{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T16:32:37Z","timestamp":1791390757168,"version":"4.3.3"},"reference-count":107,"publisher":"Elsevier BV","issue":"3","license":[{"start":{"date-parts":[[2026,3,1]],"date-time":"2026-03-01T00:00:00Z","timestamp":1772323200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2026,3,1]],"date-time":"2026-03-01T00:00:00Z","timestamp":1772323200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2026,3,1]],"date-time":"2026-03-01T00:00:00Z","timestamp":1772323200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-017"},{"start":{"date-parts":[[2026,3,1]],"date-time":"2026-03-01T00:00:00Z","timestamp":1772323200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2026,3,1]],"date-time":"2026-03-01T00:00:00Z","timestamp":1772323200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-012"},{"start":{"date-parts":[[2026,3,1]],"date-time":"2026-03-01T00:00:00Z","timestamp":1772323200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2026,3,1]],"date-time":"2026-03-01T00:00:00Z","timestamp":1772323200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-004"}],"funder":[{"DOI":"10.13039\/501100019540","name":"Science Fund for Distinguished Young Scholars of Zhejiang Province","doi-asserted-by":"publisher","award":["LR23H140001"],"award-info":[{"award-number":["LR23H140001"]}],"id":[{"id":"10.13039\/501100019540","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100022963","name":"Key Research and Development Program of Zhejiang Province","doi-asserted-by":"publisher","award":["2024SSYS0022"],"award-info":[{"award-number":["2024SSYS0022"]}],"id":[{"id":"10.13039\/100022963","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100022963","name":"Key Research and Development Program of Zhejiang Province","doi-asserted-by":"publisher","award":["2022C03088"],"award-info":[{"award-number":["2022C03088"]}],"id":[{"id":"10.13039\/100022963","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["82470973"],"award-info":[{"award-number":["82470973"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["82170953"],"award-info":[{"award-number":["82170953"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012226","name":"Fundamental Research Funds for the Central Universities","doi-asserted-by":"publisher","award":["226-2024-00202"],"award-info":[{"award-number":["226-2024-00202"]}],"id":[{"id":"10.13039\/501100012226","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002858","name":"China Postdoctoral Science Foundation","doi-asserted-by":"publisher","award":["2024M762880"],"award-info":[{"award-number":["2024M762880"]}],"id":[{"id":"10.13039\/501100002858","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2025YFF0512800"],"award-info":[{"award-number":["2025YFF0512800"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["cell.com","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Cell Host &amp; Microbe"],"published-print":{"date-parts":[[2026,3]]},"DOI":"10.1016\/j.chom.2026.01.017","type":"journal-article","created":{"date-parts":[[2026,2,19]],"date-time":"2026-02-19T16:06:26Z","timestamp":1771517186000},"page":"526-543.e6","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":5,"title":["Single-cell profiling of the subgingival bacteria reveals transcriptional heterogeneity and niche-specific programs"],"prefix":"10.1016","volume":"34","author":[{"given":"Liguo","family":"Ding","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lu","family":"Song","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yibing","family":"Han","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jianing","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuexiao","family":"Lyu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mengdi","family":"Song","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaoyue","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wentao","family":"He","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qianming","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pei-Hui","family":"Ding","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2820-4243","authenticated-orcid":false,"given":"Yongcheng","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.chom.2026.01.017_bib1","doi-asserted-by":"crossref","first-page":"1045","DOI":"10.1177\/0022034514552491","article-title":"Global burden of severe periodontitis in 1990\u20132010: a systematic review and meta-regression","volume":"93","author":"Kassebaum","year":"2014","journal-title":"J. Dent. Res."