{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,12]],"date-time":"2026-10-12T19:10:23Z","timestamp":1791832223587,"version":"4.3.4"},"reference-count":57,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2025,3,8]],"date-time":"2025-03-08T00:00:00Z","timestamp":1741392000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"},{"start":{"date-parts":[[2025,3,8]],"date-time":"2025-03-08T00:00:00Z","timestamp":1741392000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["npj Biofilms Microbiomes"],"DOI":"10.1038\/s41522-025-00660-7","type":"journal-article","created":{"date-parts":[[2025,3,8]],"date-time":"2025-03-08T05:48:56Z","timestamp":1741412936000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["V-ATPase contributes to the cariogenicity of Candida albicans- Streptococcus mutans biofilm"],"prefix":"10.1038","volume":"11","author":[{"given":"Qian","family":"Jiang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mengmeng","family":"Xu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hong","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yao","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuting","family":"Sun","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6109-3480","authenticated-orcid":false,"given":"Li","family":"Tao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zheng","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Deqin","family":"Yang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2025,3,8]]},"reference":[{"key":"660_CR1","doi-asserted-by":"publisher","DOI":"10.1038\/nrdp.2017.30","volume":"3","author":"NB Pitts","year":"2017","unstructured":"Pitts, N. B. et al. Dental caries. Nat. Rev. Dis. Primers 3, 17030 (2017).","journal-title":"Nat. Rev. Dis. Primers"},{"key":"660_CR2","doi-asserted-by":"publisher","first-page":"681","DOI":"10.1177\/0022034521992011","volume":"100","author":"FN Hugo","year":"2021","unstructured":"Hugo, F. N., Kassebaum, N. J., Marcenes, W. & Bernab\u00e9, E. Role of dentistry in global health: challenges and research priorities. J. Dental Res. 100, 681\u2013685 (2021).","journal-title":"J. Dental Res."},{"key":"660_CR3","doi-asserted-by":"publisher","first-page":"1789","DOI":"10.1016\/S0140-6736(18)32279-7","volume":"392","author":"Collaborators, G.D.a.I.I.a.P.","year":"2018","unstructured":"Collaborators, G.D.a.I.I.a.P. Global, regional, and national incidence, prevalence, and years lived with disability for 354 diseases and injuries for 195 countries and territories, 1990\u20132017: a systematic analysis for the Global Burden of Disease Study 2017. Lancet 392, 1789\u20131858 (2018).","journal-title":"Lancet"},{"key":"660_CR4","doi-asserted-by":"publisher","first-page":"362","DOI":"10.1177\/0022034520908533","volume":"99","author":"E Bernabe","year":"2020","unstructured":"Bernabe, E. et al. Global, regional, and national levels and trends in burden of oral conditions from 1990 to 2017: a systematic analysis for the global burden of disease 2017 Study. J. Dental Res. 99, 362\u2013373 (2020).","journal-title":"J. Dental Res."},{"key":"660_CR5","doi-asserted-by":"publisher","first-page":"745","DOI":"10.1038\/s41579-018-0089-x","volume":"16","author":"RJ Lamont","year":"2018","unstructured":"Lamont, R. J., Koo, H. & Hajishengallis, G. The oral microbiota: dynamic communities and host interactions. Nat. Rev. Microbiol. 16, 745\u2013759 (2018).","journal-title":"Nat. Rev. Microbiol."},{"key":"660_CR6","doi-asserted-by":"publisher","first-page":"525","DOI":"10.1007\/s00203-018-1505-3","volume":"200","author":"D Verma","year":"2018","unstructured":"Verma, D., Garg, P. K. & Dubey, A. K. Insights into the human oral microbiome. Archiv. Microbiol. 200, 525\u2013540 (2018).","journal-title":"Archiv. Microbiol."