{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,19]],"date-time":"2026-09-19T03:33:48Z","timestamp":1789788828849,"version":"4.0.1"},"reference-count":91,"publisher":"MDPI AG","issue":"5","license":[{"start":{"date-parts":[[2020,5,6]],"date-time":"2020-05-06T00:00:00Z","timestamp":1588723200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Microorganisms"],"abstract":"<jats:p>Oral bacteria possess the ability to form biofilms on solid surfaces. After the penetration of oral bacteria into the pulp, the contact between biofilms and pulp tissue may result in pulpitis, pulp necrosis and\/or periapical lesion. Depending on the environmental conditions and the availability of nutrients in the pulp chamber and root canals, mainly Gram-negative anaerobic microorganisms predominate and form the intracanal endodontic biofilm. The objective of the present study was to investigate the role of different substrates on biofilm formation as well as the separate and collective incorporation of six endodontic pathogens, namely Enterococcus faecalis, Staphylococcus aureus, Prevotella nigrescens, Selenomonas sputigena, Parvimonas micra and Treponema denticola into a nine-species \u201cbasic biofilm\u201d. This biofilm was formed in vitro as a standard subgingival biofilm, comprising Actinomyces oris, Veillonella dispar, Fusobacterium nucleatum, Streptococcus anginosus, Streptococcus oralis, Prevotella intermedia, Campylobacter rectus, Porphyromonas gingivalis, and Tannerella forsythia. The resulting endodontic-like biofilms were grown 64 h under the same conditions on hydroxyapatite and dentin discs. After harvesting the endodontic-like biofilms, the bacterial growth was determined using quantitative real-time PCR, were labeled using fluorescence in situ hybridization (FISH) and analyzed by confocal laser scanning microscopy (CLSM). The addition of six endodontic pathogens to the \u201cbasic biofilm\u201d induced a decrease in the cell number of the \u201cbasic\u201d species. Interestingly, C. rectus counts increased in biofilms containing E. faecalis, S. aureus, P. nigrescens and S. sputigena, respectively, both on hydroxyapatite and on dentin discs, whereas P. intermedia counts increased only on dentin discs by addition of E. faecalis. The growth of E. faecalis on hydroxyapatite discs and of E. faecalis and S. aureus on dentin discs were significantly higher in the biofilm containing all species than in the \u201cbasic biofilm\u201d. Contrarily, the counts of P. nigrescens, S. sputigena and P. micra on hydroxyapatite discs as well as counts of P. micra and T. denticola on dentin discs decreased in the all-species biofilm. Overall, all bacterial species associated with endodontic infections were successfully incorporated into the standard multispecies biofilm model both on hydroxyapatite and dentin discs. Thus, future investigations on endodontic infections can rely on this newly established endodontic-like multispecies biofilm model.<\/jats:p>","DOI":"10.3390\/microorganisms8050674","type":"journal-article","created":{"date-parts":[[2020,5,7]],"date-time":"2020-05-07T03:10:38Z","timestamp":1588821038000},"page":"674","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":36,"title":["Endodontic-Like Oral Biofilms as Models for Multispecies Interactions in Endodontic Diseases"],"prefix":"10.3390","volume":"8","author":[{"given":"Dejana","family":"Lukic","sequence":"first","affiliation":[{"name":"Clinic of Conservative and Preventive Dentistry, Center of Dental Medicine, University of Zurich, 8032 Zurich, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7893-0393","authenticated-orcid":false,"given":"Lamprini","family":"Karygianni","sequence":"additional","affiliation":[{"name":"Clinic of Conservative and Preventive Dentistry, Center of Dental Medicine, University of Zurich, 8032 Zurich, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Manuela","family":"Flury","sequence":"additional","affiliation":[{"name":"Clinic of Conservative and Preventive Dentistry, Center of Dental Medicine, University of Zurich, 8032 Zurich, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6141-1263","authenticated-orcid":false,"given":"Thomas","family":"Attin","sequence":"additional","affiliation":[{"name":"Clinic of Conservative and Preventive Dentistry, Center of Dental Medicine, University of Zurich, 8032 Zurich, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8615-8209","authenticated-orcid":false,"given":"Thomas","family":"Thurnheer","sequence":"additional","affiliation":[{"name":"Clinic of Conservative and Preventive Dentistry, Center of Dental Medicine, University of Zurich, 8032 Zurich, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2020,5,6]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1674","DOI":"10.1177\/00220345980770090301","article-title":"Commensal communism and the oral cavity","volume":"77","author":"Henderson","year":"1998","journal-title":"J. Dent. Res."