},{"key":"10.1016\/j.chom.2026.01.017_bib2","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/jcpe.13218","article-title":"Diagnostic sensitivity and specificity of host-derived salivary biomarkers in periodontal disease amongst adults: Systematic review","volume":"47","author":"Kc","year":"2020","journal-title":"J. Clin. Periodontol."},{"key":"10.1016\/j.chom.2026.01.017_bib3","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1016\/S0140-6736(19)31146-8","article-title":"Oral diseases: a global public health challenge","volume":"394","author":"Peres","year":"2019","journal-title":"Lancet"},{"key":"10.1016\/j.chom.2026.01.017_bib4","doi-asserted-by":"crossref","first-page":"1809","DOI":"10.1016\/S0140-6736(05)67728-8","article-title":"Periodontal diseases","volume":"366","author":"Pihlstrom","year":"2005","journal-title":"Lancet"},{"key":"10.1016\/j.chom.2026.01.017_bib5","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1111\/prd.12616","article-title":"Periodontal disease: A systemic condition","volume":"96","author":"Villoria","year":"2024","journal-title":"Periodontol. 2000"},{"key":"10.1016\/j.chom.2026.01.017_bib6","doi-asserted-by":"crossref","first-page":"897","DOI":"10.1016\/S0140-6736(24)02811-3","article-title":"Trends in the global, regional, and national burden of oral conditions from 1990 to 2021: a systematic analysis for the Global Burden of Disease Study 2021","volume":"405","year":"2025","journal-title":"Lancet"},{"key":"10.1016\/j.chom.2026.01.017_bib7","doi-asserted-by":"crossref","DOI":"10.1038\/nrdp.2017.38","article-title":"Periodontal diseases","volume":"3","author":"Kinane","year":"2017","journal-title":"Nat. Rev. Dis. Primers"},{"key":"10.1016\/j.chom.2026.01.017_bib8","doi-asserted-by":"crossref","first-page":"73","DOI":"10.1111\/odi.14516","article-title":"WHO\u2019s global oral health status report 2022: Actions, discussion and implementation","volume":"30","author":"Jain","year":"2024","journal-title":"Oral Dis."},{"key":"10.1016\/j.chom.2026.01.017_bib9","doi-asserted-by":"crossref","first-page":"134","DOI":"10.1111\/j.1600-051X.1998.tb02419.x","article-title":"Microbial complexes in subgingival plaque","volume":"25","author":"Socransky","year":"1998","journal-title":"J. Clin. Periodontol."},{"key":"10.1016\/j.chom.2026.01.017_bib10","doi-asserted-by":"crossref","first-page":"1176","DOI":"10.1038\/ismej.2011.191","article-title":"Distinct and complex bacterial profiles in human periodontitis and health revealed by 16S pyrosequencing","volume":"6","author":"Griffen","year":"2012","journal-title":"ISME J."},{"key":"10.1016\/j.chom.2026.01.017_bib11","doi-asserted-by":"crossref","first-page":"1879","DOI":"10.1038\/ismej.2014.28","article-title":"Phylogenetic and functional gene structure shifts of the oral microbiomes in periodontitis patients","volume":"8","author":"Li","year":"2014","journal-title":"ISME J."},{"key":"10.1016\/j.chom.2026.01.017_bib12","doi-asserted-by":"crossref","DOI":"10.1038\/srep38993","article-title":"Comparative metagenomics reveals taxonomically idiosyncratic yet functionally congruent communities in periodontitis","volume":"6","author":"Dabdoub","year":"2016","journal-title":"Sci. Rep."},{"key":"10.1016\/j.chom.2026.01.017_bib13","doi-asserted-by":"crossref","first-page":"5298","DOI":"10.3390\/ijms22105298","article-title":"Taxonomic and Gene Category Analyses of Subgingival Plaques from a Group of Japanese Individuals with and without Periodontitis","volume":"22","author":"Izawa","year":"2021","journal-title":"Int. J. Mol. Sci."},{"key":"10.1016\/j.chom.2026.01.017_bib14","article-title":"Metagenomic sequencing reveals microbiota and its functional potential associated with periodontal disease","volume":"3","author":"Wang","year":"2013","journal-title":"Sci. Rep."},{"key":"10.1016\/j.chom.2026.01.017_bib15","doi-asserted-by":"crossref","first-page":"1659","DOI":"10.1038\/ismej.2014.23","article-title":"Community-wide transcriptome of the oral microbiome in subjects with and without periodontitis","volume":"8","author":"Duran-Pinedo","year":"2014","journal-title":"ISME J."},{"key":"10.1016\/j.chom.2026.01.017_bib16","doi-asserted-by":"crossref","DOI":"10.1128\/mBio.01012-14","article-title":"Metatranscriptomics of the human oral microbiome during health and disease","volume":"5","author":"Jorth","year":"2014","journal-title":"mBio"},{"key":"10.1016\/j.chom.2026.01.017_bib17","doi-asserted-by":"crossref","DOI":"10.1038\/npjbiofilms.2015.17","article-title":"Functional biomarkers for chronic periodontitis and insights into the roles of Prevotella nigrescens and Fusobacterium nucleatum; a metatranscriptome analysis","volume":"1","author":"Szafra\u0144ski","year":"2015","journal-title":"NPJ Biofilms Microbiomes"},{"key":"10.1016\/j.chom.2026.01.017_bib18","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1186\/s13073-015-0153-3","article-title":"Functional signatures of oral dysbiosis during periodontitis progression revealed by microbial metatranscriptome analysis","volume":"7","author":"Yost","year":"2015","journal-title":"Genome Med."