{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,2]],"date-time":"2026-10-02T01:24:34Z","timestamp":1790904274139,"version":"4.1.0"},"reference-count":54,"publisher":"Microbiology Society","issue":"1","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2006,1,1]]},"abstract":"<jats:p>A significant proportion of oral bacteria are unable to undergo cultivation by existing techniques. In this regard, the microbiota from root canals still requires complementary characterization. The present study aimed at the identification of bacteria by sequence analysis of 16S rDNA clone libraries from seven endodontically infected teeth. Samples were collected from the root canals, subjected to the PCR with universal 16S rDNA primers, cloned and partially sequenced. Clones were clustered into groups of closely related sequences (phylotypes) and identification to the species level was performed by comparative analysis with the GenBank, EMBL and DDBJ databases, according to a 98\u200a% minimum identity. All samples were positive for bacteria and the number of phylotypes detected per subject varied from two to 14. The majority of taxa (65\u00b72\u200a%) belonged to the phylum <jats:italic>Firmicutes<\/jats:italic> of the Gram-positive bacteria, followed by <jats:italic>Proteobacteria<\/jats:italic> (10\u00b79\u200a%), <jats:italic>Spirochaetes<\/jats:italic> (4\u00b73\u200a%), <jats:italic>Bacteroidetes<\/jats:italic> (6\u00b75\u200a%), <jats:italic>Actinobacteria<\/jats:italic> (2\u00b72\u200a%) and <jats:italic>Deferribacteres<\/jats:italic> (2\u00b72\u200a%). A total of 46 distinct taxonomic units was identified. Four clones with low similarity to sequences previously deposited in the databases were sequenced to nearly full extent and were classified taxonomically as novel representatives of the order <jats:italic>Clostridiales<\/jats:italic>, including a putative novel species of <jats:italic>Mogibacterium<\/jats:italic>. The identification of novel phylotypes associated with endodontic infections suggests that the endodontium may still harbour a relevant proportion of uncharacterized taxa.<\/jats:p>","DOI":"10.1099\/jmm.0.46212-0","type":"journal-article","created":{"date-parts":[[2005,12,30]],"date-time":"2005-12-30T21:02:36Z","timestamp":1135976556000},"page":"101-107","source":"Crossref","is-referenced-by-count":70,"title":["Identification of bacteria in endodontic infections by sequence analysis of 16S rDNA clone libraries"],"prefix":"10.1099","volume":"55","author":[{"given":"Daniel","family":"Saito","sequence":"first","affiliation":[{"name":"Department of Oral Diagnosis, Dental School of Piracicaba, State University of Campinas (UNICAMP), Av. Limeira 90, Piracicaba, 13414-903 S\u00e3o Paulo, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Renato","family":"de Toledo Leonardo","sequence":"additional","affiliation":[{"name":"Department of Restorative Dentistry, Dental School of Araraquara, State University of S\u00e3o Paulo, Araraquara, S\u00e3o Paulo, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jorge Luiz Mazza","family":"Rodrigues","sequence":"additional","affiliation":[{"name":"Laboratory of Cell and Molecular Biology, Center of Nuclear Energy in Agriculture, University of S\u00e3o Paulo, Piracicaba, S\u00e3o Paulo, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Siu Mui","family":"Tsai","sequence":"additional","affiliation":[{"name":"Laboratory of Cell and Molecular Biology, Center of Nuclear Energy in Agriculture, University of S\u00e3o Paulo, Piracicaba, S\u00e3o Paulo, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jos\u00e9 Francisco","family":"H\u00f6fling","sequence":"additional","affiliation":[{"name":"Department of Oral Diagnosis, Dental School of Piracicaba, State University of Campinas (UNICAMP), Av. Limeira 90, Piracicaba, 13414-903 S\u00e3o