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"409","DOI":"10.1111\/j.2041-1014.2012.00663.x","article-title":"Beyond the red complex and into more complexity: The polymicrobial synergy and dysbiosis (PSD) model of periodontal disease etiology","volume":"27","author":"Hajishengallis","year":"2012","journal-title":"Mol. Oral Microbiol."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"1","DOI":"10.4103\/2231-0762.151956","article-title":"Biofilm in endodontics: A review","volume":"5","author":"Jhajharia","year":"2015","journal-title":"J. Int. Soc. Prev. Community Dent."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"435","DOI":"10.1146\/annurev.mi.41.100187.002251","article-title":"Bacterial biofilms in nature and disease","volume":"41","author":"Costerton","year":"1987","journal-title":"Annu. Rev. Microbiol."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"711","DOI":"10.1146\/annurev.mi.49.100195.003431","article-title":"Microbial biofilms","volume":"49","author":"Costerton","year":"1995","journal-title":"Annu. Rev. Microbiol."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1111\/iej.13202","article-title":"The influence of substrate surface conditioning and biofilm age on the composition of Enterococcus faecalis biofilms","volume":"53","author":"Ali","year":"2020","journal-title":"Int. Endod. J."},{"key":"ref_7","doi-asserted-by":"crossref","unstructured":"Karygianni, L., Ren, Z., Koo, H., and Thurnheer, T. (2020). Biofilm Matrixome: Extracellular Components in Structured Microbial Communities. Trends Microbiol.","DOI":"10.1016\/j.tim.2020.03.016"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"115576","DOI":"10.1016\/j.watres.2020.115576","article-title":"Biofouling and me: My Stockholm syndrome with biofilms","volume":"173","author":"Flemming","year":"2020","journal-title":"Water Res."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"471","DOI":"10.1038\/nrmicro2381","article-title":"Oral multispecies biofilm development and the key role of cell-cell distance","volume":"8","author":"Kolenbrander","year":"2010","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"187","DOI":"10.1146\/annurev.micro.56.012302.160705","article-title":"Biofilms as complex differentiated communities","volume":"56","author":"Stoodley","year":"2002","journal-title":"Annu. Rev. Microbiol."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"376","DOI":"10.1111\/apm.12688","article-title":"Dental biofilm infections\u2014An update","volume":"125","author":"Larsen","year":"2017","journal-title":"Apmis"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"233","DOI":"10.4103\/0972-0707.73386","article-title":"Endodontic microbiology","volume":"13","author":"Narayanan","year":"2010","journal-title":"J. Conserv Dent."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1111\/jicd.12109","article-title":"Microbial invasion of dentinal tubules: A literature review and a new perspective","volume":"5","author":"Taschieri","year":"2014","journal-title":"J. Investig Clin. Dent."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.cden.2016.08.001","article-title":"Endodontic Microbiology and Pathobiology: Current State of Knowledge","volume":"61","author":"Fouad","year":"2017","journal-title":"Dent. Clin. N. Am."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"59","DOI":"10.4103\/2319-4170.110400","article-title":"Microbial biofilms in endodontic infections: An update review","volume":"36","author":"Mohammadi","year":"2013","journal-title":"Biomed. J."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1016\/S0099-2399(87)80089-4","article-title":"Light and electron microscopic studies of root canal flora and periapical lesions","volume":"13","author":"Nair","year":"1987","journal-title":"J. Endod."