},{"key":"10.1016\/j.chom.2026.01.017_bib19","doi-asserted-by":"crossref","DOI":"10.1126\/science.adp6252","article-title":"Dissecting microbial communities with single-cell transcriptome analysis","volume":"389","author":"Pountain","year":"2025","journal-title":"Science"},{"key":"10.1016\/j.chom.2026.01.017_bib20","doi-asserted-by":"crossref","first-page":"1008","DOI":"10.1038\/d41586-025-00075-6","article-title":"Self-driving laboratories, advanced immunotherapies and five more technologies to watch in 2025","volume":"637","author":"Eisenstein","year":"2025","journal-title":"Nature"},{"key":"10.1016\/j.chom.2026.01.017_bib21","doi-asserted-by":"crossref","first-page":"2725","DOI":"10.1016\/j.cell.2022.06.040","article-title":"Single-cell approaches in human microbiome research","volume":"185","author":"Llor\u00e9ns-Rico","year":"2022","journal-title":"Cell"},{"key":"10.1016\/j.chom.2026.01.017_bib22","doi-asserted-by":"crossref","first-page":"1192","DOI":"10.1038\/s41564-020-0729-6","article-title":"Prokaryotic single-cell RNA sequencing by in situ combinatorial indexing","volume":"5","author":"Blattman","year":"2020","journal-title":"Nat. Microbiol."},{"key":"10.1016\/j.chom.2026.01.017_bib23","doi-asserted-by":"crossref","DOI":"10.1126\/science.aba5257","article-title":"Microbial single-cell RNA sequencing by split-pool barcoding","volume":"371","author":"Kuchina","year":"2021","journal-title":"Science"},{"key":"10.1016\/j.chom.2026.01.017_bib24","doi-asserted-by":"crossref","first-page":"877","DOI":"10.1016\/j.cell.2023.01.002","article-title":"Bacterial droplet-based single-cell RNA-seq reveals antibiotic-associated heterogeneous cellular states","volume":"186","author":"Ma","year":"2023","journal-title":"Cell"},{"key":"10.1016\/j.chom.2026.01.017_bib25","article-title":"Droplet-based high-throughput single microbe RNA sequencing by smRandom-seq","volume":"14","author":"Xu","year":"2023","journal-title":"Nat. Commun."},{"key":"10.1016\/j.chom.2026.01.017_bib26","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1093\/procel\/pwae027","article-title":"High-throughput single-microbe RNA sequencing reveals adaptive state heterogeneity and host-phage activity associations in human gut microbiome","volume":"16","author":"Shen","year":"2025","journal-title":"Protein Cell"},{"key":"10.1016\/j.chom.2026.01.017_bib27","doi-asserted-by":"crossref","DOI":"10.1002\/imt2.70035","article-title":"Single-microbe RNA sequencing uncovers unexplored specialized metabolic functions of keystone species in the human gut","volume":"4","author":"Shen","year":"2025","journal-title":"Imeta"},{"key":"10.1016\/j.chom.2026.01.017_bib28","doi-asserted-by":"crossref","first-page":"1884","DOI":"10.1038\/s41564-024-01723-9","article-title":"Single-cell transcriptomics across 2,534 microbial species reveals functional heterogeneity in the rumen microbiome","volume":"9","author":"Jia","year":"2024","journal-title":"Nat. Microbiol."},{"key":"10.1016\/j.chom.2026.01.017_bib29","doi-asserted-by":"crossref","DOI":"10.1002\/imt2.23","article-title":"The sampling strategy of oral microbiome","volume":"1","author":"Lu","year":"2022","journal-title":"Imeta"},{"key":"10.1016\/j.chom.2026.01.017_bib30","doi-asserted-by":"crossref","first-page":"5473","DOI":"10.3390\/molecules25225473","article-title":"Exploitation of Ultrasound Technique for Enhancement of Microbial Metabolites Production","volume":"25","author":"Behzadnia","year":"2020","journal-title":"Molecules"},{"key":"10.1016\/j.chom.2026.01.017_bib31","doi-asserted-by":"crossref","first-page":"788","DOI":"10.1111\/jre.13408","article-title":"Metagenomic Insights Into the Subgingival Microbiome in Periodontal Health and Different Grades of Periodontitis","volume":"60","author":"Zhao","year":"2025","journal-title":"J. Periodont. Res."