{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,19]],"date-time":"2026-10-19T21:33:10Z","timestamp":1792445590977,"version":"4.5.0"},"reference-count":65,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2026,6,8]],"date-time":"2026-06-08T00:00:00Z","timestamp":1780876800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"},{"start":{"date-parts":[[2026,6,8]],"date-time":"2026-06-08T00:00:00Z","timestamp":1780876800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"funder":[{"name":"JSPS KAKENHI","award":["24K00163"],"award-info":[{"award-number":["24K00163"]}]},{"name":"JSPS KAKENHI","award":["24K00163"],"award-info":[{"award-number":["24K00163"]}]},{"name":"JSPS KAKENHI","award":["24K00163"],"award-info":[{"award-number":["24K00163"]}]},{"name":"JSPS KAKENHI","award":["24K21381"],"award-info":[{"award-number":["24K21381"]}]},{"name":"JSPS KAKENHI","award":["24K21381"],"award-info":[{"award-number":["24K21381"]}]},{"name":"JSPS KAKENHI","award":["24K21381"],"award-info":[{"award-number":["24K21381"]}]},{"name":"JSPS KAKENHI","award":["24K00163"],"award-info":[{"award-number":["24K00163"]}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Sci Rep"],"DOI":"10.1038\/s41598-026-55286-2","type":"journal-article","created":{"date-parts":[[2026,6,8]],"date-time":"2026-06-08T09:03:22Z","timestamp":1780909402000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Insights into demographic and cultural influences on the oral microbiome from historical Japanese dental calculus"],"prefix":"10.1038","volume":"16","author":[{"given":"Yuki","family":"Kuriyama","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fuzuki","family":"Mizuno","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Takashi","family":"Yamada","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Masahiko","family":"Kumagai","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Masaki","family":"Tanaka","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Izumi","family":"Naka","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kazuaki","family":"Hirata","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Soichiro","family":"Mizushima","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shiori","family":"Yonemoto","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kyoko","family":"Funahashi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Noriko","family":"Seguchi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kazuhiro","family":"Sakaue","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eisaku","family":"Kanazawa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Masami","family":"Matsushita","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Takayuki","family":"Matsushita","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aiko","family":"Saso","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Takashi","family":"Nara","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ryohei","family":"Sawaura","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chiaki","family":"Katagiri","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tomoki","family":"Maekawa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kunihiko","family":"Kurosaki","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hisako","family":"Saitoh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shuuji","family":"Namiki","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shintaroh","family":"Ueda","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jun","family":"Ohashi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,6,8]]},"reference":[{"key":"55286_CR1","doi-asserted-by":"publisher","first-page":"509","DOI":"10.1016\/j.molmed.2014.05.002","volume":"20","author":"YE Borre","year":"2014","unstructured":"Borre, Y. E. et al. Microbiota and neurodevelopmental windows: Implications for brain disorders. Trends Mol. Med. 20, 509\u2013518 (2014).","journal-title":"Trends Mol. Med."