{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,29]],"date-time":"2026-07-29T06:58:21Z","timestamp":1785308301028,"version":"3.55.0"},"reference-count":38,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,7,29]],"date-time":"2026-07-29T00:00:00Z","timestamp":1785283200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"\n Introduction<\/jats:title>\n \n Bacteria of genus\n Aggregatibacter<\/jats:italic>\n vary with respect to dependence on exogenous nicotinamide adenine dinucleotide (NAD). The genus is incompletely resolved, as 20% of deposited\n Aggregatibacter<\/jats:italic>\n genome sequences do not belong to named species.\n <\/jats:p>\n <\/jats:sec>\n \n Methods<\/jats:title>\n \n We performed phenotypic analysis of the four named\n Aggregatibacter<\/jats:italic>\n species plus four additional genomospecies, and bioinformatics analysis of 282 genomes; 237 of these genomes represent cultured isolates.\n <\/jats:p>\n <\/jats:sec>\n \n Results<\/jats:title>\n \n Independence of NAD is ubiquitous in genomospecies related to\n Aggregatibacter actinomycetemcomitans<\/jats:italic>\n , common in\n Aggregatibacter aphrophilus<\/jats:italic>\n and\n Aggregatibacter kilianii<\/jats:italic>\n , and absent from\n Aggregatibacter segnis<\/jats:italic>\n plus the six additional genomospecies. Characterised genomospecies qualify for nomenclatural approval according to phenotype and accepted genomic boundaries. Suggested species\n Aggregatibacter valvarum<\/jats:italic>\n has clinical relevance, as three of five isolates were cultured from human blood.\n <\/jats:p>\n <\/jats:sec>\n \n Conclusion<\/jats:title>\n \n Naming of three species is proposed. A total of seven named\n Aggregatibacter<\/jats:italic>\n species will comprise 87% of deposited genome sequences from cultured strains. The benefit of naming of three other genomospecies is uncertain. Two genomospecies cannot be validly named until\n in vitro<\/jats:italic>\n culture has been accomplished.\n <\/jats:p>\n <\/jats:sec>","DOI":"10.3389\/fmicb.2026.1866808","type":"journal-article","created":{"date-parts":[[2026,7,29]],"date-time":"2026-07-29T05:58:20Z","timestamp":1785304700000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Distribution of nicotinamide phosphoribosyltransferase in genus Aggregatibacter and description of Aggregatibacter animalimorsus sp. nov., Aggregatibacter holmi sp. nov., and Aggregatibacter valvarum sp. nov."],"prefix":"10.3389","volume":"17","author":[{"given":"Anne A.","family":"Thomsen","sequence":"first","affiliation":[{"name":"Department of Clinical Microbiology, Aarhus University Hospital","place":["Aarhus, Denmark"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anne B.","family":"Jensen","sequence":"additional","affiliation":[{"name":"Department of Dentistry and Oral Health, Aarhus University","place":["Aarhus, Denmark"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dennis S.","family":"Hansen","sequence":"additional","affiliation":[{"name":"Department of Clinical Microbiology, Copenhagen University Hospital","place":["Herlev, Denmark"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Martin V.","family":"M\u00f8ller","sequence":"additional","affiliation":[{"name":"Department of Clinical Microbiology, Esbjerg Hospital, University Hospital of Southern Denmark","place":["Esbjerg, Denmark"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Niels","family":"N\u00f8rskov-Lauritsen","sequence":"additional","affiliation":[{"name":"Department of Clinical Microbiology, Esbjerg Hospital, University Hospital of Southern Denmark","place":["Esbjerg, Denmark"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,7,29]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"e0240721","DOI":"10.1128\/spectrum.02407-21","article-title":"Culture on selective media and amplicon-based sequencing of 16S rRNA from spontaneous brain abscess-the view from the diagnostic laboratory","volume":"10","author":"Andersen","year":"2022","journal-title":"Microbiol. Spectrum"},{"key":"ref2","volume-title":"Manual of Clinical Microbiology","author":"Carroll","year":"2023"},{"key":"ref3","doi-asserted-by":"publisher","first-page":"2135","DOI":"10.1099\/00221287-136-10-2135","article-title":"Differentiation between Actinobacillus (Haemophilus) actinomycetemcomitans, Haemophilus aphrophilus and Haemophilus paraphrophilus by multilocus enzyme electrophoresis","volume":"136","author":"Caugant","year":"1990","journal-title":"J. Gen. Microbiol."