},{"key":"10.1016\/j.chom.2026.01.017_bib32","doi-asserted-by":"crossref","DOI":"10.1128\/msystems.00187-18","article-title":"New Insights into Human Nostril Microbiome from the Expanded Human Oral Microbiome Database (eHOMD): a Resource for the Microbiome of the Human Aerodigestive Tract","volume":"3","author":"Escapa","year":"2018","journal-title":"mSystems"},{"key":"10.1016\/j.chom.2026.01.017_bib33","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1186\/1471-2105-4-41","article-title":"The COG database: an updated version includes eukaryotes","volume":"4","author":"Tatusov","year":"2003","journal-title":"BMC Bioinformatics"},{"key":"10.1016\/j.chom.2026.01.017_bib34","doi-asserted-by":"crossref","first-page":"708","DOI":"10.1038\/s41586-024-07944-6","article-title":"A spatial human thymus cell atlas mapped to a continuous tissue axis","volume":"635","author":"Yayon","year":"2024","journal-title":"Nature"},{"key":"10.1016\/j.chom.2026.01.017_bib35","doi-asserted-by":"crossref","first-page":"699","DOI":"10.1038\/s41586-024-07571-1","article-title":"Single-cell integration reveals metaplasia in inflammatory gut diseases","volume":"635","author":"Oliver","year":"2024","journal-title":"Nature"},{"key":"10.1016\/j.chom.2026.01.017_bib36","article-title":"hdWGCNA identifies co-expression networks in high-dimensional transcriptomics data","volume":"3","author":"Morabito","year":"2023","journal-title":"Cell Rep. Methods"},{"key":"10.1016\/j.chom.2026.01.017_bib37","article-title":"A whole-cell platform for discovering synthetic cell adhesion molecules in bacteria","volume":"15","author":"Chen","year":"2024","journal-title":"Nat. Commun."},{"key":"10.1016\/j.chom.2026.01.017_bib38","article-title":"Functional diversity of the microbial community in healthy subjects and periodontitis patients based on sole carbon source utilization","volume":"9","author":"Zhang","year":"2014","journal-title":"PLoS One"},{"key":"10.1016\/j.chom.2026.01.017_bib39","doi-asserted-by":"crossref","first-page":"1787","DOI":"10.1099\/13500872-140-7-1787","article-title":"Lautropia mirabilis gen. nov., sp. nov., a gram-negative motile coccus with unusual morphology isolated from the human mouth","volume":"140","author":"Gerner-Smidt","year":"1994","journal-title":"Microbiology (Reading)"},{"key":"10.1016\/j.chom.2026.01.017_bib40","doi-asserted-by":"crossref","first-page":"4160","DOI":"10.1128\/JCM.39.11.4160-4162.2001","article-title":"Cellular fatty acid composition of Lautropia mirabilis","volume":"39","author":"Daneshvar","year":"2001","journal-title":"J. Clin. Microbiol."},{"key":"10.1016\/j.chom.2026.01.017_bib41","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0021373","article-title":"N. elongata produces type IV pili that mediate interspecies gene transfer with N. gonorrhoeae","volume":"6","author":"Higashi","year":"2011","journal-title":"PLoS One"},{"key":"10.1016\/j.chom.2026.01.017_bib42","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1099\/00221287-60-1-67","article-title":"Neisseria elongata sp.nov., a rod-shaped member of the genus Neisseria. Re-evaluation of cell shape as a criterion in classification","volume":"60","author":"Bovre","year":"1970","journal-title":"J. Gen. Microbiol."},{"key":"10.1016\/j.chom.2026.01.017_bib43","doi-asserted-by":"crossref","first-page":"659","DOI":"10.1128\/iai.42.2.659-667.1983","article-title":"Relationship between oxygen tension and subgingival bacterial flora in untreated human periodontal pockets","volume":"42","author":"Loesche","year":"1983","journal-title":"Infect. Immun."},{"key":"10.1016\/j.chom.2026.01.017_bib44","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1111\/omi.12409","article-title":"Metabolism of periodontal pathobionts: Their regulatory roles in the dysbiotic microbiota","volume":"38","author":"Ding","year":"2023","journal-title":"Mol. Oral Microbiol."},{"key":"10.1016\/j.chom.2026.01.017_bib45","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1111\/j.1600-0757.2005.00107.x","article-title":"Periodontal microbial ecology","volume":"38","author":"Socransky","year":"2005","journal-title":"Periodontol. 2000"},{"key":"10.1016\/j.chom.2026.01.017_bib46","doi-asserted-by":"crossref","DOI":"10.1080\/20002297.2020.1808750","article-title":"Metabolic cooperativity between Porphyromonas gingivalis and Treponema denticola","volume":"12","author":"Kin","year":"2020","journal-title":"J. Oral Microbiol."},{"key":"10.1016\/j.chom.2026.01.017_bib47","doi-asserted-by":"crossref","DOI":"10.3389\/fcimb.2022.987683","article-title":"Implications of Porphyromonas gingivalis peptidyl arginine deiminase and gingipain R in human health and diseases","volume":"12","author":"Chow","year":"2022","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"10.1016\/j.chom.2026.01.017_bib48","doi-asserted-by":"crossref","first-page":"293","DOI":"10.1111\/febs.15337","article-title":"Enzymology of the pathway for ATP production by arginine breakdown","volume":"288","author":"Pols","year":"2021","journal-title":"FEBS J."},{"key":"10.1016\/j.chom.2026.01.017_bib49","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1003955","article-title":"Porphyromonas gingivalis and Treponema denticola exhibit metabolic symbioses","volume":"10","author":"Tan","year":"2014","journal-title":"PLoS Pathog."