},{"key":"55286_CR2","doi-asserted-by":"publisher","first-page":"392","DOI":"10.1038\/nm.4517","volume":"24","author":"JA Gilbert","year":"2018","unstructured":"Gilbert, J. A. et al. Current understanding of the human microbiome. Nat. Med. 24, 392\u2013400 (2018).","journal-title":"Nat. Med."},{"key":"55286_CR3","doi-asserted-by":"publisher","first-page":"22","DOI":"10.1016\/j.imlet.2014.08.017","volume":"162","author":"M Costalonga","year":"2014","unstructured":"Costalonga, M. & Herzberg, M. C. The oral microbiome and the immunobiology of periodontal disease and caries. Immunol. Lett. 162, 22\u201338 (2014).","journal-title":"Immunol. Lett."},{"key":"55286_CR4","doi-asserted-by":"publisher","first-page":"105","DOI":"10.1126\/science.1208344","volume":"334","author":"GD Wu","year":"2011","unstructured":"Wu, G. D. et al. Linking long-term dietary patterns with gut microbial enterotypes. Science 334, 105\u2013108 (2011).","journal-title":"Science"},{"key":"55286_CR5","doi-asserted-by":"publisher","first-page":"4212","DOI":"10.1172\/JCI72333","volume":"124","author":"SR Modi","year":"2014","unstructured":"Modi, S. R., Collins, J. J. & Relman, D. A. Antibiotics and the gut microbiota. J. Clin. Invest. 124, 4212\u20134218 (2014).","journal-title":"J. Clin. Invest."},{"key":"55286_CR6","doi-asserted-by":"publisher","first-page":"14","DOI":"10.1016\/j.gde.2016.07.003","volume":"41","author":"SL Schnorr","year":"2016","unstructured":"Schnorr, S. L., Sankaranarayanan, K., Lewis, C. M. & Warinner, C. Insights into human evolution from ancient and contemporary microbiome studies. Curr. Opin. Genet. Dev. 41, 14\u201326 (2016).","journal-title":"Curr. Opin. Genet. Dev."},{"key":"55286_CR7","doi-asserted-by":"publisher","first-page":"1682","DOI":"10.1016\/j.cub.2015.04.055","volume":"25","author":"S Rampelli","year":"2015","unstructured":"Rampelli, S. et al. Metagenome sequencing of the Hadza hunter-gatherer gut microbiota. Curr. Biol. 25, 1682\u20131693 (2015).","journal-title":"Curr. Biol."},{"key":"55286_CR8","doi-asserted-by":"publisher","first-page":"383","DOI":"10.1038\/s41579-019-0191-8","volume":"17","author":"ED Sonnenburg","year":"2019","unstructured":"Sonnenburg, E. D. & Sonnenburg, J. L. The ancestral and industrialized gut microbiota and implications for human health. Nat. Rev. Microbiol. 17, 383\u2013390 (2019).","journal-title":"Nat. Rev. Microbiol."},{"key":"55286_CR9","doi-asserted-by":"publisher","first-page":"4317","DOI":"10.1073\/pnas.061014798","volume":"98","author":"HN Poinar","year":"2001","unstructured":"Poinar, H. N. et al. A molecular analysis of dietary diversity for three archaic Native Americans. Proceedings of the National Academy of Sciences 98, 4317\u20134322 (2001).","journal-title":"Proceedings of the National Academy of Sciences"},{"key":"55286_CR10","doi-asserted-by":"publisher","first-page":"450","DOI":"10.1038\/ng.2536","volume":"45","author":"CJ Adler","year":"2013","unstructured":"Adler, C. J. et al. Sequencing ancient calcified dental plaque shows changes in oral microbiota with dietary shifts of the Neolithic and Industrial revolutions. Nat. Genet. 45, 450\u2013455 (2013).","journal-title":"Nat. Genet."},{"key":"55286_CR11","unstructured":"Fellows Yates, J. A. et al. The evolution and changing ecology of the African hominid oral microbiome. Proc. Natl. Acad. Sci. 118, e2021655118 (2021)."