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Specimens were cryopulverized, bacterial DNA was extracted and the V3\u2013V4 hypervariable regions of the 16\u2009S rRNA gene were amplified and sequenced using the Illumina Miseq platform. Diversity and community composition were studied in the paired samples, as well as in AAP and SAP cases. Diversity indices were compared in each case by means of the Wilcoxon matched\u2010pairs signed rank and Mann\u2013Whitney <jats:italic>U<\/jats:italic> tests. Differences in the community composition were explored with multivariate statistical analysis and Linear discriminant analysis Effect Size (LEfSe). Bacterial functional study was performed through the Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) analysis.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>Twenty\u2010one paired apices and lesions were successfully sequenced and analysed, identifying a total of 21 phyla and 600 genera. A higher alpha\u2010diversity was observed in the periapical lesions, although no global differences in the community composition between the two sites were found (<jats:italic>p<\/jats:italic>\u00a0=\u00a0.87), the most prevalent genera being <jats:italic>Fusobacterium<\/jats:italic>, <jats:italic>Porphyromonas<\/jats:italic> and <jats:italic>Streptococcus<\/jats:italic>. <jats:italic>Prevotella<\/jats:italic>, <jats:italic>Clostridiales_vadinBB60_group<\/jats:italic>, <jats:italic>Bosea<\/jats:italic>, <jats:italic>Phreatobacter<\/jats:italic>, <jats:italic>Afipia<\/jats:italic> and <jats:italic>Xanthobacteriaceae_unclassified<\/jats:italic> were enriched in SAP samples, while <jats:italic>Pseudopropionibacterium<\/jats:italic>, <jats:italic>Campylobacter<\/jats:italic> and <jats:italic>Peptoniphilus<\/jats:italic> were significantly more abundant in AAP cases (<jats:italic>p<\/jats:italic>\u2009&lt;\u2009.05). Metabolic pathways involved in the amino acid metabolism or degradation and flagellum assembly were more abundant in SAP samples, whereas glucose metabolism\u2010related pathways were associated with AAP.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>The bacterial community composition was similar in the apices and periapical lesions. The microbiome was different in AAP and SAP samples, gram\u2010negative bacteria showing higher relative abundances in SAP cases. An association was observed between amino acid degradation and flagellum assembly pathways, and the development of tenderness to percussion or palpation.<\/jats:p><\/jats:sec>","DOI":"10.1111\/iej.13893","type":"journal-article","created":{"date-parts":[[2023,1,23]],"date-time":"2023-01-23T17:23:48Z","timestamp":1674494628000},"page":"622-636","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":32,"title":["Microbiome in paired root apices and periapical lesions and its association with clinical signs in persistent apical periodontitis using next\u2010generation sequencing"],"prefix":"10.1111","volume":"56","author":[{"given":"Virginia","family":"P\u00e9rez\u2010Carrasco","sequence":"first","affiliation":[{"name":"GENYO, Centre for Genomics and Oncological Research Pfizer\/University of Granada\/Andalusian Regional Government, PTS Granada  Granada Spain"},{"name":"Microbiology Unit University Hospital Virgen de las Nieves  Granada 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