},{"key":"10.1016\/j.chom.2026.01.017_bib50","doi-asserted-by":"crossref","first-page":"616","DOI":"10.1128\/jb.128.2.616-622.1976","article-title":"Arginine catabolism by Treponema denticola","volume":"128","author":"Blakemore","year":"1976","journal-title":"J. Bacteriol."},{"key":"10.1016\/j.chom.2026.01.017_bib51","doi-asserted-by":"crossref","first-page":"160","DOI":"10.1038\/s41596-025-01181-5","article-title":"Single microorganism RNA sequencing of microbiomes using smRandom-Seq","volume":"21","author":"Xu","year":"2025","journal-title":"Nat. Protoc."},{"key":"10.1016\/j.chom.2026.01.017_bib52","doi-asserted-by":"crossref","first-page":"74","DOI":"10.1038\/s41522-025-00708-8","article-title":"Oral microbiome-derived biomarkers for non-invasive diagnosis of head and neck squamous cell carcinoma","volume":"11","author":"Zhi","year":"2025","journal-title":"NPJ Biofilms Microbiomes"},{"key":"10.1016\/j.chom.2026.01.017_bib53","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1038\/nature11234","article-title":"Structure, function and diversity of the healthy human microbiome","volume":"486","year":"2012","journal-title":"Nature"},{"key":"10.1016\/j.chom.2026.01.017_bib54","doi-asserted-by":"crossref","first-page":"42","DOI":"10.1186\/s40168-018-0426-3","article-title":"Improving saliva shotgun metagenomics by chemical host DNA depletion","volume":"6","author":"Marotz","year":"2018","journal-title":"Microbiome"},{"key":"10.1016\/j.chom.2026.01.017_bib55","doi-asserted-by":"crossref","first-page":"1431","DOI":"10.1038\/s41564-025-02013-8","article-title":"Secretory IgM regulates gut microbiota homeostasis and metabolism","volume":"10","author":"Ding","year":"2025","journal-title":"Nat. Microbiol."},{"key":"10.1016\/j.chom.2026.01.017_bib56","doi-asserted-by":"crossref","first-page":"1421","DOI":"10.1902\/jop.2009.090185","article-title":"Comparisons of subgingival microbial profiles of refractory periodontitis, severe periodontitis, and periodontal health using the human oral microbe identification microarray","volume":"80","author":"Colombo","year":"2009","journal-title":"J. Periodontol."},{"key":"10.1016\/j.chom.2026.01.017_bib57","doi-asserted-by":"crossref","first-page":"927","DOI":"10.1177\/0022034512456039","article-title":"Microbiological characterization in children with aggressive periodontitis","volume":"91","author":"Shaddox","year":"2012","journal-title":"J. Dent. Res."},{"key":"10.1016\/j.chom.2026.01.017_bib58","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1111\/prd.12362","article-title":"Microbial signatures of health, gingivitis, and periodontitis","volume":"86","author":"Abusleme","year":"2021","journal-title":"Periodontol. 2000"},{"key":"10.1016\/j.chom.2026.01.017_bib59","doi-asserted-by":"crossref","DOI":"10.1016\/j.foodchem.2020.128328","article-title":"Prebiotic mannooligosaccharides: Synthesis, characterization and bioactive properties","volume":"342","author":"Jana","year":"2021","journal-title":"Food Chem."},{"key":"10.1016\/j.chom.2026.01.017_bib60","doi-asserted-by":"crossref","DOI":"10.3389\/fnut.2022.798543","article-title":"Mango Pectic Oligosaccharides: A Novel Prebiotic for Functional Food","volume":"9","author":"Wongkaew","year":"2022","journal-title":"Front. Nutr."},{"key":"10.1016\/j.chom.2026.01.017_bib61","doi-asserted-by":"crossref","first-page":"1078","DOI":"10.1111\/jcpe.12987","article-title":"Effects of the prebiotic mannan oligosaccharide on the experimental periodontitis in rats","volume":"45","author":"Levi","year":"2018","journal-title":"J. Clin. Periodontol."},{"key":"10.1016\/j.chom.2026.01.017_bib62","first-page":"609","article-title":"Commensal Neisseria inhibit Porphyromonas gingivalis invasion of gingival epithelial cells","volume":"22","author":"Fukuda","year":"2024","journal-title":"Oral Health Prev. Dent."},{"key":"10.1016\/j.chom.2026.01.017_bib63","article-title":"Commensal Neisseria species share immune suppressive mechanisms with Neisseria gonorrhoeae","volume":"18","author":"Zhu","year":"2023","journal-title":"PLoS One"},{"key":"10.1016\/j.chom.2026.01.017_bib64","doi-asserted-by":"crossref","DOI":"10.1126\/science.adr0932","article-title":"Highly multiplexed spatial transcriptomics in bacteria","volume":"387","author":"Sarfatis","year":"2025","journal-title":"Science"},{"key":"10.1016\/j.chom.2026.01.017_bib65","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1111\/prd.12107","article-title":"Gingival crevicular fluid as a source of biomarkers for periodontitis","volume":"70","author":"Barros","year":"2016","journal-title":"Periodontol. 