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"509","DOI":"10.1016\/j.joen.2015.12.014","article-title":"Complex Apical Intraradicular Infection and Extraradicular Mineralized Biofilms as the Cause of Wet Canals and Treatment Failure: Report of 2 Cases","volume":"42","author":"Ricucci","year":"2016","journal-title":"J. Endod."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"1277","DOI":"10.1016\/j.joen.2010.04.007","article-title":"Biofilms and apical periodontitis: Study of prevalence and association with clinical and histopathologic findings","volume":"36","author":"Ricucci","year":"2010","journal-title":"J. Endod."},{"key":"ref_19","doi-asserted-by":"crossref","unstructured":"Neelakantan, P., Romero, M., Vera, J., Daood, U., Khan, A.U., Yan, A., and Cheung, G.S.P. (2017). Biofilms in Endodontics-Current Status and Future Directions. Int. J. Mol. Sci., 18.","DOI":"10.3390\/ijms18081748"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"275","DOI":"10.1111\/j.1399-302X.2007.00423.x","article-title":"Molecular analysis of the root canal microbiota associated with endodontic treatment failures","volume":"23","author":"Sakamoto","year":"2008","journal-title":"Oral Microbiol. Immunol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1046\/j.0902-0055.2003.00116.x","article-title":"Microbiological examination of infected dental root canals","volume":"19","author":"Gomes","year":"2004","journal-title":"Oral Microbiol. Immunol."},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Ammann, T.W., Belibasakis, G.N., and Thurnheer, T. (2013). Impact of early colonizers on in vitro subgingival biofilm formation. PLoS ONE, 8 12.","DOI":"10.1371\/journal.pone.0083090"},{"key":"ref_23","doi-asserted-by":"crossref","unstructured":"Ammann, T., Gmur, R., and Thurnheer, T. (2012). Advancement of the 10-species subgingival Zurich Biofilm model by examining different nutritional conditions and defining the structure of the in vitro biofilms. BMC Microbiol., 12.","DOI":"10.1186\/1471-2180-12-227"},{"key":"ref_24","doi-asserted-by":"crossref","unstructured":"Guggenheim, B., Gmur, R., Galicia, J., Stathopoulou, P., Benakanakere, M., Meier, A., Thurnheer, T., and Kinane, D. (2009). In vitro modeling of host-parasite interactions: The \u2018subgingival\u2019 biofilm challenge of primary human epithelial cells. BMC Microbiol., 9.","DOI":"10.1186\/1471-2180-9-280"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"363","DOI":"10.1177\/00220345010800011201","article-title":"Validation of an in vitro biofilm model of supragingival plaque","volume":"80","author":"Guggenheim","year":"2001","journal-title":"J. Dent. Res."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"343","DOI":"10.1902\/jop.2013.130167","article-title":"Validation of antibiotic efficacy on in vitro subgingival biofilms","volume":"85","author":"Belibasakis","year":"2014","journal-title":"J. Periodontol."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"977","DOI":"10.1016\/j.archoralbio.2014.05.023","article-title":"Colonisation of gingival epithelia by subgingival biofilms in vitro: Role of \u201cred complex\u201d bacteria","volume":"59","author":"Thurnheer","year":"2014","journal-title":"Arch. Oral Biol."},{"key":"ref_28","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":"ref_29","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":"ref_30","doi-asserted-by":"crossref","first-page":"285","DOI":"10.1016\/j.tripleo.2006.05.010","article-title":"Detection of Porphyromonas gingivalis, Porphyromonas endodontalis, Prevotella intermedia, and Prevotella nigrescens in chronic endodontic infection","volume":"103","author":"Tomazinho","year":"2007","journal-title":"Oral Surg. Oral Med. Oral Pathol. Oral Radiol. Endod."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"517","DOI":"10.1111\/jre.12034","article-title":"Validation of a quantitative real-time PCR assay and comparison with fluorescence microscopy and selective agar plate counting for species-specific quantification of an in vitro subgingival biofilm model","volume":"48","author":"Ammann","year":"2013","journal-title":"J. Periodontal. Res."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"890","DOI":"10.1111\/clr.12715","article-title":"Incorporation of staphylococci into titanium-grown biofilms: An in vitro \u201csubmucosal\u201d biofilm model for peri-implantitis","volume":"27","author":"Thurnheer","year":"2016","journal-title":"Clin. Oral Implant. Res."