{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,22]],"date-time":"2026-10-22T05:37:27Z","timestamp":1792647447671,"version":"4.5.0"},"reference-count":132,"publisher":"Elsevier BV","issue":"11","license":[{"start":{"date-parts":[[2025,11,1]],"date-time":"2025-11-01T00:00:00Z","timestamp":1761955200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2025,11,1]],"date-time":"2025-11-01T00:00:00Z","timestamp":1761955200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2025,11,1]],"date-time":"2025-11-01T00:00:00Z","timestamp":1761955200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-017"},{"start":{"date-parts":[[2025,11,1]],"date-time":"2025-11-01T00:00:00Z","timestamp":1761955200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2025,11,1]],"date-time":"2025-11-01T00:00:00Z","timestamp":1761955200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-012"},{"start":{"date-parts":[[2025,11,1]],"date-time":"2025-11-01T00:00:00Z","timestamp":1761955200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2025,11,1]],"date-time":"2025-11-01T00:00:00Z","timestamp":1761955200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-004"}],"funder":[{"DOI":"10.13039\/501100003052","name":"Korea Ministry of Trade Industry and Energy","doi-asserted-by":"publisher","award":["20022947"],"award-info":[{"award-number":["20022947"]}],"id":[{"id":"10.13039\/501100003052","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003725","name":"National Research Foundation of Korea","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100003725","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100014188","name":"Korea Ministry of Science and ICT","doi-asserted-by":"publisher","award":["2022M3A9F3016364"],"award-info":[{"award-number":["2022M3A9F3016364"]}],"id":[{"id":"10.13039\/501100014188","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100014188","name":"Korea Ministry of Science and ICT","doi-asserted-by":"publisher","award":["2022R1A2C1092062"],"award-info":[{"award-number":["2022R1A2C1092062"]}],"id":[{"id":"10.13039\/501100014188","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":[[2025,11]]},"DOI":"10.1016\/j.chom.2025.10.001","type":"journal-article","created":{"date-parts":[[2025,10,29]],"date-time":"2025-10-29T14:35:00Z","timestamp":1761748500000},"page":"1977-1994.e8","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":22,"title":["A high-quality genomic catalog of the human oral microbiome broadens its phylogeny and clinical insights"],"prefix":"10.1016","volume":"33","author":[{"given":"Jun Hyung","family":"Cha","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nayeon","family":"Kim","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Junyeong","family":"Ma","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sungho","family":"Lee","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Geon","family":"Koh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sunmo","family":"Yang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Samuel","family":"Beck","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Iksu","family":"Byeon","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Byungwook","family":"Lee","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3146-6180","authenticated-orcid":false,"given":"Insuk","family":"Lee","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.chom.2025.10.001_bib1","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1038\/s41579-023-00963-6","article-title":"The oral microbiome: diversity, biogeography and human health","volume":"22","author":"Baker","year":"2024","journal-title":"Nat. Rev. Microbiol."},{"key":"10.1016\/j.chom.2025.10.001_bib2","doi-asserted-by":"crossref","first-page":"745","DOI":"10.1038\/s41579-018-0089-x","article-title":"The oral microbiota: dynamic communities and host interactions","volume":"16","author":"Lamont","year":"2018","journal-title":"Nat. Rev. Microbiol."},{"key":"10.1016\/j.chom.2025.10.001_bib3","doi-asserted-by":"crossref","DOI":"10.1038\/s41368-022-00163-7","article-title":"Oral microbiota in human systematic diseases","volume":"14","author":"Peng","year":"2022","journal-title":"Int. J. Oral Sci."},{"key":"10.1016\/j.chom.2025.10.001_bib4","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.2025.10.001_bib5","doi-asserted-by":"crossref","first-page":"1501","DOI":"10.1038\/s12276-024-01262-7","article-title":"Genome-resolved metagenomics: a game changer for microbiome medicine","volume":"56","author":"Kim","year":"2024","journal-title":"Exp. Mol. Med."},{"key":"10.1016\/j.chom.2025.10.001_bib6","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1038\/s41587-020-0603-3","article-title":"A unified catalog of 204,938 reference genomes from the human gut microbiome","volume":"39","author":"Almeida","year":"2021","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.chom.2025.10.001_bib7","doi-asserted-by":"crossref","DOI":"10.1186\/s13073-021-00950-7","article-title":"Human reference gut microbiome catalog including newly assembled genomes from under-represented Asian metagenomes","volume":"13","author":"Kim","year":"2021","journal-title":"Genome Med."