},{"key":"660_CR7","doi-asserted-by":"publisher","unstructured":"Lemos, J. A. et al. The Biology of S. mutans. Microbiol. Spectrum 7, https:\/\/doi.org\/10.1128\/microbiolspec.GPP3-0051-2018 (2019).","DOI":"10.1128\/microbiolspec.GPP3-0051-2018"},{"key":"660_CR8","doi-asserted-by":"publisher","first-page":"667","DOI":"10.1080\/1040841X.2021.1915959","volume":"47","author":"Y Lin","year":"2021","unstructured":"Lin, Y., Chen, J., Zhou, X. & Li, Y. Inhibition of S. mutans biofilm formation by strategies targeting the metabolism of exopolysaccharides. Crit. Rev. MicrobiolM 47, 667\u2013677 (2021).","journal-title":"Crit. Rev. MicrobiolM"},{"key":"660_CR9","doi-asserted-by":"publisher","first-page":"1643","DOI":"10.3390\/ijms17101643","volume":"17","author":"VK Chin","year":"2016","unstructured":"Chin, V. K., Lee, T. Y., Rusliza, B. & Chong, P. P. Dissecting C. albicans Infection from the Perspective of C. albicans Virulence and omics approaches on host-pathogen interaction: a review. Int. J. Mol. Sci. 17, 1643 (2016).","journal-title":"Int. J. Mol. Sci."},{"key":"660_CR10","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1038\/nrmicro.2017.107","volume":"16","author":"MB Lohse","year":"2018","unstructured":"Lohse, M. B., Gulati, M., Johnson, A. D. & Nobile, C. J. Development and regulation of single- and multi-species C. albicans biofilms. Nat. Rev. Microbiol. 16, 19\u201331 (2018).","journal-title":"Nat. Rev. Microbiol."},{"key":"660_CR11","doi-asserted-by":"publisher","first-page":"e1000713","DOI":"10.1371\/journal.ppat.1000713","volume":"6","author":"MA Ghannoum","year":"2010","unstructured":"Ghannoum, M. A. et al. Characterization of the oral fungal microbiome (mycobiome) in healthy individuals. PLoS Pathog. 6, e1000713 (2010).","journal-title":"PLoS Pathog."},{"key":"660_CR12","doi-asserted-by":"publisher","DOI":"10.1002\/mbo3.1381","volume":"12","author":"TK Lueyar","year":"2023","unstructured":"Lueyar, T. K., Karygianni, L., Attin, T. & Thurnheer, T. Dynamic interactions between C. albicans and different streptococcal species in a multispecies oral biofilm. MicrobiologyOpen 12, e1381 (2023).","journal-title":"MicrobiologyOpen"},{"key":"660_CR13","doi-asserted-by":"publisher","first-page":"1036","DOI":"10.3389\/fmicb.2017.01036","volume":"8","author":"J He","year":"2017","unstructured":"He, J. et al. RNA-Seq reveals enhanced sugar metabolism in S. mutans Co-cultured with C. albicans within mixed-species biofilms. Front. MicrobiolM 8, 1036 (2017).","journal-title":"Front. MicrobiolM"},{"key":"660_CR14","doi-asserted-by":"publisher","first-page":"1968","DOI":"10.1128\/IAI.00087-14","volume":"82","author":"ML Falsetta","year":"2014","unstructured":"Falsetta, M. L. et al. Symbiotic relationship between S. mutans and C. albicans synergizes virulence of plaque biofilms in vivo. Infection Immunity 82, 1968\u20131981 (2014).","journal-title":"Infection Immunity"},{"key":"660_CR15","doi-asserted-by":"publisher","first-page":"2256","DOI":"10.1038\/ismej.2014.73","volume":"8","author":"H Sztajer","year":"2014","unstructured":"Sztajer, H. et al. Cross-feeding and interkingdom communication in dual-species biofilms of S. mutans and C. albicans. ISME J. 8, 2256\u20132271 (2014).","journal-title":"ISME J."},{"key":"660_CR16","doi-asserted-by":"publisher","first-page":"e1006407","DOI":"10.1371\/journal.ppat.1006407","volume":"13","author":"G Hwang","year":"2017","unstructured":"Hwang, G. et al. C. albicans mannans mediate S. mutans exoenzyme GtfB binding to modulate cross-kingdom biofilm development in vivo. PLoS Pathog. 13, e1006407 (2017).","journal-title":"PLoS Pathog."},{"key":"660_CR17","doi-asserted-by":"publisher","first-page":"102","DOI":"10.1159\/000481833","volume":"52","author":"J Xiao","year":"2018","unstructured":"Xiao, J. et al. C. albicans and early childhood caries: a systematic review and meta-analysis. Caries Res. 52, 102\u2013112 (2018).","journal-title":"Caries Res."