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"459","DOI":"10.1128\/iai.42.2.459-470.1983","article-title":"Antigenic heterogeneity of Bacteroides intermedius as recognized by monoclonal antibodies","volume":"42","author":"Guggenheim","year":"1983","journal-title":"Infect. Immun."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"575","DOI":"10.1016\/j.archoralbio.2004.10.017","article-title":"Quantitative real-time PCR detection of oral Enterococcus faecalis in humans","volume":"50","author":"Sedgley","year":"2005","journal-title":"Arch. Oral Biol."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"827","DOI":"10.1111\/j.1365-2591.2011.01888.x","article-title":"Potential systematic error in laboratory experiments on microbial leakage through filled root canals: An experimental study","volume":"44","author":"Rechenberg","year":"2011","journal-title":"Int. Endod. J."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1016\/j.mimet.2003.09.003","article-title":"Multiplex FISH analysis of a six-species bacterial biofilm","volume":"56","author":"Thurnheer","year":"2004","journal-title":"J. Microbiol. Methods"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"1379","DOI":"10.1099\/00221287-148-5-1379","article-title":"Direct quantitative differentiation between Prevotella intermedia and Prevotella nigrescens in clinical specimens","volume":"148","author":"Thurnheer","year":"2002","journal-title":"Microbiology"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"226","DOI":"10.1111\/omi.12166","article-title":"FISHing for gutta-percha-adhered biofilms in purulent post-treatment apical periodontitis","volume":"32","author":"Zehnder","year":"2017","journal-title":"Mol. Oral Microbiol."},{"key":"ref_39","doi-asserted-by":"crossref","unstructured":"Zijnge, V., van Leeuwen, M., Degener, J., Abbas, F., Thurnheer, T., Gmur, R., and Harmsen, H. (2010). Oral biofilm architecture on natural teeth. PLoS ONE, 5.","DOI":"10.1371\/journal.pone.0009321"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"258","DOI":"10.4161\/21505594.2014.967608","article-title":"Integration of non-oral bacteria into in vitro oral biofilms","volume":"6","author":"Thurnheer","year":"2015","journal-title":"Virulence"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"5311","DOI":"10.1128\/AEM.03039-05","article-title":"Improved in situ hybridization efficiency with locked-nucleic-acid-incorporated DNA probes","volume":"72","author":"Kubota","year":"2006","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1016\/0022-2836(81)90508-8","article-title":"Gene organization and primary structure of a ribosomal RNA operon from Escherichia coli","volume":"148","author":"Brosius","year":"1981","journal-title":"J. Mol. Biol."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"488","DOI":"10.1007\/s13238-018-0548-1","article-title":"Oral microbiomes: More and more importance in oral cavity and whole body","volume":"9","author":"Gao","year":"2018","journal-title":"Protein Cell"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1111\/j.1600-0757.2009.00318.x","article-title":"Quorum sensing regulation of biofilm growth and gene expression by oral bacteria and periodontal pathogens","volume":"52","author":"Shao","year":"2010","journal-title":"Periodontology 2000"},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1111\/j.1574-6968.2005.00001.x","article-title":"Quorum sensing: The many languages of bacteria","volume":"254","author":"Reading","year":"2006","journal-title":"FEMS Microbiol. Lett."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1146\/annurev.micro.55.1.165","article-title":"Quorum sensing in bacteria","volume":"55","author":"Miller","year":"2001","journal-title":"Annu. Rev. Microbiol."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"271","DOI":"10.1016\/j.femsle.2005.07.019","article-title":"Synergistic biofilm formation by Treponema denticola and Porphyromonas gingivalis","volume":"250","author":"Yamada","year":"2005","journal-title":"FEMS Microbiol. Lett."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"7193","DOI":"10.1128\/JB.187.21.7193-7203.2005","article-title":"Competition and coexistence between Streptococcus mutans and Streptococcus sanguinis in the dental biofilm","volume":"187","author":"Kreth","year":"2005","journal-title":"J. Bacteriol."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1159\/000057866","article-title":"An in vitro oral biofilm model for comparing the efficacy of antimicrobial mouthrinses","volume":"36","author":"Shapiro","year":"2002","journal-title":"Caries Res."