},{"key":"10.1016\/j.chom.2025.10.001_bib8","doi-asserted-by":"crossref","DOI":"10.1186\/s40168-021-01114-w","article-title":"HumGut: a comprehensive human gut prokaryotic genomes collection filtered by metagenome data","volume":"9","author":"Hiseni","year":"2021","journal-title":"Microbiome"},{"key":"10.1016\/j.chom.2025.10.001_bib9","doi-asserted-by":"crossref","first-page":"246","DOI":"10.1016\/j.gpb.2021.05.001","article-title":"Over 50,000 Metagenomically Assembled Draft Genomes for the Human Oral Microbiome Reveal New Taxa","volume":"20","author":"Zhu","year":"2022","journal-title":"Genomics Proteomics Bioinformatics"},{"key":"10.1016\/j.chom.2025.10.001_bib10","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.2025.10.001_bib11","doi-asserted-by":"crossref","first-page":"629","DOI":"10.1038\/s41579-018-0076-2","article-title":"Biosynthetic capacity, metabolic variety and unusual biology in the CPR and DPANN radiations","volume":"16","author":"Castelle","year":"2018","journal-title":"Nat. Rev. Microbiol."},{"key":"10.1016\/j.chom.2025.10.001_bib12","doi-asserted-by":"crossref","first-page":"D92","DOI":"10.1093\/nar\/gkad1067","article-title":"The European Nucleotide Archive in 2023","volume":"52","author":"Yuan","year":"2024","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.chom.2025.10.001_bib13","doi-asserted-by":"crossref","first-page":"D387","DOI":"10.1093\/nar\/gkab1053","article-title":"The Sequence Read Archive: a decade more of explosive growth","volume":"50","author":"Katz","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.chom.2025.10.001_bib14","first-page":"799","article-title":"CNGBdb: China National GeneBank DataBase","volume":"42","author":"Chen","year":"2020","journal-title":"Yi Chuan"},{"key":"10.1016\/j.chom.2025.10.001_bib15","doi-asserted-by":"crossref","first-page":"D92","DOI":"10.1093\/nar\/gkaa1023","article-title":"GenBank","volume":"49","author":"Sayers","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.chom.2025.10.001_bib16","doi-asserted-by":"crossref","first-page":"D1020","DOI":"10.1093\/nar\/gkaa1105","article-title":"RefSeq: expanding the Prokaryotic Genome Annotation Pipeline reach with protein family model curation","volume":"49","author":"Li","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.chom.2025.10.001_bib17","first-page":"D606","article-title":"The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities","volume":"48","author":"Davis","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.chom.2025.10.001_bib18","doi-asserted-by":"crossref","first-page":"1043","DOI":"10.1101\/gr.186072.114","article-title":"CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes","volume":"25","author":"Parks","year":"2015","journal-title":"Genome Res."},{"key":"10.1016\/j.chom.2025.10.001_bib19","doi-asserted-by":"crossref","first-page":"208","DOI":"10.1038\/nature14486","article-title":"Unusual biology across a group comprising more than 15% of domain Bacteria","volume":"523","author":"Brown","year":"2015","journal-title":"Nature"},{"key":"10.1016\/j.chom.2025.10.001_bib20","doi-asserted-by":"crossref","first-page":"1203","DOI":"10.1038\/s41592-023-01940-w","article-title":"CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning","volume":"20","author":"Chklovski","year":"2023","journal-title":"Nat. Methods"},{"key":"10.1016\/j.chom.2025.10.001_bib21","doi-asserted-by":"crossref","DOI":"10.1186\/s13059-021-02393-0","article-title":"GUNC: detection of chimerism and contamination in prokaryotic genomes","volume":"22","author":"Orakov","year":"2021","journal-title":"Genome Biol."},{"key":"10.1016\/j.chom.2025.10.001_bib22","doi-asserted-by":"crossref","first-page":"5315","DOI":"10.1093\/bioinformatics\/btac672","article-title":"GTDB-Tk v2: memory friendly classification with the genome taxonomy database","volume":"38","author":"Chaumeil","year":"2022","journal-title":"Bioinformatics"},{"key":"10.1016\/j.chom.2025.10.001_bib23","doi-asserted-by":"crossref","DOI":"10.1038\/s41522-023-00414-3","article-title":"A catalog of bacterial reference genomes from cultivated human oral bacteria","volume":"9","author":"Li","year":"2023","journal-title":"NPJ Biofilms Microbiomes"},{"key":"10.1016\/j.chom.2025.10.001_bib24","doi-asserted-by":"crossref","first-page":"D753","DOI":"10.1093\/nar\/gkac1080","article-title":"MGnify: the microbiome sequence data analysis resource in 2023","volume":"51","author":"Richardson","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.chom.2025.10.001_bib25","doi-asserted-by":"crossref","DOI":"10.1186\/s13059-019-1891-0","article-title":"Improved metagenomic analysis with Kraken 2","volume":"20","author":"Wood","year":"2019","journal-title":"Genome Biol."