2000"},{"key":"10.1016\/j.chom.2026.01.017_bib66","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1111\/prd.12154","article-title":"Gingival crevicular fluid and its immune mediators in the proteomic era","volume":"76","author":"Bostanci","year":"2018","journal-title":"Periodontol. 2000"},{"key":"10.1016\/j.chom.2026.01.017_bib67","doi-asserted-by":"crossref","first-page":"2426","DOI":"10.3390\/nu14122426","article-title":"A cross-talk between diet and the oral microbiome: balance of nutrition on inflammation and immune system\u2019s response during periodontitis","volume":"14","author":"Santonocito","year":"2022","journal-title":"Nutrients"},{"key":"10.1016\/j.chom.2026.01.017_bib68","doi-asserted-by":"crossref","first-page":"9982","DOI":"10.1073\/pnas.0506824104","article-title":"Receptor-mediated activation of nitric oxide synthesis by arginine in endothelial cells","volume":"104","author":"Joshi","year":"2007","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.chom.2026.01.017_bib69","doi-asserted-by":"crossref","first-page":"320","DOI":"10.1902\/jop.2010.100199","article-title":"Arginine-nitric oxide-polyamine metabolism in periodontal disease","volume":"82","author":"Ozer","year":"2011","journal-title":"J. Periodontol."},{"key":"10.1016\/j.chom.2026.01.017_bib70","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1016\/j.neulet.2009.03.093","article-title":"Activation of I2-imidazoline receptors by agmatine improved insulin sensitivity through two mechanisms in type-2 diabetic rats","volume":"457","author":"Su","year":"2009","journal-title":"Neurosci. Lett."},{"key":"10.1016\/j.chom.2026.01.017_bib71","doi-asserted-by":"crossref","first-page":"13844","DOI":"10.1073\/pnas.241443798","article-title":"Helicobacter pylori arginase inhibits nitric oxide production by eukaryotic cells: a strategy for bacterial survival","volume":"98","author":"Gobert","year":"2001","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.chom.2026.01.017_bib72","doi-asserted-by":"crossref","first-page":"1628","DOI":"10.1177\/0022034515606045","article-title":"Oral Microbiome Metabolism: From \u201cWho Are They?\u201d to \u201cWhat Are They Doing?\u201d","volume":"94","author":"Takahashi","year":"2015","journal-title":"J. Dent. Res."},{"key":"10.1016\/j.chom.2026.01.017_bib73","doi-asserted-by":"crossref","first-page":"541","DOI":"10.1007\/s00018-013-1527-6","article-title":"Urocanate as a potential signaling molecule for bacterial recognition of eukaryotic hosts","volume":"71","author":"Zhang","year":"2014","journal-title":"Cell. Mol. Life Sci."},{"key":"10.1016\/j.chom.2026.01.017_bib74","doi-asserted-by":"crossref","first-page":"2051","DOI":"10.1016\/j.dental.2024.09.011","article-title":"Matrix metalloproteinases in dentin: Assessing their presence, activity, and inhibitors - a review of current trends","volume":"40","author":"Anumula","year":"2024","journal-title":"Dent. Mater."},{"key":"10.1016\/j.chom.2026.01.017_bib75","doi-asserted-by":"crossref","DOI":"10.3389\/froh.2023.1210200","article-title":"Microbial metabolites in the pathogenesis of periodontal diseases: a narrative review","volume":"4","author":"Basic","year":"2023","journal-title":"Front. Oral Health"},{"key":"10.1016\/j.chom.2026.01.017_bib76","doi-asserted-by":"crossref","first-page":"371","DOI":"10.1038\/s41423-025-01271-0","article-title":"Inflammation-triggered Gli1+ stem cells engage with extracellular vesicles to prime aberrant neutrophils to exacerbate periodontal immunopathology","volume":"22","author":"Cai","year":"2025","journal-title":"Cell. Mol. Immunol."},{"key":"10.1016\/j.chom.2026.01.017_bib77","doi-asserted-by":"crossref","first-page":"234","DOI":"10.1007\/BF00424897","article-title":"Amino acid and glucose fermentation by Treponema denticola","volume":"78","author":"Hespell","year":"1971","journal-title":"Arch. Mikrobiol."},{"key":"10.1016\/j.chom.2026.01.017_bib78","doi-asserted-by":"crossref","first-page":"147","DOI":"10.1007\/BF01573470","article-title":"Chemically defined and minimal media forBacteroides gingivalis","volume":"17","author":"Seddon","year":"1988","journal-title":"Curr. Microbiol."},{"key":"10.1016\/j.chom.2026.01.017_bib79","article-title":"Preferential dipeptide incorporation of Porphyromonas gingivalis mediated by proton-dependent oligopeptide transporter (Pot)","volume":"367","author":"Ohara-Nemoto","year":"2020","journal-title":"FEMS Microbiol. Lett."},{"key":"10.1016\/j.chom.2026.01.017_bib80","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1111\/omi.12317","article-title":"Dipeptidyl-peptidases: Key enzymes producing entry forms of extracellular proteins in asaccharolytic periodontopathic bacterium Porphyromonas gingivalis","volume":"36","author":"Nemoto","year":"2021","journal-title":"Mol. Oral Microbiol."