},{"key":"ref4","doi-asserted-by":"publisher","first-page":"2221","DOI":"10.1099\/00207713-51-6-2221","article-title":"Is characterization of a single isolate sufficient for valid publication of a new genus or species? Proposal to modify recommendation 30b of the bacteriological code (1990 revision)","volume":"51","author":"Christensen","year":"2001","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref5","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1016\/S0025-6196(25)18690-4","article-title":"Symposium on infective endocarditis. III. Endocarditis due to gram-negative bacteria. Report of 56 cases","volume":"57","author":"Geraci","year":"1982","journal-title":"Mayo Clin. Proc."},{"key":"ref6","doi-asserted-by":"publisher","first-page":"6719","DOI":"10.1128\/JB.00432-06","article-title":"NAD1 utilization in Pasteurellaceae: simplification of a complex pathway","volume":"188","author":"Gerlach","year":"2006","journal-title":"J. Bacteriol."},{"key":"ref7","doi-asserted-by":"publisher","first-page":"D243","DOI":"10.1093\/nar\/gkae1038","article-title":"NCBI RefSeq: reference sequence standards through 25 years of curation and annotation","volume":"53","author":"Goldfarb","year":"2025","journal-title":"Nucleic Acids Res."},{"key":"ref8","doi-asserted-by":"publisher","first-page":"237","DOI":"10.1016\/S0140-6736(08)60135-X","article-title":"Risk of aggressive periodontitis in adolescent carriers of the JP2 clone of Aggregatibacter (Actinobacillus) actinomycetemcomitans in Morocco: a prospective longitudinal cohort study","volume":"371","author":"Haubek","year":"2008","journal-title":"Lancet"},{"key":"ref9","doi-asserted-by":"publisher","first-page":"1531","DOI":"10.1099\/00207713-49-4-1531","article-title":"Identification of Enterobacteriaceae by partial sequencing of the gene encoding translation initiation factor 2","volume":"49","author":"Hedegaard","year":"2001","journal-title":"Int. J. Syst. Bacteriol."},{"key":"ref10","doi-asserted-by":"publisher","first-page":"235","DOI":"10.1111\/j.1699-0463.1954.tb00821.x","article-title":"The influence of carbon-dioxide on the growth of Actinobacillus actinomycetemcomitans (bacterium actinomycetem comitans (Klinger 1912))","volume":"34","author":"Holm","year":"1954","journal-title":"Acta Pathologica Microbiologica Scandinavica"},{"key":"ref11","doi-asserted-by":"publisher","first-page":"846","DOI":"10.1111\/jcpe.13148","article-title":"Comprehensive antimicrobial susceptibility testing of a large collection of clinical strains of Aggregatibacter actinomycetemcomitans does not identify resistance to amoxicillin","volume":"46","author":"Jensen","year":"2019","journal-title":"J. Clin. Periodontol."},{"key":"ref12","doi-asserted-by":"publisher","first-page":"1005","DOI":"10.1099\/mic.0.055459-0","article-title":"Ribosomal multilocus sequence typing: universal characterization of bacteria from domain to strain","volume":"158","author":"Jolley","year":"2012","journal-title":"Microbiology"},{"key":"ref13","doi-asserted-by":"publisher","first-page":"124","DOI":"10.12688\/wellcomeopenres.14826.1","article-title":"Open-access bacterial population genomics: BIGSdb software, the PubMLST.Org website and their applications","volume":"3","author":"Jolley","year":"2018","journal-title":"Wellcome Open Res."},{"key":"ref14","doi-asserted-by":"publisher","first-page":"e00309","DOI":"10.1128\/mbio.00309-12","article-title":"An evolutionary link between natural transformation and CRISPR adaptive immunity","volume":"3","author":"Jorth","year":"2012","journal-title":"MBio"},{"key":"ref15","doi-asserted-by":"publisher","first-page":"1181","DOI":"10.1128\/JCM.40.4.1181-1187.2002","article-title":"Population structure and genetic diversity of Actinobacillus actinomycetemcomitans strains isolated from localized juvenile periodontitis patients","volume":"40","author":"Kaplan","year":"2002","journal-title":"J. Clin. Microbiol."},{"key":"ref16","doi-asserted-by":"publisher","first-page":"1275","DOI":"10.1128\/JB.06710-11","article-title":"Genome sequence of Aggregatibacter actinomycetemcomitans RHAA1, isolated from a rhesus macaque, an Old World primate","volume":"194","author":"Karched","year":"2012","journal-title":"J. Bacteriol."},{"key":"ref17","doi-asserted-by":"publisher","DOI":"10.21105\/joss.01762","article-title":"Mashtree: a rapid comparison of whole genome sequence files","volume":"4","author":"Katz","year":"2019","journal-title":"J. Open Source Softw."