},{"key":"10.1016\/j.chom.2025.10.001_bib26","doi-asserted-by":"crossref","first-page":"1633","DOI":"10.1038\/s41587-023-01688-w","article-title":"Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4","volume":"41","author":"Blanco-M\u00edguez","year":"2023","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.chom.2025.10.001_bib27","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.2025.10.001_bib28","doi-asserted-by":"crossref","first-page":"618","DOI":"10.1038\/s41592-021-01141-3","article-title":"Challenges in benchmarking metagenomic profilers","volume":"18","author":"Sun","year":"2021","journal-title":"Nat. Methods"},{"key":"10.1016\/j.chom.2025.10.001_bib29","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1002608","article-title":"The accessory genome as a cradle for adaptive evolution in pathogens","volume":"8","author":"Croll","year":"2012","journal-title":"PLOS Pathog."},{"key":"10.1016\/j.chom.2025.10.001_bib30","doi-asserted-by":"crossref","DOI":"10.1038\/nmicrobiol.2016.48","article-title":"A new view of the tree of life","volume":"1","author":"Hug","year":"2016","journal-title":"Nat. Microbiol."},{"key":"10.1016\/j.chom.2025.10.001_bib31","doi-asserted-by":"crossref","first-page":"1533","DOI":"10.1038\/s41564-017-0012-7","article-title":"Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life","volume":"2","author":"Parks","year":"2017","journal-title":"Nat. Microbiol."},{"key":"10.1016\/j.chom.2025.10.001_bib32","doi-asserted-by":"crossref","first-page":"996","DOI":"10.1038\/nbt.4229","article-title":"A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life","volume":"36","author":"Parks","year":"2018","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.chom.2025.10.001_bib33","doi-asserted-by":"crossref","first-page":"243","DOI":"10.1007\/s00248-015-0711-7","article-title":"Phenotypic and Physiological Characterization of the Epibiotic Interaction Between TM7x and Its Basibiont Actinomyces","volume":"71","author":"Bor","year":"2016","journal-title":"Microb. Ecol."},{"key":"10.1016\/j.chom.2025.10.001_bib34","doi-asserted-by":"crossref","DOI":"10.1128\/cmr.00140-21","article-title":"Candidate Phyla Radiation, an Underappreciated Division of the Human Microbiome, and Its Impact on Health and Disease","volume":"35","author":"Naud","year":"2022","journal-title":"Clin. Microbiol. Rev."},{"key":"10.1016\/j.chom.2025.10.001_bib35","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1038\/s41564-022-01257-y","article-title":"Ancient origin and constrained evolution of the division and cell wall gene cluster in Bacteria","volume":"7","author":"Megrian","year":"2022","journal-title":"Nat. Microbiol."},{"key":"10.1016\/j.chom.2025.10.001_bib36","doi-asserted-by":"crossref","first-page":"500","DOI":"10.1177\/0022034519831671","article-title":"Saccharibacteria (TM7) in the Human Oral Microbiome","volume":"98","author":"Bor","year":"2019","journal-title":"J. Dent. Res."},{"key":"10.1016\/j.chom.2025.10.001_bib37","doi-asserted-by":"crossref","DOI":"10.1038\/s41467-019-12171-z","article-title":"The distinction of CPR bacteria from other bacteria based on protein family content","volume":"10","author":"M\u00e9heust","year":"2019","journal-title":"Nat. Commun."},{"key":"10.1016\/j.chom.2025.10.001_bib38","doi-asserted-by":"crossref","first-page":"2757","DOI":"10.1099\/mic.0.040196-0","article-title":"Role of Vibrio polysaccharide (vps) genes in VPS production, biofilm formation and Vibrio cholerae pathogenesis","volume":"156","author":"Fong","year":"2010","journal-title":"Microbiology (Reading)"},{"key":"10.1016\/j.chom.2025.10.001_bib39","doi-asserted-by":"crossref","first-page":"5147","DOI":"10.1128\/JB.00401-09","article-title":"Overexpression of VpsS, a hybrid sensor kinase, enhances biofilm formation in Vibrio cholerae","volume":"191","author":"Shikuma","year":"2009","journal-title":"J. Bacteriol."},{"key":"10.1016\/j.chom.2025.10.001_bib40","article-title":"Resuscitation-Promoting Factors Are Required for Mycobacterium smegmatis Biofilm Formation","volume":"84","author":"Ealand","year":"2018","journal-title":"Appl. Environ. Microbiol."},{"key":"10.1016\/j.chom.2025.10.001_bib41","doi-asserted-by":"crossref","first-page":"153","DOI":"10.1016\/j.jmb.2008.10.042","article-title":"Crystal structure of the resuscitation-promoting factor (DeltaDUF)RpfB from M. tuberculosis","volume":"385","author":"Ruggiero","year":"2009","journal-title":"J. Mol. Biol."},{"key":"10.1016\/j.chom.2025.10.001_bib42","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1007074","article-title":"Pseudomonas aeruginosa type IV minor pilins and PilY1 regulate virulence by modulating FimS-AlgR activity","volume":"14","author":"Marko","year":"2018","journal-title":"PLOS Pathog."},{"key":"10.1016\/j.chom.2025.10.001_bib43","doi-asserted-by":"crossref","first-page":"4285","DOI":"10.1128\/JB.00803-12","article-title":"Type IV pilus assembly in Pseudomonas aeruginosa over a broad range of cyclic di-GMP concentrations","volume":"194","author":"Jain","year":"2012","journal-title":"J. Bacteriol."},{"key":"10.1016\/j.chom.2025.10.001_bib44","doi-asserted-by":"crossref","first-page":"2331","DOI":"10.1111\/j.1462-2920.2008.01658.x","article-title":"Roles of type IV pili, flagellum-mediated motility and extracellular DNA in the formation of mature multicellular structures in Pseudomonas aeruginosa biofilms","volume":"10","author":"Barken","year":"2008","journal-title":"Environ. Microbiol."