},{"key":"10.1016\/j.chom.2026.01.017_bib81","doi-asserted-by":"crossref","first-page":"255","DOI":"10.1038\/nature17626","article-title":"The evolution of cooperation within the gut microbiota","volume":"533","author":"Rakoff-Nahoum","year":"2016","journal-title":"Nature"},{"key":"10.1016\/j.chom.2026.01.017_bib82","doi-asserted-by":"crossref","first-page":"1658","DOI":"10.1093\/bioinformatics\/btl158","article-title":"Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences","volume":"22","author":"Li","year":"2006","journal-title":"Bioinformatics"},{"key":"10.1016\/j.chom.2026.01.017_bib83","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","article-title":"STAR: ultrafast universal RNA-seq aligner","volume":"29","author":"Dobin","year":"2013","journal-title":"Bioinformatics"},{"key":"10.1016\/j.chom.2026.01.017_bib84","doi-asserted-by":"crossref","first-page":"366","DOI":"10.1038\/s41592-021-01101-x","article-title":"Sensitive protein alignments at tree-of-life scale using DIAMOND","volume":"18","author":"Buchfink","year":"2021","journal-title":"Nat. Methods"},{"key":"10.1016\/j.chom.2026.01.017_bib85","doi-asserted-by":"crossref","first-page":"2815","DOI":"10.1038\/s41596-022-00738-y","article-title":"Metagenome analysis using the Kraken software suite","volume":"17","author":"Lu","year":"2022","journal-title":"Nat. Protoc."},{"key":"10.1016\/j.chom.2026.01.017_bib86","doi-asserted-by":"crossref","DOI":"10.7717\/peerj-cs.104","article-title":"Bracken: estimating species abundance in metagenomics data","volume":"3","author":"Lu","year":"2017","journal-title":"PeerJ Comput. Sci."},{"key":"10.1016\/j.chom.2026.01.017_bib87","doi-asserted-by":"crossref","DOI":"10.1093\/gigascience\/giy083","article-title":"Clustering trees: a visualization for evaluating clusterings at multiple resolutions","volume":"7","author":"Zappia","year":"2018","journal-title":"GigaScience"},{"key":"10.1016\/j.chom.2026.01.017_bib88","doi-asserted-by":"crossref","first-page":"3573","DOI":"10.1016\/j.cell.2021.04.048","article-title":"Integrated analysis of multimodal single-cell data","volume":"184","author":"Hao","year":"2021","journal-title":"Cell"},{"key":"10.1016\/j.chom.2026.01.017_bib89","doi-asserted-by":"crossref","first-page":"1289","DOI":"10.1038\/s41592-019-0619-0","article-title":"Fast, sensitive and accurate integration of single-cell data with Harmony","volume":"16","author":"Korsunsky","year":"2019","journal-title":"Nat. Methods"},{"key":"10.1016\/j.chom.2026.01.017_bib90","doi-asserted-by":"crossref","DOI":"10.1038\/s41467-020-19894-4","article-title":"muscat detects subpopulation-specific state transitions from multi-sample multi-condition single-cell transcriptomics data","volume":"11","author":"Crowell","year":"2020","journal-title":"Nat. Commun."},{"key":"10.1016\/j.chom.2026.01.017_bib91","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1038\/nbt.2859","article-title":"The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells","volume":"32","author":"Trapnell","year":"2014","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.chom.2026.01.017_bib92","doi-asserted-by":"crossref","first-page":"3292","DOI":"10.1038\/s41596-024-01020-z","article-title":"Using clusterProfiler to characterize multiomics data","volume":"19","author":"Xu","year":"2024","journal-title":"Nat. Protoc."},{"key":"10.1016\/j.chom.2026.01.017_bib93","doi-asserted-by":"crossref","first-page":"W6","DOI":"10.1093\/nar\/gkl164","article-title":"BLAST: improvements for better sequence analysis","volume":"34","author":"Ye","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.chom.2026.01.017_bib94","doi-asserted-by":"crossref","first-page":"626","DOI":"10.1007\/s11427-022-2172-x","article-title":"SecReT6 update: a comprehensive resource of bacterial Type VI Secretion Systems","volume":"66","author":"Zhang","year":"2023","journal-title":"Sci. China Life Sci."},{"key":"10.1016\/j.chom.2026.01.017_bib95","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1093\/bioinformatics\/btn578","article-title":"DNAPlotter: circular and linear interactive genome visualization","volume":"25","author":"Carver","year":"2009","journal-title":"Bioinformatics"},{"key":"10.1016\/j.chom.2026.01.017_bib96","doi-asserted-by":"crossref","first-page":"121","DOI":"10.3109\/00016356408993968","article-title":"Periodontal Disease in Pregnancy. Ii. Correlation Between Oral Hygiene and Periodontal Condtion","volume":"22","author":"Silness","year":"1964","journal-title":"Acta Odontol. Scand."