},{"key":"55286_CR12","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0051146","volume":"7","author":"RY Tito","year":"2012","unstructured":"Tito, R. Y. et al. Insights from characterizing extinct human gut microbiomes. PLOS ONE 7, e51146 (2012).","journal-title":"PLOS ONE"},{"key":"55286_CR13","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1038\/nature21674","volume":"544","author":"LS Weyrich","year":"2017","unstructured":"Weyrich, L. S. et al. Neanderthal behaviour, diet, and disease inferred from ancient DNA in dental calculus. Nature 544, 357\u2013361 (2017).","journal-title":"Nature"},{"key":"55286_CR14","doi-asserted-by":"publisher","first-page":"234","DOI":"10.1038\/s41586-021-03532-0","volume":"594","author":"MC Wibowo","year":"2021","unstructured":"Wibowo, M. C. et al. Reconstruction of ancient microbial genomes from the human gut. Nature 594, 234\u2013239 (2021).","journal-title":"Nature"},{"key":"55286_CR15","doi-asserted-by":"publisher","first-page":"197","DOI":"10.1186\/s40168-021-01132-8","volume":"9","author":"L Graneh\u00e4ll","year":"2021","unstructured":"Graneh\u00e4ll, L. et al. Metagenomic analysis of ancient dental calculus reveals unexplored diversity of oral archaeal Methanobrevibacter. Microbiome 9, 197 (2021).","journal-title":"Microbiome"},{"key":"55286_CR16","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msae017","volume":"41","author":"I Jackson","year":"2024","unstructured":"Jackson, I., Woodman, P., Dowd, M., Fibiger, L. & Cassidy, L. M. Ancient genomes from Bronze Age remains reveal deep diversity and recent adaptive episodes for human oral pathobionts. Mol. Biol. Evol. 41, msae017 (2024).","journal-title":"Mol. Biol. Evol."},{"key":"55286_CR17","doi-asserted-by":"publisher","first-page":"336","DOI":"10.1038\/ng.2906","volume":"46","author":"C Warinner","year":"2014","unstructured":"Warinner, C. et al. Pathogens and host immunity in the ancient human oral cavity. Nat. Genet. 46, 336\u2013344 (2014).","journal-title":"Nat. Genet."},{"key":"55286_CR18","doi-asserted-by":"publisher","first-page":"10191","DOI":"10.1038\/s41467-024-53920-z","volume":"15","author":"IM Velsko","year":"2024","unstructured":"Velsko, I. M. et al. Exploring the potential of dental calculus to shed light on past human migrations in Oceania. Nat. Commun. 15, 10191 (2024).","journal-title":"Nat. Commun."},{"key":"55286_CR19","doi-asserted-by":"publisher","first-page":"149","DOI":"10.1080\/15564894.2017.1382620","volume":"14","author":"R Eisenhofer","year":"2019","unstructured":"Eisenhofer, R., Anderson, A., Dobney, K., Cooper, A. & Weyrich, L. S. Ancient Microbial DNA in Dental Calculus: A New method for Studying Rapid Human Migration Events. J. Isl Coast Archaeol. 14, 149\u2013162 (2019).","journal-title":"J. Isl Coast Archaeol."},{"key":"55286_CR20","doi-asserted-by":"publisher","first-page":"723821","DOI":"10.3389\/fcimb.2021.723821","volume":"11","author":"T Shiba","year":"2021","unstructured":"Shiba, T. et al. Comparison of Periodontal Bacteria of Edo and Modern Periods Using Novel Diagnostic Approach for Periodontitis With Micro-CT. Front. Cell. Infect. Microbiol. 11, 723821 (2021).","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"55286_CR21","doi-asserted-by":"publisher","first-page":"2415734","DOI":"10.1080\/20002297.2024.2415734","volume":"16","author":"V Pilliol","year":"2024","unstructured":"Pilliol, V. et al. Methanobrevibacter oralis: a comprehensive review. J. Oral Microbiol. 16, 2415734 (2024).","journal-title":"J. Oral Microbiol."},{"key":"55286_CR22","doi-asserted-by":"publisher","first-page":"20190578","DOI":"10.1098\/rstb.2019.0578","volume":"375","author":"R Eisenhofer","year":"2020","unstructured":"Eisenhofer, R., Kanzawa-Kiriyama, H., Shinoda, K. & Weyrich, L. S. Investigating the demographic history of Japan using ancient oral microbiota. Philos. Trans. R Soc. B Biol. Sci. 375, 20190578 (2020).","journal-title":"Philos. Trans. R Soc. B Biol. Sci."