},{"key":"10.1016\/j.chom.2025.10.001_bib45","doi-asserted-by":"crossref","DOI":"10.1093\/femspd\/ftw061","article-title":"Type IV pili promote early biofilm formation by Clostridium difficile","volume":"74","author":"Maldarelli","year":"2016","journal-title":"Pathog. Dis."},{"key":"10.1016\/j.chom.2025.10.001_bib46","doi-asserted-by":"crossref","first-page":"6783","DOI":"10.1128\/AEM.00974-09","article-title":"Conjugative plasmid transfer and adhesion dynamics in an Escherichia coli biofilm","volume":"75","author":"Ong","year":"2009","journal-title":"Appl. Environ. Microbiol."},{"key":"10.1016\/j.chom.2025.10.001_bib47","doi-asserted-by":"crossref","first-page":"354","DOI":"10.1038\/s41564-020-00840-5","article-title":"Genome-resolved metagenomics reveals site-specific diversity of episymbiotic CPR bacteria and DPANN archaea in groundwater ecosystems","volume":"6","author":"He","year":"2021","journal-title":"Nat. Microbiol."},{"key":"10.1016\/j.chom.2025.10.001_bib48","doi-asserted-by":"crossref","DOI":"10.1016\/j.celrep.2020.107939","article-title":"Acquisition and Adaptation of Ultra-small Parasitic Reduced Genome Bacteria to Mammalian Hosts","volume":"32","author":"McLean","year":"2020","journal-title":"Cell Rep."},{"key":"10.1016\/j.chom.2025.10.001_bib49","doi-asserted-by":"crossref","DOI":"10.1002\/mbo3.412","article-title":"Convergent evolution of the arginine deiminase pathway: the ArcD and ArcE arginine\/ornithine exchangers","volume":"6","author":"Noens","year":"2017","journal-title":"MicrobiologyOpen"},{"key":"10.1016\/j.chom.2025.10.001_bib50","doi-asserted-by":"crossref","first-page":"4803","DOI":"10.1016\/j.cell.2023.08.017","article-title":"Genetic manipulation of Patescibacteria provides mechanistic insights into microbial dark matter and the epibiotic lifestyle","volume":"186","author":"Wang","year":"2023","journal-title":"Cell"},{"key":"10.1016\/j.chom.2025.10.001_bib51","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.2215990119","article-title":"Type IV pili trigger episymbiotic association of Saccharibacteria with its bacterial host","volume":"119","author":"Xie","year":"2022","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.chom.2025.10.001_bib52","doi-asserted-by":"crossref","first-page":"1471","DOI":"10.1128\/JB.01293-13","article-title":"Natural competence and the evolution of DNA uptake specificity","volume":"196","author":"Mell","year":"2014","journal-title":"J. Bacteriol."},{"key":"10.1016\/j.chom.2025.10.001_bib53","doi-asserted-by":"crossref","first-page":"1123","DOI":"10.1126\/science.ade2574","article-title":"Evolutionary-scale prediction of atomic-level protein structure with a language model","volume":"379","author":"Lin","year":"2023","journal-title":"Science"},{"key":"10.1016\/j.chom.2025.10.001_bib54","doi-asserted-by":"crossref","first-page":"D439","DOI":"10.1093\/nar\/gkab1061","article-title":"AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models","volume":"50","author":"Varadi","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.chom.2025.10.001_bib55","doi-asserted-by":"crossref","first-page":"637","DOI":"10.1038\/s41586-023-06510-w","article-title":"Clustering predicted structures at the scale of the known protein universe","volume":"622","author":"Barrio-Hernandez","year":"2023","journal-title":"Nature"},{"key":"10.1016\/j.chom.2025.10.001_bib56","doi-asserted-by":"crossref","first-page":"297","DOI":"10.1093\/emboj\/18.2.297","article-title":"The structure of a PKD domain from polycystin-1: implications for polycystic kidney disease","volume":"18","author":"Bycroft","year":"1999","journal-title":"EMBO J."},{"key":"10.1016\/j.chom.2025.10.001_bib57","doi-asserted-by":"crossref","first-page":"23433","DOI":"10.1074\/jbc.M200811200","article-title":"CPG70 is a novel basic metallocarboxypeptidase with C-terminal polycystic kidney disease domains from Porphyromonas gingivalis","volume":"277","author":"Chen","year":"2002","journal-title":"J. Biol. Chem."},{"key":"10.1016\/j.chom.2025.10.001_bib58","doi-asserted-by":"crossref","first-page":"791","DOI":"10.1038\/s41579-024-01075-5","article-title":"The oral-gut microbiome axis in health and disease","volume":"22","author":"Kunath","year":"2024","journal-title":"Nat. Rev. Microbiol."},{"key":"10.1016\/j.chom.2025.10.001_bib59","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.42693","article-title":"Extensive transmission of microbes along the gastrointestinal tract","volume":"8","author":"Schmidt","year":"2019","journal-title":"eLife"},{"key":"10.1016\/j.chom.2025.10.001_bib60","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pbio.1002533","article-title":"Revised Estimates for the Number of Human and Bacteria Cells in the Body","volume":"14","author":"Sender","year":"2016","journal-title":"PLOS Biol."