},{"key":"10.1016\/j.chom.2026.01.017_bib97","doi-asserted-by":"crossref","first-page":"S162","DOI":"10.1111\/jcpe.12946","article-title":"Periodontitis: Consensus report of workgroup 2 of the 2017 World Workshop on the Classification of Periodontal and Peri-Implant Diseases and Conditions","volume":"45","author":"Papapanou","year":"2018","journal-title":"J. Clin. Periodontol."},{"key":"10.1016\/j.chom.2026.01.017_bib98","doi-asserted-by":"crossref","first-page":"905","DOI":"10.1111\/jcpe.13793","article-title":"Subgingival microbiome in periodontal health, gingivitis and different stages of periodontitis","volume":"50","author":"Iniesta","year":"2023","journal-title":"J. Clin. Periodontol."},{"key":"10.1016\/j.chom.2026.01.017_bib99","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","article-title":"BEDTools: a flexible suite of utilities for comparing genomic features","volume":"26","author":"Quinlan","year":"2010","journal-title":"Bioinformatics"},{"key":"10.1016\/j.chom.2026.01.017_bib100","doi-asserted-by":"crossref","first-page":"2848","DOI":"10.1093\/bioinformatics\/btab216","article-title":"A critical assessment of gene catalogs for metagenomic analysis","volume":"37","author":"Commichaux","year":"2021","journal-title":"Bioinformatics"},{"key":"10.1016\/j.chom.2026.01.017_bib101","doi-asserted-by":"crossref","DOI":"10.1038\/s41598-020-61942-y","article-title":"Co-abundance analysis reveals hidden players associated with high methane yield phenotype in sheep rumen microbiome","volume":"10","author":"Ghanbari Maman","year":"2020","journal-title":"Sci. Rep."},{"key":"10.1016\/j.chom.2026.01.017_bib102","doi-asserted-by":"crossref","first-page":"D274","DOI":"10.1093\/nar\/gkaa1018","article-title":"COG database update: focus on microbial diversity, model organisms, and widespread pathogens","volume":"49","author":"Galperin","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.chom.2026.01.017_bib103","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1089\/cmb.2012.0021","article-title":"SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing","volume":"19","author":"Bankevich","year":"2012","journal-title":"J. Comput. Biol."},{"key":"10.1016\/j.chom.2026.01.017_bib104","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1093\/nar\/28.1.45","article-title":"The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000","volume":"28","author":"Bairoch","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.chom.2026.01.017_bib105","doi-asserted-by":"crossref","first-page":"1421","DOI":"10.1007\/s00253-015-7039-6","article-title":"Denitrifying sulfide removal process on high-salinity wastewaters in the presence of Halomonas sp","volume":"100","author":"Liu","year":"2016","journal-title":"Appl. Microbiol. Biotechnol."},{"key":"10.1016\/j.chom.2026.01.017_bib106","doi-asserted-by":"crossref","first-page":"581","DOI":"10.1038\/nmeth.3869","article-title":"DADA2: High-resolution sample inference from Illumina amplicon data","volume":"13","author":"Callahan","year":"2016","journal-title":"Nat. Methods"},{"key":"10.1016\/j.chom.2026.01.017_bib107","doi-asserted-by":"crossref","first-page":"852","DOI":"10.1038\/s41587-019-0209-9","article-title":"Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2","volume":"37","author":"Bolyen","year":"2019","journal-title":"Nat. Biotechnol."}],"container-title":["Cell Host &amp; Microbe"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1931312826000429?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1931312826000429?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,8,25]],"date-time":"2026-08-25T04:18:41Z","timestamp":1787631521000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S1931312826000429"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,3]]},"references-count":107,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2026,3]]}},"alternative-id":["S1931312826000429"],"URL":"https:\/\/doi.org\/10.1016\/j.chom.2026.01.017","relation":{},"ISSN":["1931-3128"],"issn-type":[{"value":"1931-3128","type":"print"}],"subject":[],"published":{"date-parts":[[2026,3]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Single-cell profiling of the subgingival bacteria reveals transcriptional heterogeneity and niche-specific programs","name":"articletitle","label":"Article Title"},{"value":"Cell Host & Microbe","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.chom.2026.01.017","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2026 Elsevier Inc. All rights are reserved, including those for text and data mining, AI training, and similar technologies.","name":"copyright","label":"Copyright"}]}}