},{"key":"55286_CR23","doi-asserted-by":"publisher","first-page":"605","DOI":"10.1126\/science.aam9695","volume":"356","author":"V Slon","year":"2017","unstructured":"Slon, V. et al. Neandertal and Denisovan DNA from Pleistocene sediments. Science 356, 605\u2013608 (2017).","journal-title":"Science"},{"key":"55286_CR24","doi-asserted-by":"publisher","DOI":"10.1002\/imt2.107","volume":"2","author":"S Chen","year":"2023","unstructured":"Chen, S. Ultrafast one-pass FASTQ data preprocessing, quality control, and deduplication using fastp. iMeta 2, e107 (2023).","journal-title":"iMeta"},{"key":"55286_CR25","doi-asserted-by":"publisher","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","volume":"34","author":"S Chen","year":"2018","unstructured":"Chen, S., Zhou, Y., Chen, Y. & Gu, J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34, i884\u2013i890 (2018).","journal-title":"Bioinformatics"},{"key":"55286_CR26","doi-asserted-by":"publisher","first-page":"243","DOI":"10.1186\/s40168-023-01670-3","volume":"11","author":"C Duitama Gonz\u00e1lez","year":"2023","unstructured":"Duitama Gonz\u00e1lez, C. et al. decOM: similarity-based microbial source tracking of ancient oral samples using k-mer-based methods. Microbiome 11, 243 (2023).","journal-title":"Microbiome"},{"key":"55286_CR27","doi-asserted-by":"publisher","first-page":"366","DOI":"10.1038\/s41592-021-01101-x","volume":"18","author":"B Buchfink","year":"2021","unstructured":"Buchfink, B., Reuter, K. & Drost, H. G. Sensitive protein alignments at tree-of-life scale using DIAMOND. Nat. Methods. 18, 366\u2013368 (2021).","journal-title":"Nat. Methods"},{"key":"55286_CR28","doi-asserted-by":"publisher","DOI":"10.1002\/cpz1.59","volume":"1","author":"C Ba\u011fc\u0131","year":"2021","unstructured":"Ba\u011fc\u0131, C., Patz, S. & Huson, D. H. DIAMOND+MEGAN: Fast and easy taxonomic and functional analysis of short and long microbiome sequences. Curr. Protoc. 1, e59 (2021).","journal-title":"Curr. Protoc."},{"key":"55286_CR29","doi-asserted-by":"publisher","first-page":"377","DOI":"10.1101\/gr.5969107","volume":"17","author":"DH Huson","year":"2007","unstructured":"Huson, D. H., Auch, A. F., Qi, J. & Schuster, S. C. MEGAN analysis of metagenomic data. Genome Res. 17, 377\u2013386 (2007).","journal-title":"Genome Res."},{"key":"55286_CR30","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1004957","volume":"12","author":"DH Huson","year":"2016","unstructured":"Huson, D. H. et al. MEGAN Community Edition - Interactive exploration and analysis of large-scale microbiome sequencing data. PLoS Comput. Biol. 12, e1004957 (2016).","journal-title":"PLoS Comput. Biol."},{"key":"55286_CR31","doi-asserted-by":"publisher","unstructured":"Escapa, I. F. et al. New Insights into Human Nostril Microbiome from the Expanded Human Oral Microbiome Database (eHOMD): a Resource for the Microbiome of the Human Aerodigestive Tract. mSystems 3, (2018). https:\/\/doi.org\/10.1128\/msystems.001. 87\u201318.","DOI":"10.1128\/msystems.001"},{"key":"55286_CR32","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-12-S1-S21","volume":"12","author":"S Mitra","year":"2011","unstructured":"Mitra, S. et al. Functional analysis of metagenomes and metatranscriptomes using SEED and KEGG. BMC Bioinformatics 12, S21 (2011).","journal-title":"BMC Bioinformatics"},{"key":"55286_CR33","doi-asserted-by":"crossref","unstructured":"Ottoni, C. et al. Tracking the transition to agriculture in Southern Europe through ancient DNA analysis of dental calculus. Proc. Natl. Acad. Sci. 118, e2102116118 (2021).","DOI":"10.1073\/pnas.2102116118"},{"key":"55286_CR34","doi-asserted-by":"publisher","unstructured":"Blanco-Miguez, A. et al. Extending and improving metagenomic taxonomic profiling with uncharacterized species with MetaPhlAn 4. 