},{"key":"10.1016\/j.chom.2025.10.001_bib61","doi-asserted-by":"crossref","DOI":"10.1080\/20002297.2019.1586422","article-title":"Can oral bacteria affect the microbiome of the gut?","volume":"11","author":"Olsen","year":"2019","journal-title":"J. Oral Microbiol."},{"key":"10.1016\/j.chom.2025.10.001_bib62","article-title":"A human gut metagenome-assembled genome catalogue spanning 41 countries supports genome-scale metabolic models","author":"Junyeong","year":"2024","journal-title":"Preprint at bioRxiv"},{"key":"10.1016\/j.chom.2025.10.001_bib63","doi-asserted-by":"crossref","DOI":"10.1186\/s13059-023-02924-x","article-title":"Metabolic independence drives gut microbial colonization and resilience in health and disease","volume":"24","author":"Watson","year":"2023","journal-title":"Genome Biol."},{"key":"10.1016\/j.chom.2025.10.001_bib64","doi-asserted-by":"crossref","DOI":"10.1186\/s13059-021-02428-6","article-title":"Host adaptation in gut Firmicutes is associated with sporulation loss and altered transmission cycle","volume":"22","author":"Browne","year":"2021","journal-title":"Genome Biol."},{"key":"10.1016\/j.chom.2025.10.001_bib65","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1016\/j.tim.2022.08.010","article-title":"Fusobacterium nucleatum, a key pathogenic factor and microbial biomarker for colorectal cancer","volume":"31","author":"Wang","year":"2023","journal-title":"Trends Microbiol."},{"key":"10.1016\/j.chom.2025.10.001_bib66","doi-asserted-by":"crossref","first-page":"1555","DOI":"10.1038\/s41564-024-01680-3","article-title":"Oral bacteria relative abundance in faeces increases due to gut microbiota depletion and is linked with patient outcomes","volume":"9","author":"Liao","year":"2024","journal-title":"Nat. Microbiol."},{"key":"10.1016\/j.chom.2025.10.001_bib78","doi-asserted-by":"crossref","first-page":"D785","DOI":"10.1093\/nar\/gkab776","article-title":"GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy","volume":"50","author":"Parks","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.chom.2025.10.001_bib111","doi-asserted-by":"crossref","first-page":"D488","DOI":"10.1093\/nar\/gkab651","article-title":"DRAMP 3.0: an enhanced comprehensive data repository of antimicrobial peptides","volume":"50","author":"Shi","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.chom.2025.10.001_bib101","doi-asserted-by":"crossref","first-page":"D760","DOI":"10.1093\/nar\/gkac1078","article-title":"proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes","volume":"51","author":"Fullam","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.chom.2025.10.001_bib98","doi-asserted-by":"crossref","first-page":"1282","DOI":"10.1093\/bioinformatics\/btm098","article-title":"UniRef: comprehensive and non-redundant UniProt reference clusters","volume":"23","author":"Suzek","year":"2007","journal-title":"Bioinformatics"},{"key":"10.1016\/j.chom.2025.10.001_bib109","doi-asserted-by":"crossref","DOI":"10.1093\/database\/bas003","article-title":"AntiFam: a tool to help identify spurious ORFs in protein annotation","volume":"2012","author":"Eberhardt","year":"2012","journal-title":"Database (Oxford)"},{"key":"10.1016\/j.chom.2025.10.001_bib67","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for Illumina sequence data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"10.1016\/j.chom.2025.10.001_bib69","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with Bowtie 2","volume":"9","author":"Langmead","year":"2012","journal-title":"Nat. Methods"},{"key":"10.1016\/j.chom.2025.10.001_bib70","doi-asserted-by":"crossref","first-page":"824","DOI":"10.1101\/gr.213959.116","article-title":"metaSPAdes: a new versatile metagenomic assembler","volume":"27","author":"Nurk","year":"2017","journal-title":"Genome Res."},{"key":"10.1016\/j.chom.2025.10.001_bib71","doi-asserted-by":"crossref","first-page":"1674","DOI":"10.1093\/bioinformatics\/btv033","article-title":"MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph","volume":"31","author":"Li","year":"2015","journal-title":"Bioinformatics"},{"key":"10.1016\/j.chom.2025.10.001_bib72","doi-asserted-by":"crossref","DOI":"10.7717\/peerj.7359","article-title":"MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies","volume":"7","author":"Kang","year":"2019","journal-title":"PeerJ"},{"key":"10.1016\/j.chom.2025.10.001_bib73","doi-asserted-by":"crossref","first-page":"605","DOI":"10.1093\/bioinformatics\/btv638","article-title":"MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets","volume":"32","author":"Wu","year":"2016","journal-title":"Bioinformatics"},{"key":"10.1016\/j.chom.2025.10.001_bib74","doi-asserted-by":"crossref","first-page":"1144","DOI":"10.1038\/nmeth.3103","article-title":"Binning metagenomic contigs by coverage and composition","volume":"11","author":"Alneberg","year":"2014","journal-title":"Nat. Methods"},{"key":"10.1016\/j.chom.2025.10.001_bib76","doi-asserted-by":"crossref","DOI":"10.1186\/s40168-018-0541-1","article-title":"MetaWRAP-a flexible pipeline for genome-resolved metagenomic data analysis","volume":"6","author":"Uritskiy","year":"2018","journal-title":"Microbiome"},{"key":"10.1016\/j.chom.2025.10.001_bib77","author":"Seemann"},{"key":"10.1016\/j.chom.2025.10.001_bib79","doi-asserted-by":"crossref","first-page":"9077","DOI":"10.1093\/nar\/gkab688","article-title":"tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes","volume":"49","author":"Chan","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.chom.2025.10.001_bib81","doi-asserted-by":"crossref","DOI":"10.1186\/s13059-016-0997-x","article-title":"Mash: fast genome and metagenome distance estimation using MinHash","volume":"17","author":"Ondov","year":"2016","journal-title":"Genome Biol."