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"212","DOI":"10.1159\/000077757","article-title":"Application of the Z\u00fcrich biofilm model to problems of cariology","volume":"38","author":"Guggenheim","year":"2004","journal-title":"Caries Res."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"1343","DOI":"10.1128\/AEM.67.3.1343-1350.2001","article-title":"Spatial arrangements and associative behavior of species in an in vitro oral biofilm model","volume":"67","author":"Guggenheim","year":"2001","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1016\/j.archoralbio.2018.02.010","article-title":"Effect of sodium fluoride on oral biofilm microbiota and enamel demineralization","volume":"89","author":"Thurnheer","year":"2018","journal-title":"Arch. Oral Biol."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1111\/omi.12108","article-title":"Microbial dynamics during conversion from supragingival to subgingival biofilms in an in vitro model","volume":"31","author":"Thurnheer","year":"2016","journal-title":"Mol. Oral Microbiol."},{"key":"ref_54","doi-asserted-by":"crossref","unstructured":"Thurnheer, T., Karygianni, L., Flury, M., and Belibasakis, G.N. (2019). Fusobacterium Species and Subspecies Differentially Affect the Composition and Architecture of Supra- and Subgingival Biofilms Models. Front. Microbiol., 10.","DOI":"10.3389\/fmicb.2019.01716"},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"166","DOI":"10.1016\/j.mimet.2010.03.002","article-title":"Visualization of initial bacterial colonization on dentine and enamel in situ","volume":"81","author":"Jung","year":"2010","journal-title":"J. Microbiol. Methods"},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"315","DOI":"10.1097\/00004770-200405000-00004","article-title":"Association of Enterococcus faecalis with different forms of periradicular diseases","volume":"30","author":"Rocas","year":"2004","journal-title":"J. Endod."},{"key":"ref_57","doi-asserted-by":"crossref","unstructured":"Dioguardi, M., Di Gioia, G., Illuzzi, G., Arena, C., Caponio, V.C.A., Caloro, G.A., Zhurakivska, K., Adipietro, I., Troiano, G., and Lo Muzio, L. (2019). Inspection of the Microbiota in Endodontic Lesions. Dent. J. Basel, 7.","DOI":"10.3390\/dj7020047"},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"652","DOI":"10.1016\/j.joen.2006.11.004","article-title":"Redefining the persistent infection in root canals: Possible role of biofilm communities","volume":"33","year":"2007","journal-title":"J. Endod."},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"158","DOI":"10.1080\/00016357.2018.1533142","article-title":"In vitro treatment of Enterococcus faecalis with calcium hydroxide impairs phagocytosis by human macrophages","volume":"77","author":"Ponce","year":"2019","journal-title":"Acta Odontol. Scand."},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"689","DOI":"10.1097\/00004770-200210000-00003","article-title":"Biofilm formation in medicated root canals","volume":"28","author":"Distel","year":"2002","journal-title":"J. Endod."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"86","DOI":"10.1016\/S1079-2104(98)90404-8","article-title":"Microbiologic analysis of teeth with failed endodontic treatment and the outcome of conservative re-treatment","volume":"85","author":"Sundqvist","year":"1998","journal-title":"Oral Surg. Oral Med. Oral Pathol. Oral Radiol. Endod."},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"916","DOI":"10.1111\/iej.12501","article-title":"Strains of Enterococcus faecalis differ in their ability to coexist in biofilms with other root canal bacteria","volume":"48","author":"Davies","year":"2015","journal-title":"Int. Endod. J."},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1111\/adj.12324","article-title":"Exploration of the mechanisms of biofilm formation by Enterococcus faecalis in glucose starvation environments","volume":"60","author":"Ran","year":"2015","journal-title":"Aust. Dent. J."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1111\/j.1399-302X.2007.00378.x","article-title":"Bacterial examination of endodontic infections by clonal analysis in concert with denaturing high-performance liquid chromatography","volume":"22","author":"Jacinto","year":"2007","journal-title":"Oral Microbiol. Immunol."