Paulo, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Reginaldo Bruno","family":"Gon\u00e7alves","sequence":"additional","affiliation":[{"name":"Department of Oral Diagnosis, Dental School of Piracicaba, State University of Campinas (UNICAMP), Av. Limeira 90, Piracicaba, 13414-903 S\u00e3o Paulo, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"345","reference":[{"key":"R1","doi-asserted-by":"crossref","first-page":"2629","DOI":"10.1128\/JB.186.9.2629-2635.2004","article-title":"Divergence and redundancy of 16S rRNA sequences in genomes with multiple rrn operons","volume":"186","author":"Acinas","year":"2004","journal-title":"J Bacteriol"},{"key":"R2","doi-asserted-by":"crossref","first-page":"194","DOI":"10.1046\/j.1365-2591.1999.00299.x","article-title":"Detection of bacterial virulence genes associated with infective endocarditis in infected root canals","volume":"33","author":"Bate","year":"2000","journal-title":"Int Endod J"},{"key":"R3","doi-asserted-by":"crossref","first-page":"794","DOI":"10.1097\/00004770-200312000-00002","article-title":"Identification of spirochetes (treponemes) in endodontic infections","volume":"29","author":"Baumgartner","year":"2003","journal-title":"J Endod"},{"key":"R4","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1097\/00004770-200403000-00004","article-title":"Geographical differences in bacteria detected in endodontic infections using polymerase chain reaction","volume":"30","author":"Baumgartner","year":"2004","journal-title":"J Endod"},{"key":"R5","doi-asserted-by":"crossref","first-page":"1001","DOI":"10.1128\/JCM.40.3.1001-1009.2002","article-title":"Molecular analysis of bacterial species associated with childhood caries","volume":"40","author":"Becker","year":"2002","journal-title":"J Clin Microbiol"},{"key":"R6","first-page":"555","article-title":"16-year remission of rheumatoid arthritis after unusually vigorous treatment of closed dental foci","volume":"20","author":"Breebaart","year":"2002","journal-title":"Clin Exp Rheumatol"},{"key":"R7","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1016\/S0378-1097(03)00717-1","article-title":"Intragenomic heterogeneity between multiple 16S ribosomal RNA operons in sequenced bacterial genomes","volume":"228","author":"Coenye","year":"2003","journal-title":"FEMS Microbiol Lett"},{"key":"R8","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1034\/j.1399-302x.2000.150410.x","article-title":"Importance of Dialister pneumosintes in human periodontitis","volume":"15","author":"Contreras","year":"2000","journal-title":"Oral Microbiol Immunol"},{"key":"R9","doi-asserted-by":"crossref","first-page":"196","DOI":"10.1034\/j.1399-302x.2000.150308.x","article-title":"The diversity of periodontal spirochetes by 16S rRNA analysis","volume":"15","author":"Dewhirst","year":"2000","journal-title":"Oral Microbiol Immunol"},{"key":"R10","doi-asserted-by":"crossref","first-page":"1937","DOI":"10.1099\/ijs.0.02640-0","article-title":"Dialister invisus sp. nov., isolated from the human oral cavity","volume":"53","author":"Downes","year":"2003","journal-title":"Int J Syst Evol Microbiol"},{"key":"R11","doi-asserted-by":"crossref","first-page":"3623","DOI":"10.1128\/JCM.38.10.3623-3630.2000","article-title":"16S ribosomal DNA sequence analysis of a large collection of environmental and clinical unidentifiable bacterial isolates","volume":"38","author":"Drancourt","year":"2000","journal-title":"J Clin Microbiol"},{"key":"R12","doi-asserted-by":"crossref","first-page":"3223","DOI":"10.1128\/JCM.40.9.3223-3231.2002","article-title":"PCR-based identification of bacteria associated with endodontic infections","volume":"40","author":"Fouad","year":"2002","journal-title":"J Clin Microbiol"},{"key":"R13","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1034\/j.1600-0765.2002.05019.x","article-title":"Dialister