},{"key":"10.1016\/j.chom.2025.10.001_bib82","doi-asserted-by":"crossref","first-page":"2864","DOI":"10.1038\/ismej.2017.126","article-title":"dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication","volume":"11","author":"Olm","year":"2017","journal-title":"ISME J."},{"key":"10.1016\/j.chom.2025.10.001_bib83","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1005944","article-title":"MUMmer4: A fast and versatile genome alignment system","volume":"14","author":"Mar\u00e7ais","year":"2018","journal-title":"PLOS Comput. Biol."},{"key":"10.1016\/j.chom.2025.10.001_bib84","doi-asserted-by":"crossref","first-page":"1","DOI":"10.18637\/jss.v053.i09","article-title":"fastcluster: Fast hierarchical, agglomerative clustering routines for R and Python","volume":"53","author":"M\u00fcllner","year":"2013","journal-title":"J. Stat. Software"},{"key":"10.1016\/j.chom.2025.10.001_bib86","doi-asserted-by":"crossref","first-page":"1530","DOI":"10.1093\/molbev\/msaa015","article-title":"IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era","volume":"37","author":"Minh","year":"2020","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.chom.2025.10.001_bib87","doi-asserted-by":"crossref","DOI":"10.1186\/s13059-020-02090-4","article-title":"Producing polished prokaryotic pangenomes with the Panaroo pipeline","volume":"21","author":"Tonkin-Hill","year":"2020","journal-title":"Genome Biol."},{"key":"10.1016\/j.chom.2025.10.001_bib88","doi-asserted-by":"crossref","first-page":"1026","DOI":"10.1038\/nbt.3988","article-title":"MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets","volume":"35","author":"Steinegger","year":"2017","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.chom.2025.10.001_bib89","doi-asserted-by":"crossref","DOI":"10.1186\/s40168-019-0633-6","article-title":"CAMISIM: simulating metagenomes and microbial communities","volume":"7","author":"Fritz","year":"2019","journal-title":"Microbiome"},{"key":"10.1016\/j.chom.2025.10.001_bib90","first-page":"2825","article-title":"Scikit-learn: Machine learning in Python","volume":"12","author":"Pedregosa","year":"2011","journal-title":"J. Mach. Learn. Res."},{"key":"10.1016\/j.chom.2025.10.001_bib91","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1038\/s41592-019-0686-2","article-title":"SciPy 1.0: fundamental algorithms for scientific computing in Python","volume":"17","author":"Virtanen","year":"2020","journal-title":"Nat. Methods"},{"key":"10.1016\/j.chom.2025.10.001_bib92","doi-asserted-by":"crossref","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","article-title":"Prokka: rapid prokaryotic genome annotation","volume":"30","author":"Seemann","year":"2014","journal-title":"Bioinformatics"},{"key":"10.1016\/j.chom.2025.10.001_bib93","doi-asserted-by":"crossref","first-page":"5825","DOI":"10.1093\/molbev\/msab293","article-title":"eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale","volume":"38","author":"Cantalapiedra","year":"2021","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.chom.2025.10.001_bib94","doi-asserted-by":"crossref","first-page":"D309","DOI":"10.1093\/nar\/gky1085","article-title":"eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses","volume":"47","author":"Huerta-Cepas","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.chom.2025.10.001_bib95","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.2025.10.001_bib96","doi-asserted-by":"crossref","DOI":"10.1093\/bioinformatics\/btaa763","article-title":"DeepGOPlus: improved protein function prediction from sequence","volume":"37","author":"Kulmanov","year":"2021","journal-title":"Bioinformatics"},{"key":"10.1016\/j.chom.2025.10.001_bib99","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."},{"key":"10.1016\/j.chom.2025.10.001_bib100","doi-asserted-by":"crossref","DOI":"10.1128\/msystems.00691-21","article-title":"Uniform Manifold Approximation and Projection (UMAP) Reveals Composite Patterns and Resolves Visualization Artifacts in Microbiome Data","volume":"6","author":"Armstrong","year":"2021","journal-title":"mSystems"},{"key":"10.1016\/j.chom.2025.10.001_bib102","doi-asserted-by":"crossref","first-page":"1416","DOI":"10.1038\/s41587-023-01675-1","article-title":"gutSMASH predicts specialized primary metabolic pathways from the human gut microbiota","volume":"41","author":"Pascal Andreu","year":"2023","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.chom.2025.10.001_bib103","doi-asserted-by":"crossref","first-page":"W29","DOI":"10.1093\/nar\/gkab335","article-title":"antiSMASH 6.0: improving cluster detection and comparison capabilities","volume":"49","author":"Blin","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.chom.2025.10.001_bib104","first-page":"205","article-title":"A new generation of homology search tools based on probabilistic inference","volume":"23","author":"Eddy","year":"2009","journal-title":"Genome Inform."