},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1016\/j.micpath.2015.09.009","article-title":"Periodontal-disease-associated biofilm: A reservoir for pathogens of medical importance","volume":"94","author":"Magalhaes","year":"2016","journal-title":"Microb. Pathog."},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"819","DOI":"10.1111\/1751-7915.12705","article-title":"Dynamics of mono- and dual-species biofilm formation and interactions between Staphylococcus aureus and Gram-negative bacteria","volume":"10","author":"Makovcova","year":"2017","journal-title":"Microb. Biotechnol."},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"841","DOI":"10.3389\/fmicb.2015.00841","article-title":"Intra- and inter-species interactions within biofilms of important foodborne bacterial pathogens","volume":"6","author":"Giaouris","year":"2015","journal-title":"Front. Microbiol."},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"620","DOI":"10.1016\/S0099-2399(97)80173-2","article-title":"Occurrence of Prevotella nigrescens and Prevotella intermedia in infections of endodontic origin","volume":"23","author":"Bae","year":"1997","journal-title":"J. Endod."},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1902\/jop.1994.65.1.56","article-title":"Characterization of Prevotella intermedia and Prevotella nigrescens isolates from periodontic and endodontic infections","volume":"65","author":"Gharbia","year":"1994","journal-title":"J. Periodontol."},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1111\/j.1399-302X.2005.00214.x","article-title":"Porphyromonas gingivalis, Porphyromonas endodontalis, Prevotella intermedia and Prevotella nigrescens in endodontic lesions detected by culture and by PCR","volume":"20","author":"Gomes","year":"2005","journal-title":"Oral Microbiol. Immunol."},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"355","DOI":"10.1034\/j.1600-0765.2001.360602.x","article-title":"Effects of glucose on formation of cytotoxic end-products and proteolytic activity of Prevotella intermedia, Prevotella nigrescens and Porphyromonas gingivalis","volume":"36","author":"Saito","year":"2001","journal-title":"J. Periodontal. Res."},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"1044","DOI":"10.1128\/JB.01270-08","article-title":"Response of Porphyromonas gingivalis to heme limitation in continuous culture","volume":"191","author":"Dashper","year":"2009","journal-title":"J. Bacteriol."},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"323","DOI":"10.1111\/j.1399-302X.1997.tb00733.x","article-title":"Acid tolerance and acid-neutralizing activity of Porphyromonas gingivalis, Prevotella intermedia and Fusobacterium nucleatum","volume":"12","author":"Takahashi","year":"1997","journal-title":"Oral Microbiol. Immunol."},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"1206","DOI":"10.1016\/j.joen.2011.05.026","article-title":"Analysis of symptomatic and asymptomatic primary root canal infections in adult Norwegian patients","volume":"37","author":"Rocas","year":"2011","journal-title":"J. Endod."},{"key":"ref_75","doi-asserted-by":"crossref","unstructured":"Zhu, Y., Dashper, S., Chen, Y., Crawford, S., Slakeski, N., and Reynolds, E. (2013). Porphyromonas gingivalis and Treponema denticola synergistic polymicrobial biofilm development. PLoS ONE, 8.","DOI":"10.1371\/journal.pone.0071727"},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"555","DOI":"10.4103\/0972-0707.144604","article-title":"Investigate the correlation between clinical sign and symptoms and the presence of P. gingivalis, T. denticola, and T. forsythia individually or as a \u201cRed complex\u201d by a multiplex PCR method","volume":"17","author":"Sanghavi","year":"2014","journal-title":"J. Conserv. Dent."},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"124","DOI":"10.3389\/fmicb.2018.00124","article-title":"Worlds Apart\u2014Transcriptome Profiles of Key Oral Microbes in the Periodontal Pocket Compared to Single Laboratory Culture Reflect Synergistic Interactions","volume":"9","author":"Deng","year":"2018","journal-title":"Front. Microbiol."