pneumosintes , a new putative periodontal pathogen","volume":"37","author":"Ghayoumi","year":"2002","journal-title":"J Periodontal Res"},{"key":"R14","doi-asserted-by":"crossref","first-page":"177","DOI":"10.1093\/clinids\/6.Supplement_1.S177","article-title":"Role of anaerobic bacteria in bite-wound infections","volume":"6","author":"Goldstein","year":"1984","journal-title":"Rev Infect Dis"},{"key":"R15","doi-asserted-by":"crossref","first-page":"955","DOI":"10.1016\/S0030-4220(78)80018-8","article-title":"Brain abscess following dental infection","volume":"45","author":"Henig","year":"1978","journal-title":"Oral Surg Oral Med Oral Pathol"},{"key":"R16","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1099\/mic.0.25791-0","article-title":"Molecular analysis of bacteria in periodontitis: evaluation of clone libraries, novel phylotypes and putative pathogens","volume":"149","author":"Hutter","year":"2003","journal-title":"Microbiology"},{"key":"R17","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1016\/B978-1-4832-3211-9.50009-7","article-title":"Evolution of protein molecules","volume-title":"In Mammalian Protein Metabolism","author":"Jukes","year":"1969"},{"key":"R18","doi-asserted-by":"crossref","first-page":"599","DOI":"10.1097\/00004770-200010000-00006","article-title":"Molecular epidemiology and association of putative pathogens in root canal infection","volume":"26","author":"Jung","year":"2000","journal-title":"J Endod"},{"key":"R19","doi-asserted-by":"crossref","first-page":"340","DOI":"10.1016\/0030-4220(65)90166-0","article-title":"The effects of surgical exposures of dental pulps in germ-free and conventional laboratory rats","volume":"20","author":"Kakehashi","year":"1965","journal-title":"Oral Surg Oral Med Oral Pathol"},{"key":"R20","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1111\/j.1600-9657.1990.tb00378.x","article-title":"Similarities in the microfloras of root canals and deep periodontal pockets","volume":"6","author":"Kerekes","year":"1990","journal-title":"Endod Dent Traumatol"},{"key":"R21","doi-asserted-by":"crossref","first-page":"14547","DOI":"10.1073\/pnas.96.25.14547","article-title":"Bacterial diversity within the human subgingival crevice","volume":"96","author":"Kroes","year":"1999","journal-title":"Proc Natl Acad Sci U S A"},{"key":"R22","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1136\/ard.58.2.103","article-title":"Optimised sample preparation of synovial fluid for detection of Chlamydia trachomatis DNA by polymerase chain reaction","volume":"58","author":"Kuipers","year":"1999","journal-title":"Ann Rheum Dis"},{"key":"R23","doi-asserted-by":"crossref","first-page":"1244","DOI":"10.1093\/bioinformatics\/17.12.1244","article-title":"mega2: molecular evolutionary genetics analysis software","volume":"17","author":"Kumar","year":"2001","journal-title":"Bioinformatics"},{"key":"R24","first-page":"115","article-title":"16S\/ 23S rRNA sequencing","volume-title":"In Nucleic Acid Techniques in Bacterial Systematics","author":"Lane","year":"1991"},{"key":"R25","doi-asserted-by":"crossref","first-page":"318","DOI":"10.1111\/j.1399-302X.1997.tb00397.x","article-title":"Evaluation of root canal bacteria and their antimicrobial susceptibility in teeth with necrotic pulp","volume":"12","author":"Le Goff","year":"1997","journal-title":"Oral Microbiol Immunol"},{"key":"R26","doi-asserted-by":"crossref","first-page":"320","DOI":"10.3109\/00016488609132845","article-title":"Chronic maxillary sinusitis. Definition, diagnosis and relation to dental infections and nasal polyposis","volume":"101","author":"Melen","year":"1986","journal-title":"Acta Otolaryngol"},{"key":"R27","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1046\/j.1365-2591.1998.t01-1-00111.x","article-title":"Microbiological status of root-filled teeth with apical