},{"key":"10.1016\/j.chom.2025.10.001_bib105","doi-asserted-by":"crossref","first-page":"D690","DOI":"10.1093\/nar\/gkac920","article-title":"CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database","volume":"51","author":"Alcock","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.chom.2025.10.001_bib107","doi-asserted-by":"crossref","DOI":"10.1038\/s41467-022-30269-9","article-title":"Systematic and quantitative view of the antiviral arsenal of prokaryotes","volume":"13","author":"Tesson","year":"2022","journal-title":"Nat. Commun."},{"key":"10.1016\/j.chom.2025.10.001_bib108","doi-asserted-by":"crossref","DOI":"10.21105\/joss.04296","article-title":"Pyrodigal: Python bindings and interface to Prodigal, an efficient method for gene prediction in prokaryotes","volume":"7","author":"Larralde","year":"2022","journal-title":"J. Open Source Software"},{"key":"10.1016\/j.chom.2025.10.001_bib110","doi-asserted-by":"crossref","DOI":"10.7717\/peerj.10555","article-title":"Macrel: antimicrobial peptide screening in genomes and metagenomes","volume":"8","author":"Santos-J\u00fanior","year":"2020","journal-title":"PeerJ"},{"key":"10.1016\/j.chom.2025.10.001_bib112","doi-asserted-by":"crossref","first-page":"3150","DOI":"10.1093\/bioinformatics\/bts565","article-title":"CD-HIT: accelerated for clustering the next-generation sequencing data","volume":"28","author":"Fu","year":"2012","journal-title":"Bioinformatics"},{"key":"10.1016\/j.chom.2025.10.001_bib114","doi-asserted-by":"crossref","first-page":"128","DOI":"10.1002\/prot.22499","article-title":"Fast and accurate automatic structure prediction with HHpred","volume":"77","author":"Hildebrand","year":"2009","journal-title":"Proteins"},{"key":"10.1016\/j.chom.2025.10.001_bib116","doi-asserted-by":"crossref","first-page":"755","DOI":"10.1093\/bioinformatics\/14.9.755","article-title":"Profile hidden Markov models","volume":"14","author":"Eddy","year":"1998","journal-title":"Bioinformatics"},{"key":"10.1016\/j.chom.2025.10.001_bib117","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1038\/s41564-020-00834-3","article-title":"Community-led, integrated, reproducible multi-omics with anvi'o","volume":"6","author":"Eren","year":"2021","journal-title":"Nat. Microbiol."},{"key":"10.1016\/j.chom.2025.10.001_bib118","doi-asserted-by":"crossref","DOI":"10.24072\/pcjournal.250","article-title":"MacSyFinder v2: Improved modelling and search engine to identify molecular systems in genomes","volume":"3","author":"N\u00e9ron","year":"2023","journal-title":"Peer Community J."},{"key":"10.1016\/j.chom.2025.10.001_bib119","doi-asserted-by":"crossref","first-page":"1236","DOI":"10.1093\/bioinformatics\/btu031","article-title":"InterProScan 5: genome-scale protein function classification","volume":"30","author":"Jones","year":"2014","journal-title":"Bioinformatics"},{"key":"10.1016\/j.chom.2025.10.001_bib122","unstructured":"Lun, A., Hicks, S., Courbayre, B., Borman, T., and Lahti, L. (2024). bluster: Clustering Algorithms for Bioconductor. R package version 1.14.0."},{"key":"10.1016\/j.chom.2025.10.001_bib123","first-page":"1","article-title":"The igraph software","volume":"1695","author":"Csardi","year":"2006","journal-title":"Complex Syst."},{"key":"10.1016\/j.chom.2025.10.001_bib124","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1009442","article-title":"Multivariable association discovery in population-scale meta-omics studies","volume":"17","author":"Mallick","year":"2021","journal-title":"PLOS Comput. Biol."},{"key":"10.1016\/j.chom.2025.10.001_bib125","doi-asserted-by":"crossref","DOI":"10.1186\/s13059-022-02753-4","article-title":"Population structure discovery in meta-analyzed microbial communities and inflammatory bowel disease using MMUPHin","volume":"23","author":"Ma","year":"2022","journal-title":"Genome Biol."},{"key":"10.1016\/j.chom.2025.10.001_bib126","doi-asserted-by":"crossref","DOI":"10.1186\/1471-2105-10-421","article-title":"BLAST+: architecture and applications","volume":"10","author":"Camacho","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"10.1016\/j.chom.2025.10.001_bib127","doi-asserted-by":"crossref","DOI":"10.1186\/s13059-021-02306-1","article-title":"Microbiome meta-analysis and cross-disease comparison enabled by the SIAMCAT machine learning toolbox","volume":"22","author":"Wirbel","year":"2021","journal-title":"Genome Biol."},{"key":"10.1016\/j.chom.2025.10.001_bib128","doi-asserted-by":"crossref","DOI":"10.1038\/s41467-020-17041-7","article-title":"Analysis of compositions of microbiomes with bias correction","volume":"11","author":"Lin","year":"2020","journal-title":"Nat. Commun."