},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"54","DOI":"10.1016\/j.anaerobe.2018.10.007","article-title":"Parvimonas micra stimulates expression of gingipains from Porphyromonas gingivalis in multi-species communities","volume":"55","author":"Neilands","year":"2019","journal-title":"Anaerobe"},{"key":"ref_79","doi-asserted-by":"crossref","first-page":"1927","DOI":"10.1099\/mic.0.2008\/016576-0","article-title":"Oral bacteria in biofilms exhibit slow reactivation from nutrient deprivation","volume":"154","author":"Hamilton","year":"2008","journal-title":"Microbiology"},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"174","DOI":"10.1046\/j.1365-2591.2003.00636.x","article-title":"Campylobacter gracilis and Campylobacter rectus in primary endodontic infections","volume":"36","author":"Siqueira","year":"2003","journal-title":"Int. Endod. J."},{"key":"ref_81","doi-asserted-by":"crossref","first-page":"156","DOI":"10.1038\/s41579-018-0129-6","article-title":"Fusobacterium nucleatum-symbiont, opportunist and oncobacterium","volume":"17","author":"Brennan","year":"2019","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_82","doi-asserted-by":"crossref","first-page":"4729","DOI":"10.1128\/IAI.66.10.4729-4732.1998","article-title":"Role of Fusobacterium nucleatum and coaggregation in anaerobe survival in planktonic and biofilm oral microbial communities during aeration","volume":"66","author":"Bradshaw","year":"1998","journal-title":"Infect. Immun."},{"key":"ref_83","doi-asserted-by":"crossref","first-page":"399","DOI":"10.1046\/j.1365-2591.2001.00437.x","article-title":"Enterococcus faecalis--a mechanism for its role in endodontic failure","volume":"34","author":"Love","year":"2001","journal-title":"Int. Endod. J."},{"key":"ref_84","doi-asserted-by":"crossref","first-page":"044017","DOI":"10.1117\/1.2957972","article-title":"Influence of endodontic chemical treatment on Enterococcus faecalis adherence to collagen studied with laser scanning confocal microscopy and optical tweezers: A preliminary study","volume":"13","author":"Sum","year":"2008","journal-title":"J. Biomed. Opt."},{"key":"ref_85","doi-asserted-by":"crossref","first-page":"S87","DOI":"10.1016\/j.joen.2017.06.011","article-title":"Inflammation and Regeneration in the Dentin-pulp Complex: Net Gain or Net Loss?","volume":"43","author":"Cooper","year":"2017","journal-title":"J. Endod."},{"key":"ref_86","doi-asserted-by":"crossref","first-page":"335","DOI":"10.1111\/j.1574-695X.2012.00956.x","article-title":"Combination of microscopic techniques reveals a comprehensive visual impression of biofilm structure and composition","volume":"65","author":"Alhede","year":"2012","journal-title":"FEMS Immunol. Med. Microbiol."},{"key":"ref_87","doi-asserted-by":"crossref","first-page":"124","DOI":"10.1111\/j.1365-2818.2009.03201.x","article-title":"Imaging of endodontic biofilms by combined microscopy (FISH\/cLSM-SEM)","volume":"235","author":"Schaudinn","year":"2009","journal-title":"J. Microsc."},{"key":"ref_88","doi-asserted-by":"crossref","first-page":"263","DOI":"10.1016\/j.mimet.2011.09.007","article-title":"Molecular pathogen detection in biosolids with a focus on quantitative PCR using propidium monoazide for viable cell enumeration","volume":"87","author":"Trevors","year":"2011","journal-title":"J. Microbiol. Methods"},{"key":"ref_89","doi-asserted-by":"crossref","first-page":"86","DOI":"10.1186\/s40168-017-0285-3","article-title":"Schrodinger\u2019s microbes: Tools for distinguishing the living from the dead in microbial ecosystems","volume":"5","author":"Emerson","year":"2017","journal-title":"Microbiome"},{"key":"ref_90","doi-asserted-by":"crossref","first-page":"756","DOI":"10.1111\/eci.12801","article-title":"Talking the talk, but not walking the walk: RT-qPCR as a paradigm for the lack of reproducibility in molecular research","volume":"47","author":"Bustin","year":"2017","journal-title":"Eur. J. Clin. Investig."},{"key":"ref_91","doi-asserted-by":"crossref","first-page":"1559","DOI":"10.1038\/nprot.2006.236","article-title":"Quantification of mRNA using real-time RT-PCR","volume":"1","author":"Nolan","year":"2006","journal-title":"Nat. Protoc."}],"container-title":["Microorganisms"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-2607\/8\/5\/674\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T09:26:07Z","timestamp":1760174767000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-2607\/8\/5\/674"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,5,6]]},"references-count":91,"journal-issue":{"issue":"5","published-online":{"date-parts":[[2020,5]]}},"alternative-id":["microorganisms8050674"],"URL":"https:\/\/doi.org\/10.3390\/microorganisms8050674","relation":{},"ISSN":["2076-2607"],"issn-type":[{"value":"2076-2607","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,5,6]]}}}