08.22.504593 Preprint at (2022). https:\/\/doi.org\/10.1101\/2022.08.22.504593 (2022).","DOI":"10.1101\/2022.08.22.504593"},{"key":"55286_CR35","doi-asserted-by":"publisher","first-page":"626","DOI":"10.1101\/gr.216242.116","volume":"27","author":"DT Truong","year":"2017","unstructured":"Truong, D. T., Tett, A., Pasolli, E., Huttenhower, C. & Segata, N. Microbial strain-level population structure and genetic diversity from metagenomes. Genome Res. 27, 626\u2013638 (2017).","journal-title":"Genome Res."},{"key":"55286_CR36","doi-asserted-by":"publisher","first-page":"3022","DOI":"10.1093\/molbev\/msab120","volume":"38","author":"K Tamura","year":"2021","unstructured":"Tamura, K., Stecher, G. & Kumar, S. MEGA11: Molecular Evolutionary Genetics Analysis version 11. Mol. Biol. Evol. 38, 3022\u20133027 (2021).","journal-title":"Mol. Biol. Evol."},{"key":"55286_CR37","doi-asserted-by":"publisher","first-page":"1674","DOI":"10.1093\/bioinformatics\/btv033","volume":"31","author":"D Li","year":"2015","unstructured":"Li, D., Liu, C. M., Luo, R., Sadakane, K. & Lam, T. W. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics 31, 1674\u20131676 (2015).","journal-title":"Bioinformatics"},{"key":"55286_CR38","doi-asserted-by":"publisher","first-page":"605","DOI":"10.1093\/bioinformatics\/btv638","volume":"32","author":"YW Wu","year":"2016","unstructured":"Wu, Y. W., Simmons, B. A. & Singer, S. W. MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets. Bioinformatics 32, 605\u2013607 (2016).","journal-title":"Bioinformatics"},{"key":"55286_CR39","doi-asserted-by":"publisher","first-page":"e1165","DOI":"10.7717\/peerj.1165","volume":"3","author":"DD Kang","year":"2015","unstructured":"Kang, D. D., Froula, J., Egan, R. & Wang, Z. MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities. PeerJ 3, e1165 (2015).","journal-title":"PeerJ"},{"key":"55286_CR40","doi-asserted-by":"publisher","first-page":"e7359","DOI":"10.7717\/peerj.7359","volume":"7","author":"DD Kang","year":"2019","unstructured":"Kang, D. D. et al. MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies. PeerJ 7, e7359 (2019).","journal-title":"PeerJ"},{"key":"55286_CR41","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1038\/nmeth.1923","volume":"9","author":"B Langmead","year":"2012","unstructured":"Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357\u2013359 (2012).","journal-title":"Nat. Methods"},{"key":"55286_CR42","doi-asserted-by":"publisher","first-page":"836","DOI":"10.1038\/s41564-018-0171-1","volume":"3","author":"CMK Sieber","year":"2018","unstructured":"Sieber, C. M. K. et al. Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy. Nat. Microbiol. 3, 836\u2013843 (2018).","journal-title":"Nat. Microbiol."},{"key":"55286_CR43","doi-asserted-by":"publisher","first-page":"1043","DOI":"10.1101\/gr.186072.114","volume":"25","author":"DH Parks","year":"2015","unstructured":"Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P. & Tyson, G. W. CheckM: Assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 25, 1043\u20131055 (2015).","journal-title":"Genome Res."},{"key":"55286_CR44","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-16366-7","volume":"11","author":"F Asnicar","year":"2020","unstructured":"Asnicar, F. et al. Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0. Nat. Commun. 11, 2500 (2020).","journal-title":"Nat. Commun."},{"key":"55286_CR45","doi-asserted-by":"publisher","unstructured":"Harris, S. R. S. K. A. Split Kmer Analysis Toolkit for Bacterial Genomic Epidemiology. 453142 Preprint at (2018). https:\/\/doi.org\/10.1101\/453142","DOI":"10.1101\/453142"},{"key":"55286_CR46","volume":"2","author":"AJ Page","year":"2016","unstructured":"Page, A. J. et al. SNP-sites: Rapid efficient extraction of SNPs from multi-FASTA alignments. Microb. Genom. 2, e000056 (2016).","journal-title":"Microb. Genom."