},{"key":"660_CR18","doi-asserted-by":"publisher","first-page":"1151532","DOI":"10.3389\/fcimb.2023.1151532","volume":"13","author":"Y Lu","year":"2023","unstructured":"Lu, Y., Lin, Y., Li, M. & He, J. Roles of S. mutans-C. albicans interaction in early childhood caries: a literature review. Front. Cell. Infection Microbiol. 13, 1151532 (2023).","journal-title":"Front. Cell. Infection Microbiol."},{"key":"660_CR19","doi-asserted-by":"publisher","first-page":"1828","DOI":"10.1177\/00220345010800091101","volume":"80","author":"SR Brailsford","year":"2001","unstructured":"Brailsford, S. R. et al. The predominant aciduric microflora of root-caries lesions. J. Dental Res. 80, 1828\u20131833 (2001).","journal-title":"J. Dental Res."},{"key":"660_CR20","doi-asserted-by":"publisher","first-page":"779176","DOI":"10.3389\/fmicb.2021.779176","volume":"12","author":"Q Lv","year":"2021","unstructured":"Lv, Q., Yan, L. & Jiang, Y. The importance of vacuolar ion homeostasis and trafficking in hyphal development and virulence in C. albicans. Front. Microbiol. 12, 779176 (2021).","journal-title":"Front. Microbiol."},{"key":"660_CR21","doi-asserted-by":"publisher","first-page":"295","DOI":"10.1016\/j.tibs.2019.12.007","volume":"45","author":"T Vasanthakumar","year":"2020","unstructured":"Vasanthakumar, T. & Rubinstein, J. L. Structure and Roles of V-type ATPases. Trends Biochem. Sci. 45, 295\u2013307 (2020).","journal-title":"Trends Biochem. Sci."},{"key":"660_CR22","doi-asserted-by":"publisher","first-page":"1207","DOI":"10.1128\/EC.00135-14","volume":"13","author":"HS Rane","year":"2014","unstructured":"Rane, H. S. et al. The contribution of C. albicans vacuolar ATPase subunit V1B, encoded by VMA2, to stress response, autophagy, and virulence is independent of environmental pH. Eukaryotic Cell 13, 1207\u20131221 (2014).","journal-title":"Eukaryotic Cell"},{"key":"660_CR23","doi-asserted-by":"publisher","first-page":"1369","DOI":"10.1128\/EC.00118-13","volume":"12","author":"HS Rane","year":"2013","unstructured":"Rane, H. S. et al. C. albicans VMA3 is necessary for V-ATPase assembly and function and contributes to secretion and filamentation. Eukaryotic cell 12, 1369\u20131382 (2013).","journal-title":"Eukaryotic cell"},{"key":"660_CR24","doi-asserted-by":"publisher","first-page":"1645","DOI":"10.1099\/mic.0.27505-0","volume":"151","author":"S Poltermann","year":"2005","unstructured":"Poltermann, S. et al. The putative vacuolar ATPase subunit Vma7p of C. albicans is involved in vacuole acidification, hyphal development and virulence. Microbiology 151, 1645\u20131655 (2005).","journal-title":"Microbiology"},{"key":"660_CR25","doi-asserted-by":"publisher","first-page":"136","DOI":"10.3390\/antiox10010136","volume":"10","author":"X Mao","year":"2021","unstructured":"Mao, X. et al. Vacuole and Mitochondria Patch (vCLAMP) Protein Vam6 is involved in maintenance of mitochondrial and vacuolar functions under oxidative stress in C. albicans. Antioxidants 10, 136 (2021).","journal-title":"Antioxidants"},{"key":"660_CR26","doi-asserted-by":"publisher","first-page":"709","DOI":"10.1016\/j.funbio.2019.06.002","volume":"123","author":"SW Kim","year":"2019","unstructured":"Kim, S. W. et al. Subunits of the vacuolar H+-ATPase complex, Vma4 and Vma10, are essential for virulence and represent potential drug targets in C. albicans. Fungal Biol.123, 709\u2013722 (2019).","journal-title":"Fungal Biol."},{"key":"660_CR27","doi-asserted-by":"publisher","first-page":"1147","DOI":"10.2217\/fmb-2017-0029","volume":"12","author":"K Zhang","year":"2017","unstructured":"Zhang, K. et al. Contribution of VMA5 to vacuolar function, stress response, ion homeostasis and autophagy in C. albicans. Future Microbiol. 