},{"key":"10.1016\/j.chom.2025.10.001_bib129","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1004226","article-title":"Sparse and compositionally robust inference of microbial ecological networks","volume":"11","author":"Kurtz","year":"2015","journal-title":"PLOS Comput. Biol."},{"key":"10.1016\/j.chom.2025.10.001_bib106","article-title":"An omics-based framework for assessing the health risk of antimicrobial resistance genes","volume":"12","author":"Zhang","year":"2021","journal-title":"Nat. Commun."},{"key":"10.1016\/j.chom.2025.10.001_bib130","series-title":"ggplot2: elegant graphics for data analysis by WICKHAM, H","author":"Wilkinson","year":"2011"},{"key":"10.1016\/j.chom.2025.10.001_bib131","doi-asserted-by":"crossref","unstructured":"Ahlmann-Eltze, C., and Patil, I. (2021) Ggsignif: R Package for Displaying Significance Brackets for'ggplot2'.","DOI":"10.31234\/osf.io\/7awm6"},{"key":"10.1016\/j.chom.2025.10.001_bib132","doi-asserted-by":"crossref","DOI":"10.1002\/imt2.43","article-title":"Complex heatmap visualization","volume":"1","author":"Gu","year":"2022","journal-title":"Imeta"},{"key":"10.1016\/j.chom.2025.10.001_bib68","doi-asserted-by":"crossref","first-page":"849","DOI":"10.1101\/gr.213611.116","article-title":"Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly","volume":"27","author":"Schneider","year":"2017","journal-title":"Genome Res."},{"key":"10.1016\/j.chom.2025.10.001_bib75","doi-asserted-by":"crossref","first-page":"649","DOI":"10.1016\/j.cell.2019.01.001","article-title":"Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle","volume":"176","author":"Pasolli","year":"2019","journal-title":"Cell"},{"key":"10.1016\/j.chom.2025.10.001_bib80","doi-asserted-by":"crossref","first-page":"725","DOI":"10.1038\/nbt.3893","article-title":"Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea","volume":"35","author":"Bowers","year":"2017","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.chom.2025.10.001_bib85","doi-asserted-by":"crossref","first-page":"2520","DOI":"10.1038\/s41596-021-00508-2","article-title":"Recovering prokaryotic genomes from host-associated, short-read shotgun metagenomic sequencing data","volume":"16","author":"Saheb Kashaf","year":"2021","journal-title":"Nat. Protoc."},{"key":"10.1016\/j.chom.2025.10.001_bib97","doi-asserted-by":"crossref","first-page":"W140","DOI":"10.1093\/nar\/gkab373","article-title":"DeepGOWeb: fast and accurate protein function prediction on the (Semantic) Web","volume":"49","author":"Kulmanov","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.chom.2025.10.001_bib113","doi-asserted-by":"crossref","first-page":"149","DOI":"10.1093\/protein\/13.3.149","article-title":"Simplified amino acid alphabets for protein fold recognition and implications for folding","volume":"13","author":"Murphy","year":"2000","journal-title":"Protein Eng."},{"key":"10.1016\/j.chom.2025.10.001_bib115","doi-asserted-by":"crossref","DOI":"10.1186\/s12859-019-3019-7","article-title":"HH-suite3 for fast remote homology detection and deep protein annotation","volume":"20","author":"Steinegger","year":"2019","journal-title":"BMC Bioinformatics"},{"key":"10.1016\/j.chom.2025.10.001_bib120","doi-asserted-by":"crossref","first-page":"567","DOI":"10.1006\/jmbi.2000.4315","article-title":"Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes","volume":"305","author":"Krogh","year":"2001","journal-title":"J. Mol. Biol."},{"key":"10.1016\/j.chom.2025.10.001_bib121","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.89862","article-title":"Microbes with higher metabolic independence are enriched in human gut microbiomes under stress","volume":"12","author":"Veseli","year":"2025","journal-title":"eLife"}],"container-title":["Cell Host &amp; Microbe"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1931312825004159?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1931312825004159?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,3,12]],"date-time":"2026-03-12T14:51:17Z","timestamp":1773327077000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S1931312825004159"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,11]]},"references-count":132,"journal-issue":{"issue":"11","published-print":{"date-parts":[[2025,11]]}},"alternative-id":["S1931312825004159"],"URL":"https:\/\/doi.org\/10.1016\/j.chom.2025.10.001","relation":{"is-basis-for":[{"id-type":"doi","id":"10.52843\/cassyni.3tktg8","asserted-by":"object"}]},"ISSN":["1931-3128"],"issn-type":[{"value":"1931-3128","type":"print"}],"subject":[],"published":{"date-parts":[[2025,11]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"A high-quality genomic catalog of the human oral microbiome broadens its phylogeny and clinical insights","name":"articletitle","label":"Article Title"},{"value":"Cell Host & Microbe","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.chom.2025.10.001","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2025 Elsevier Inc. All rights are reserved, including those for text and data mining, AI training, and similar technologies.","name":"copyright","label":"Copyright"}]}}