},{"key":"55286_CR47","doi-asserted-by":"publisher","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","volume":"25","author":"H Li","year":"2009","unstructured":"Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows\u2013Wheeler transform. Bioinformatics 25, 1754\u20131760 (2009).","journal-title":"Bioinformatics"},{"key":"55286_CR48","doi-asserted-by":"publisher","first-page":"giab008","DOI":"10.1093\/gigascience\/giab008","volume":"10","author":"P Danecek","year":"2021","unstructured":"Danecek, P. et al. Twelve years of SAMtools and BCFtools. GigaScience 10, giab008 (2021).","journal-title":"GigaScience"},{"key":"55286_CR49","doi-asserted-by":"publisher","first-page":"1682","DOI":"10.1093\/bioinformatics\/btt193","volume":"29","author":"H J\u00f3nsson","year":"2013","unstructured":"J\u00f3nsson, H., Ginolhac, A., Schubert, M., Johnson, P. L. F. & Orlando, L. mapDamage2.0: Fast approximate Bayesian estimates of ancient DNA damage parameters. Bioinformatics 29, 1682\u20131684 (2013).","journal-title":"Bioinformatics"},{"key":"55286_CR50","doi-asserted-by":"publisher","first-page":"1037","DOI":"10.1093\/bioinformatics\/btx713","volume":"34","author":"Y Tanizawa","year":"2018","unstructured":"Tanizawa, Y., Fujisawa, T. & Nakamura, Y. DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication. Bioinformatics 34, 1037\u20131039 (2018).","journal-title":"Bioinformatics"},{"key":"55286_CR51","doi-asserted-by":"publisher","first-page":"5825","DOI":"10.1093\/molbev\/msab293","volume":"38","author":"CP Cantalapiedra","year":"2021","unstructured":"Cantalapiedra, C. P., Hern\u00e1ndez-Plaza, A., Letunic, I., Bork, P. & Huerta-Cepas, J. eggNOG-mapper v2: Functional annotation, orthology assignments, and domain prediction at the metagenomic scale. Mol. Biol. Evol. 38, 5825\u20135829 (2021).","journal-title":"Mol. Biol. Evol."},{"key":"55286_CR52","doi-asserted-by":"crossref","unstructured":"Cosentino, S., Sriswasdi, S. & Iwasaki, W. SonicParanoid2: Fast, accurate, and comprehensive orthology inference with machine learning and language models. Genome Biol. 25195. (2024).","DOI":"10.1101\/2023.05.14.540736"},{"key":"55286_CR53","doi-asserted-by":"publisher","first-page":"1530","DOI":"10.1093\/molbev\/msaa015","volume":"37","author":"BQ Minh","year":"2020","unstructured":"Minh, B. Q. et al. IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era. Mol. Biol. Evol. 37, 1530\u20131534 (2020).","journal-title":"Mol. Biol. Evol."},{"key":"55286_CR54","doi-asserted-by":"crossref","unstructured":"Socransky, S., Haffajee, A., Cugini, M., Smith, C. & Kent, R. L. Jr. Microbial complexes in subgingival plaque. J. Clin. Periodontol. 25, 134\u2013144 (1998).","DOI":"10.1111\/j.1600-051X.1998.tb02419.x"},{"key":"55286_CR55","first-page":"217","volume":"12","author":"T Ezure","year":"1987","unstructured":"Ezure, T. et al. A report of clinical example concerning the tooth black. Dent. J. Iwate Med. Univ. 12, 217\u2013221 (1987). (in Japanese).","journal-title":"Dent. J. Iwate Med. Univ."},{"key":"55286_CR56","doi-asserted-by":"publisher","first-page":"353","DOI":"10.1246\/cl.200774","volume":"50","author":"T Watanabe","year":"2021","unstructured":"Watanabe, T. & Shima, S. MvhB-type Polyferredoxin as an Electron-transfer Chain in Putative Redox-enzyme Complexes. Chem. Lett. 50, 353\u2013360 (2021).","journal-title":"Chem. Lett."},{"key":"55286_CR57","doi-asserted-by":"publisher","first-page":"915","DOI":"10.2217\/fmb-2018-0043","volume":"13","author":"B Zhu","year":"2018","unstructured":"Zhu, B., Macleod, L. C., Kitten, T. & Xu, P. Streptococcus sanguinis biofilm formation & interaction with oral pathogens. Future Microbiol. 13, 915\u2013932 (2018).","journal-title":"Future Microbiol."