12, 1147\u20131166 (2017).","journal-title":"Future Microbiol."},{"key":"660_CR28","doi-asserted-by":"publisher","first-page":"1422","DOI":"10.1016\/j.biocel.2012.05.014","volume":"44","author":"A Qin","year":"2012","unstructured":"Qin, A. et al. V-ATPases in osteoclasts: structure, function and potential inhibitors of bone resorption. Int. J. Biochem. Cell Biol. 44, 1422\u20131435 (2012).","journal-title":"Int. J. Biochem. Cell Biol."},{"key":"660_CR29","doi-asserted-by":"publisher","first-page":"318","DOI":"10.1152\/physiol.00007.2013","volume":"28","author":"S Breton","year":"2013","unstructured":"Breton, S. & Brown, D. Regulation of luminal acidification by the V-ATPase. Physiology 28, 318\u2013329 (2013).","journal-title":"Physiology"},{"key":"660_CR30","doi-asserted-by":"publisher","first-page":"569","DOI":"10.3390\/pathogens9070569","volume":"9","author":"X Chen","year":"2020","unstructured":"Chen, X. et al. Microbial etiology and prevention of dental caries: exploiting natural products to inhibit cariogenic biofilms. Pathogens 9, 569 (2020).","journal-title":"Pathogens"},{"key":"660_CR31","doi-asserted-by":"publisher","first-page":"1106231","DOI":"10.3389\/fcimb.2023.1106231","volume":"13","author":"Y Li","year":"2023","unstructured":"Li, Y., Huang, S., Du, J., Wu, M. & Huang, X. Current and prospective therapeutic strategies: tackling C. albicans and S. mutans cross-kingdom biofilm. Front. Cell. Infection Microbiol. 13, 1106231 (2023).","journal-title":"Front. Cell. Infection Microbiol."},{"key":"660_CR32","doi-asserted-by":"crossref","unstructured":"Duangthip, D. & Duangthip, D. Early childhood caries and C. albicans. Evid. Based Dent. 19, 100\u2013101 (2018).","DOI":"10.1038\/sj.ebd.6401337"},{"key":"660_CR33","doi-asserted-by":"publisher","first-page":"296","DOI":"10.1016\/j.chom.2015.08.005","volume":"18","author":"F Teng","year":"2015","unstructured":"Teng, F. et al. Prediction of early childhood caries via spatial-temporal variations of oral microbiota. Cell Host Microbe 18, 296\u2013306 (2015).","journal-title":"Cell Host Microbe"},{"key":"660_CR34","doi-asserted-by":"publisher","first-page":"134","DOI":"10.2174\/138920312800493205","volume":"13","author":"Y Zhang","year":"2012","unstructured":"Zhang, Y. & Rao, R. The V-ATPase as a target for antifungal drugs. Curr. Protein Peptide Sci. 13, 134\u2013140 (2012).","journal-title":"Curr. Protein Peptide Sci."},{"key":"660_CR35","first-page":"1049","volume":"38","author":"L Pan","year":"2016","unstructured":"Pan, L. et al. Phenotypic transitions and their regulatory mechanisms in the human fungal pathogen C. albicans. Chin. J. Cell Biol. 38, 1049\u20131059 (2016).","journal-title":"Chin. J. Cell Biol."},{"key":"660_CR36","doi-asserted-by":"publisher","first-page":"30","DOI":"10.1038\/s41368-021-00137-1","volume":"13","author":"Q Zhang","year":"2021","unstructured":"Zhang, Q., Ma, Q., Wang, Y., Wu, H. & Zou, J. Molecular mechanisms of inhibiting glucosyltransferases for biofilm formation in S. mutans. Int.J. Oral Sci. 13, 30 (2021).","journal-title":"Int.J. Oral Sci."},{"key":"660_CR37","doi-asserted-by":"publisher","first-page":"211","DOI":"10.1111\/j.1399-302X.2008.00497.x","volume":"24","author":"Y Terao","year":"2009","unstructured":"Terao, Y., Isoda, R., Murakami, J., Hamada, S. & Kawabata, S. Molecular and biological characterization of gtf regulation-associated genes in S. mutans. Oral Microbiol. Immunol. 24, 211\u2013217 (2009).","journal-title":"Oral Microbiol. Immunol."},{"key":"660_CR38","doi-asserted-by":"publisher","first-page":"49","DOI":"10.1111\/omi.12277","volume":"35","author":"R Wang","year":"2020","unstructured":"Wang, R. et al. Nanoscale adhesion forces of glucosyltransferase B and C genes regulated Streptococcal mutans probed by AFM. Mol. Oral Microbiol. 