periodontitis","volume":"31","author":"Molander","year":"1998","journal-title":"Int Endod J"},{"key":"R28","doi-asserted-by":"crossref","first-page":"761","DOI":"10.1177\/0810761","article-title":"Molecular and cultural analysis of the microflora associated with endodontic infections","volume":"81","author":"Munson","year":"2002","journal-title":"J Dent Res"},{"key":"R29","doi-asserted-by":"crossref","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":"R30","first-page":"101","article-title":"Orbital cellulitis as a sole symptom of odontogenic infection","volume":"40","author":"Ngeow","year":"1999","journal-title":"Singapore Med J"},{"key":"R31","doi-asserted-by":"crossref","first-page":"591","DOI":"10.1099\/jmm.0.05062-0","article-title":"Molecular analysis of bacterial flora associated with chronically inflamed maxillary sinuses","volume":"52","author":"Paju","year":"2003","journal-title":"J Med Microbiol"},{"key":"R32","doi-asserted-by":"crossref","first-page":"3770","DOI":"10.1128\/JB.183.12.3770-3783.2001","article-title":"Bacterial diversity in human subgingival plaque","volume":"183","author":"Paster","year":"2001","journal-title":"J Bacteriol"},{"key":"R33","doi-asserted-by":"crossref","first-page":"2187","DOI":"10.1128\/JCM.40.6.2187-2191.2002","article-title":"& 7 other authors","volume":"40","author":"Paster","year":"2002","journal-title":"J Clin Microbiol"},{"key":"R34","doi-asserted-by":"crossref","first-page":"3724","DOI":"10.1128\/AEM.64.10.3724-3730.1998","article-title":"Bias in template-to-product ratios in multitemplate PCR","volume":"64","author":"Polz","year":"1998","journal-title":"Appl Environ Microbiol"},{"key":"R35","doi-asserted-by":"crossref","first-page":"4249","DOI":"10.1128\/AEM.69.7.4249-4255.2003","article-title":"Detection and diversity assessment of Xylella fastidiosa in field-collected plant and insect samples by using 16S rRNA and gyrB sequences","volume":"69","author":"Rodrigues","year":"2003","journal-title":"Appl Environ Microbiol"},{"key":"R36","doi-asserted-by":"crossref","first-page":"3282","DOI":"10.1128\/JCM.39.9.3282-3289.2001","article-title":"Molecular identification of microorganisms from endodontic infections","volume":"39","author":"Rolph","year":"2001","journal-title":"J Clin Microbiol"},{"key":"R37","doi-asserted-by":"crossref","first-page":"3871","DOI":"10.1128\/JCM.40.10.3871-3873.2002","article-title":"Dialister pneumosintes associated with human brain abscesses","volume":"40","author":"Rous\u00e9e","year":"2002","journal-title":"J Clin Microbiol"},{"key":"R38","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1034\/j.1600-9657.2000.016006269.x","article-title":"Comparison of profiles of key periodontal pathogens in periodontium and endodontium","volume":"16","author":"Rupf","year":"2000","journal-title":"Endod Dent Traumatol"},{"key":"R39","first-page":"406","article-title":"The neighbor-joining method: a new method for reconstructing phylogenetic trees","volume":"4","author":"Saitou","year":"1987","journal-title":"Mol Biol Evol"},{"key":"R40","doi-asserted-by":"crossref","first-page":"643","DOI":"10.1111\/j.1348-0421.2000.tb02545.x","article-title":"Comparison of the oral bacterial flora in saliva from a healthy subject and two periodontitis patients by sequence analysis of 16S rDNA libraries","volume":"44","author":"Sakamoto","year":"2000","journal-title":"Microbiol Immunol"},{"key":"R41","volume-title":"Molecular Cloning: a Laboratory Manual","author":"Sambrook","year":"1989"},{"key":"R42","doi-asserted-by":"crossref","first-page":"293","DOI":"10.1016\/j.jdent.2004.09.008","article-title":"Detection of bacteraemias during non-surgical root canal treatment","volume":"33","author":"Savarrio","year":"2005","journal-title":"J Dent"},{"key":"R43","doi-asserted-by":"crossref","first-page":"494","DOI":"10.1067\/moe.2002.125202","article-title":"Dialister