},{"key":"55286_CR58","doi-asserted-by":"publisher","first-page":"2315","DOI":"10.1038\/s41564-023-01527-3","volume":"8","author":"AS Gancz","year":"2023","unstructured":"Gancz, A. S. et al. Ancient dental calculus reveals oral microbiome shifts associated with lifestyle and disease in Great Britain. Nat. Microbiol. 8, 2315\u20132325 (2023).","journal-title":"Nat. Microbiol."},{"key":"55286_CR59","doi-asserted-by":"publisher","DOI":"10.1038\/s41522-024-00642-1","volume":"11","author":"IM Velsko","year":"2025","unstructured":"Velsko, I. M. & Warinner, C. Streptococcus abundance and oral site tropism in humans and non-human primates reflects host and lifestyle differences. Npj Biofilms Microbiomes 11, 19 (2025).","journal-title":"Npj Biofilms Microbiomes"},{"key":"55286_CR60","doi-asserted-by":"publisher","DOI":"10.1093\/pnasnexus\/pgac148","volume":"1","author":"IM Velsko","year":"2022","unstructured":"Velsko, I. M. et al. Ancient dental calculus preserves signatures of biofilm succession and interindividual variation independent of dental pathology. PNAS Nexus 1, pgac148 (2022).","journal-title":"PNAS Nexus"},{"key":"55286_CR61","unstructured":"Hanihara, K. Dual Structure Model for the Population History of the Japanese. Jpn Rev 1\u201333 (1991)."},{"key":"55286_CR62","doi-asserted-by":"crossref","unstructured":"Lepp, P. W. et al. Methanogenic Archaea and human periodontal disease. Proc. Natl. Acad. Sci. 101, 6176\u20136181 (2004).","DOI":"10.1073\/pnas.0308766101"},{"key":"55286_CR63","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2020.587750","author":"R S\u00e1nchez de la Nieta","year":"2020","unstructured":"S\u00e1nchez de la Nieta, R., Antoraz, S., Alzate, J. F., Santamar\u00eda, R. I. & D\u00edaz, M. Antibiotic production and antibiotic resistance: The two sides of AbrB1\/B2, a two-component system of Streptomyces coelicolor. Front. Microbiol. https:\/\/doi.org\/10.3389\/fmicb.2020.587750 (2020).","journal-title":"Front. Microbiol."},{"key":"55286_CR64","doi-asserted-by":"publisher","first-page":"6354","DOI":"10.1128\/JB.187.18.6354-6362.2005","volume":"187","author":"F Yao","year":"2005","unstructured":"Yao, F. & Strauch, M. A. Independent and Interchangeable Multimerization Domains of the AbrB, Abh, and SpoVT Global Regulatory Proteins. J. Bacteriol. 187, 6354\u20136362 (2005).","journal-title":"J. Bacteriol."},{"key":"55286_CR65","doi-asserted-by":"publisher","DOI":"10.1016\/j.heliyon.2019.e03013","volume":"5","author":"G Guti\u00e9rrez-Venegas","year":"2019","unstructured":"Guti\u00e9rrez-Venegas, G., G\u00f3mez-Mora, J. A., Meraz-Rodr\u00edguez, M. A., Flores-S\u00e1nchez, M. A. & Ortiz-Miranda, L. F. Effect of flavonoids on antimicrobial activity of microorganisms present in dental plaque. Heliyon 5, e03013 (2019).","journal-title":"Heliyon"}],"container-title":["Scientific Reports"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41598-026-55286-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41598-026-55286-2","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41598-026-55286-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,6,8]],"date-time":"2026-06-08T09:03:38Z","timestamp":1780909418000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41598-026-55286-2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,6,8]]},"references-count":65,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2026,12]]}},"alternative-id":["55286"],"URL":"https:\/\/doi.org\/10.1038\/s41598-026-55286-2","relation":{},"ISSN":["2045-2322"],"issn-type":[{"value":"2045-2322","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,6,8]]},"assertion":[{"value":"12 January 2026","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"23 May 2026","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"8 June 2026","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"The authors declare no competing interests.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"17522"}}