35, 49\u201355 (2020).","journal-title":"Mol. Oral Microbiol."},{"key":"660_CR39","first-page":"191","volume":"12","author":"DJ Lynch","year":"2013","unstructured":"Lynch, D. J. et al. Cariogenicity of S. mutans glucan-binding protein deletion mutants. Oral Health Dental Manag. 12, 191\u2013199 (2013).","journal-title":"Oral Health Dental Manag."},{"key":"660_CR40","doi-asserted-by":"publisher","first-page":"30","DOI":"10.1111\/j.1399-302X.2007.00318.x","volume":"22","author":"M Matsumoto-Nakano","year":"2007","unstructured":"Matsumoto-Nakano, M., Fujita, K. & Ooshima, T. Comparison of glucan-binding proteins in cariogenicity of S. mutans. Oral Microbiol. Immunol. 22, 30\u201335 (2007).","journal-title":"Oral Microbiol. Immunol."},{"key":"660_CR41","doi-asserted-by":"publisher","first-page":"213","DOI":"10.1111\/j.1348-0421.2003.tb03389.x","volume":"47","author":"M Matsumura","year":"2003","unstructured":"Matsumura, M. et al. The role of glucan-binding proteins in the cariogenicity of S. mutans. Microbiol. Immunol. 47, 213\u2013215 (2003).","journal-title":"Microbiol. Immunol."},{"key":"660_CR42","doi-asserted-by":"publisher","first-page":"51","DOI":"10.1111\/omi.12253","volume":"34","author":"Y Yang","year":"2019","unstructured":"Yang, Y. et al. Regulation of water-soluble glucan synthesis by the S. mutans dexA gene effects biofilm aggregation and cariogenic pathogenicity. Mol. Oral Microbiol. 34, 51\u201363 (2019).","journal-title":"Mol. Oral Microbiol."},{"key":"660_CR43","doi-asserted-by":"publisher","first-page":"2929","DOI":"10.1099\/13500872-141-11-2929","volume":"141","author":"SM Colby","year":"1995","unstructured":"Colby, S. M., Whiting, G. C., Tao, L. & Russell, R. R. Insertional inactivation of the S. mutans dexA (dextranase) gene results in altered adherence and dextran catabolism. Microbiology 141, 2929\u20132936 (1995).","journal-title":"Microbiology"},{"key":"660_CR44","doi-asserted-by":"publisher","first-page":"193","DOI":"10.1034\/j.1399-302X.2002.170310.x","volume":"17","author":"T Igarashi","year":"2002","unstructured":"Igarashi, T. et al. An essential amino acid residue for catalytic activity of the dextranase of S.mutans. Oral Microbiol. Immunol. 17, 193\u2013196 (2002).","journal-title":"Oral Microbiol. Immunol."},{"key":"660_CR45","doi-asserted-by":"publisher","first-page":"e0129903","DOI":"10.1371\/journal.pone.0129903","volume":"10","author":"HF Chen","year":"2015","unstructured":"Chen, H. F. et al. Role of SFP1 in the Regulation of C. albicans biofilm formation. PloS ONE 10, e0129903 (2015).","journal-title":"PloS ONE"},{"key":"660_CR46","doi-asserted-by":"publisher","first-page":"280","DOI":"10.3389\/fmicb.2016.00280","volume":"7","author":"LL Hoyer","year":"2016","unstructured":"Hoyer, L. L. et al. C. albicans Agglutinin-Like Sequence (Als) Family Vignettes: a review of als protein structure and function. Front. Microbiol. 7, 280 (2016).","journal-title":"Front. Microbiol."},{"key":"660_CR47","doi-asserted-by":"publisher","first-page":"6357","DOI":"10.1128\/AEM.05203-11","volume":"77","author":"S Gregoire","year":"2011","unstructured":"Gregoire, S. et al. Role of glucosyltransferase B in interactions of C. albicans with S. mutans and with an experimental pellicle on hydroxyapatite surfaces. Appl. Environ. Microbiol. 77, 6357\u20136367 (2011).","journal-title":"Appl. Environ. Microbiol."