":"2026-10-12T16:20:45Z","timestamp":1791822045069,"version":"4.3.4"},"reference-count":67,"publisher":"Wiley","issue":"8","license":[{"start":{"date-parts":[[2024,5,3]],"date-time":"2024-05-03T00:00:00Z","timestamp":1714694400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"},{"start":{"date-parts":[[2024,5,3]],"date-time":"2024-05-03T00:00:00Z","timestamp":1714694400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"funder":[{"DOI":"10.13039\/100002569","name":"American Association of Endodontists Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100002569","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100019822","name":"Institute for Clinical and Translational Research, University of Maryland, Baltimore","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100019822","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Int Endodontic J"],"published-print":{"date-parts":[[2024,8]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Aim<\/jats:title>\n                    <jats:p>To investigate the bacteriome present in teeth with primary endodontic infection (PEI) and apical periodontitis (AP) and to determine quantitatively and qualitatively the impact of chemomechanical preparation (CMP) using 2.5% sodium hypochlorite NAOCl on the bacteriome found in PEI with AP using the Illumina MiSeq platform.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methodology<\/jats:title>\n                    <jats:p>Thirty\u2010six paired samples from 18 patients were successfully sequenced and analysed. Samples were collected at two sampling times: before (s1) and after (s2) CMP using 2.5% NaOCl. The DNA was extracted from s1 and s2 samples and quantified using quantitative PCR (qPCR). All 36 samples were sequenced using the Illumina MiSeq platform. Raw V3\u2013V4 amplicon sequencing data were processed with the DADA2 pipeline to generate amplicon sequence variants (ASVs). Alpha diversity metrics representing abundance (Chao1) and diversity and evenness (Shannon, Simpson) were computed. The paired\u2010sample Wilcoxon's test was used to compare alpha diversity metrics and qPCR counts between s1 and s2. The PERMANOVA method (with 999 permutations) was applied to compare community composition between sample types (s1 versus s2) and between patient IDs. ALDEx2 (ANOVA\u2010like differential expression tool for high\u2010throughput sequencing data) to investigate differentially abundant taxa between s1 and s2. A paired\u2010sample Wilcoxon's test was used to compare alpha diversity metrics and qPCR counts between s1 and s2.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      The qPCR counts were significantly higher in s1 compared to s2 (\n                      <jats:italic>p<\/jats:italic>\n                      \u2009=\u2009.0007). The Chao1 index indicated no difference in alpha diversity (\n                      <jats:italic>p<\/jats:italic>\n                      \u2009&lt;\u2009.7019); whereas Shannon (\n                      <jats:italic>p<\/jats:italic>\n                      \u2009=\u2009.0056) and Simpson (\n                      <jats:italic>p<\/jats:italic>\n                      \u2009=\u2009.02685) indexes showed higher values in s2. The PERMANOVA test using Adonis2 showed a significant effect of sample time on community composition (\n                      <jats:italic>R<\/jats:italic>\n                      <jats:sup>2<\/jats:sup>\n                      \u2009=\u2009.0630,\n                      <jats:italic>p<\/jats:italic>\n                      \u2009=\u2009.012). Patient ID also showed a significant effect on community composition (\n                      <jats:italic>R<\/jats:italic>\n                      <jats:sup>2<\/jats:sup>\n                      \u2009=\u2009.6961,\n                      <jats:italic>p<\/jats:italic>\n                      \u2009=\u2009.001). At the genus level,\n                      <jats:italic>Dialister<\/jats:italic>\n                      ,\n                      <jats:italic>Mogibacterium<\/jats:italic>\n                      ,\n                      <jats:italic>Prevotella<\/jats:italic>\n                      , and\n                      <jats:italic>Olsenella<\/jats:italic>\n                      were differentially enriched at s1, while\n                      <jats:italic>Actinomyces, Stenotrophomonas_unclassified<\/jats:italic>\n                      ,\n                      <jats:italic>Enterococcus_unclassified<\/jats:italic>\n                      , and\n                      <jats:italic>Actinomyces_unclassified<\/jats:italic>\n                      were differentially enriched in s2.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>The bacteriome present in teeth with PEI with AP is complex and diverse. CMP using 2.5% NaOCl showed a high quantitatively and qualitatively disinfectant impact on the bacteriome present in PEI with AP.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1111\/iej.14074","type":"journal-article","created":{"date-parts":[[2024,5,3]],"date-time":"2024-05-03T11:25:36Z","timestamp":1714735536000},"page":"1124-1135","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":19,"title":["Impact of root canal disinfection on the bacteriome present in primary endodontic infection: A next generation sequencing study"],"prefix":"10.1111","volume":"57","author":[{"given":"Theeb Abdullah","family":"Alquria","sequence":"first","affiliation":[{"name":"Department of Advanced Oral Sciences and Therapeutics, School of Dentistry University of Maryland  Baltimore Maryland USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aneesha","family":"Acharya","sequence":"additional","affiliation":[{"name":"Department of Periodontics and Oral Implantology Dr D.Y. 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