pneumosintes can be a suspected endodontic pathogen","volume":"94","author":"Siqueira","year":"2002","journal-title":"Oral Surg Oral Med Oral Pathol Oral Radiol Endod"},{"key":"R44","doi-asserted-by":"crossref","first-page":"85","DOI":"10.1016\/S1079-2104(03)00353-6","article-title":"Polymerase chain reaction-based analysis of microorganisms associated with failed endodontic treatment","volume":"97","author":"Siqueira","year":"2004","journal-title":"Oral Surg Oral Med Oral Pathol Oral Radiol Endod"},{"key":"R45","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1111\/j.1399-302X.1989.tb00406.x","article-title":"Rapid method for the purification of DNA from subgingival microorganisms","volume":"4","author":"Smith","year":"1989","journal-title":"Oral Microbiol Immunol"},{"key":"R46","doi-asserted-by":"crossref","first-page":"846","DOI":"10.1099\/00207713-44-4-846","article-title":"Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology","volume":"44","author":"Stackebrandt","year":"1994","journal-title":"Int J Syst Bacteriol"},{"key":"R47","article-title":"Bacteriological studies of necrotic dental pulps","author":"Sundqvist","year":"1976"},{"key":"R48","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1111\/j.1399-302X.1992.tb00584.x","article-title":"Associations between microbial species in dental root canal infections","volume":"7","author":"Sundqvist","year":"1992a","journal-title":"Oral Microbiol Immunol"},{"key":"R49","doi-asserted-by":"crossref","first-page":"427","DOI":"10.1016\/S0099-2399(06)80842-3","article-title":"Ecology of the root canal flora","volume":"18","author":"Sundqvist","year":"1992b","journal-title":"J Endod"},{"key":"R50","doi-asserted-by":"crossref","first-page":"625","DOI":"10.1128\/AEM.62.2.625-630.1996","article-title":"Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR","volume":"62","author":"Suzuki","year":"1996","journal-title":"Appl Environ Microbiol"},{"key":"R51","doi-asserted-by":"crossref","first-page":"4673","DOI":"10.1093\/nar\/22.22.4673","article-title":"clustal w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice","volume":"22","author":"Thompson","year":"1994","journal-title":"Nucleic Acids Res"},{"key":"R52","doi-asserted-by":"crossref","first-page":"S235","DOI":"10.1086\/516215","article-title":"Molecular detection of novel anaerobic species in dentoalveolar abscesses","volume":"25 (Suppl. 2)","author":"Wade","year":"1997","journal-title":"Clin Infect Dis"},{"key":"R53","doi-asserted-by":"crossref","first-page":"156","DOI":"10.1111\/j.1834-7819.1997.tb00113.x","article-title":"Serious complications of endodontic infections: some cautionary tales","volume":"42","author":"Walsh","year":"1997","journal-title":"Aust Dent J"},{"key":"R54","doi-asserted-by":"crossref","first-page":"697","DOI":"10.1128\/JB.173.2.697-703.1991","article-title":"16S ribosomal DNA amplification for phylogenetic study","volume":"173","author":"Weisburg","year":"1991","journal-title":"J Bacteriol"}],"container-title":["Journal of Medical Microbiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.microbiologyresearch.org\/content\/journal\/jmm\/10.1099\/jmm.0.46212-0?crawler=true","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,9,23]],"date-time":"2020-09-23T05:19:25Z","timestamp":1600838365000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.microbiologyresearch.org\/content\/journal\/jmm\/10.1099\/jmm.0.46212-0"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2006,1,1]]},"references-count":54,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2006,1,1]]}},"URL":"https:\/\/doi.org\/10.1099\/jmm.0.46212-0","relation":{},"ISSN":["0022-2615","1473-5644"],"issn-type":[{"value":"0022-2615","type":"print"},{"value":"1473-5644","type":"electronic"}],"subject":[],"published":{"date-parts":[[2006,1,1]]}}}