},{"key":"660_CR48","doi-asserted-by":"publisher","first-page":"3167","DOI":"10.1091\/mbc.e03-11-0782","volume":"15","author":"T Doedt","year":"2004","unstructured":"Doedt, T. et al. APSES proteins regulate morphogenesis and metabolism in C. albicans. Mol. Biol. cell 15, 3167\u20133180 (2004).","journal-title":"Mol. Biol. cell"},{"key":"660_CR49","doi-asserted-by":"publisher","first-page":"e02320","DOI":"10.1128\/mBio.02320-18","volume":"10","author":"Y Lu","year":"2019","unstructured":"Lu, Y. et al. CO (2) Signaling through the Ptc2-Ssn3 axis governs sustained hyphal development of C. albicans by reducing Ume6 phosphorylation and degradation. mBio 10, e02320\u201318 (2019).","journal-title":"mBio"},{"key":"660_CR50","doi-asserted-by":"publisher","first-page":"298","DOI":"10.1128\/EC.4.2.298-309.2005","volume":"4","author":"SM Noble","year":"2005","unstructured":"Noble, S. M. & Johnson, A. D. Strains and strategies for large-scale gene deletion studies of the diploid human fungal pathogen C. albicans. Eukaryotic cell 4, 298\u2013309 (2005).","journal-title":"Eukaryotic cell"},{"key":"660_CR51","unstructured":"Organization, W.H. Oral health surveys: basic methods-5th ed. Geneva (Switzerland): World Health Organization (2013)."},{"key":"660_CR52","doi-asserted-by":"publisher","first-page":"1432","DOI":"10.3389\/fmicb.2015.01432","volume":"6","author":"L Lei","year":"2015","unstructured":"Lei, L. et al. Modulation of biofilm exopolysaccharides by the S. mutans vicX Gene. Front. Microbiol. 6, 1432 (2015).","journal-title":"Front. Microbiol."},{"key":"660_CR53","first-page":"2967","volume":"20","author":"B Klug","year":"2011","unstructured":"Klug, B. et al. Oral biofilm analysis of palatal expanders by fluorescence in-situ hybridization and confocal laser scanning microscopy. J. Visualized Exp. JoVE 20, 2967 (2011).","journal-title":"J. Visualized Exp. JoVE"},{"key":"660_CR54","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-12-323","volume":"12","author":"B Li","year":"2011","unstructured":"Li, B. & Dewey, C. N. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinform. 12, 323 (2011).","journal-title":"BMC Bioinform."},{"key":"660_CR55","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-014-0550-8","volume":"15","author":"MI Love","year":"2014","unstructured":"Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).","journal-title":"Genome Biol."},{"key":"660_CR56","doi-asserted-by":"publisher","first-page":"W316","DOI":"10.1093\/nar\/gkr483","volume":"39","author":"C Xie","year":"2011","unstructured":"Xie, C. et al. KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases. Nucleic Acids Res. 39, W316\u2013W322 (2011).","journal-title":"Nucleic Acids Res."},{"key":"660_CR57","doi-asserted-by":"publisher","first-page":"1077","DOI":"10.1177\/00220345580370060801","volume":"37","author":"PH Keyes","year":"1958","unstructured":"Keyes, P. H. Dental caries in the molar teeth of rats. I. Distribution of lesions induced by high-carbohydrate low-fat diets. J. Dental Res. 37, 1077\u20131087 (1958).","journal-title":"J. Dental Res."}],"container-title":["npj Biofilms and Microbiomes"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41522-025-00660-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41522-025-00660-7","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41522-025-00660-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,3,8]],"date-time":"2025-03-08T05:54:14Z","timestamp":1741413254000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41522-025-00660-7"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,3,8]]},"references-count":57,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2025,12]]}},"alternative-id":["660"],"URL":"https:\/\/doi.org\/10.1038\/s41522-025-00660-7","relation":{},"ISSN":["2055-5008"],"issn-type":[{"value":"2055-5008","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,3,8]]},"assertion":[{"value":"27 March 2024","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"22 January 2025","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"8 March 2025","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"41"}}