},{"key":"ref18","doi-asserted-by":"publisher","first-page":"497","DOI":"10.1002\/path.1700500312","article-title":"Endocarditis due to new species of Haemophilus","volume":"50","author":"Khairat","year":"1940","journal-title":"J. Pathol. Bacteriol."},{"key":"ref19","doi-asserted-by":"publisher","first-page":"94","DOI":"10.1177\/0022034515608163","article-title":"Evolutionary divergence of Aggregatibacter actinomycetemcomitans","volume":"95","author":"Kittichotirat","year":"2016","journal-title":"J. Dent. Res."},{"key":"ref20","doi-asserted-by":"publisher","first-page":"btaf517","DOI":"10.1093\/bioinformatics\/btaf517","article-title":"CompareM2 is a genomes-to-report pipeline for comparing microbial genomes","volume":"41","author":"Kobel","year":"2025","journal-title":"Bioinformatics"},{"key":"ref21","doi-asserted-by":"publisher","first-page":"1990","DOI":"10.1128\/JCM.00346-14","article-title":"Massive parallel sequencing provides new perspectives on bacterial brain abscesses","volume":"52","author":"Kommedal","year":"2014","journal-title":"J. Clin. Microbiol."},{"key":"ref22","doi-asserted-by":"publisher","first-page":"2567","DOI":"10.1073\/pnas.0409727102","article-title":"Genomic insights that advance the species definition for prokaryotes","volume":"102","author":"Konstantinidis","year":"2005","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref23","doi-asserted-by":"publisher","first-page":"83","DOI":"10.1016\/j.ijid.2018.01.025","article-title":"Incidence of HACEK bacteraemia in Denmark: a 6-year population-based study","volume":"68","author":"L\u00fctzen","year":"2018","journal-title":"Int. J. Infect. Dis."},{"key":"ref24","doi-asserted-by":"publisher","first-page":"D801","DOI":"10.1093\/nar\/gkab902","article-title":"TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes","volume":"50","author":"Meier-Kolthoff","year":"2022","journal-title":"Nucleic Acid Res."},{"key":"ref25","doi-asserted-by":"publisher","first-page":"e00053","DOI":"10.1128\/JCM.00053-18","article-title":"Whole-genome sequencing of Aggregatibacter species isolated from human clinical specimens and description of Aggregatibacter kilianii sp. nov","volume":"56","author":"Murra","year":"2018","journal-title":"J. Clin. Microbiol."},{"key":"ref26","doi-asserted-by":"publisher","first-page":"256","DOI":"10.3390\/pathogens8040256","article-title":"Whole genome sequencing of Aggregatibacter actinomycetemcomitans cultured from blood stream infections reveals three major phylogenetic groups including a novel lineage expressing serotype a membrane O polysaccharide","volume":"8","author":"Nedergaard","year":"2019","journal-title":"Pathogens"},{"key":"ref27","doi-asserted-by":"publisher","first-page":"214","DOI":"10.1128\/CMR.00103-13","article-title":"Classification, identification, and clinical significance of Haemophilus and Aggregatibacter species with host specificity for humans","volume":"27","author":"N\u00f8rskov-Lauritsen","year":"2014","journal-title":"Clin. Microbiol. Rev."},{"key":"ref28","doi-asserted-by":"publisher","first-page":"243","DOI":"10.3390\/pathogens8040243","article-title":"Aggregatibacter actinomycetemcomitans: clinical significance of a pathobiont subjected to ample changes in classification and nomenclature","volume":"8","author":"N\u00f8rskov-Lauritsen","year":"2019","journal-title":"Pathogens"},{"key":"ref29","doi-asserted-by":"publisher","first-page":"2135","DOI":"10.1099\/ijs.0.64207-0","article-title":"Reclassification of Actinobacillus actinomycetemcomitans, Haemophilus aphrophilus, Haemophilus paraphrophilus and Haemophilus segnis as Aggregatibacter actinomycetemcomitans gen. Nov., comb. nov., Aggregatibacter aphrophilus comb. nov. and Aggregatibacter segnis comb. nov., and emended description of Aggregatibacter aphrophilus to include V factor-dependent and V factor-independent isolates","volume":"56","author":"N\u00f8rskov-Lauritsen","year":"2006","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref30","doi-asserted-by":"publisher","first-page":"gkac1003","DOI":"10.1093\/nar\/gkac1003","article-title":"Introducing the bacterial and viral bioinformatics resource center (BV-BRC): a resource combining PATRIC, IRD and ViPR","volume":"9","author":"Olson","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"ref31","doi-asserted-by":"publisher","first-page":"1079","DOI":"10.1038\/s41587-020-0501-8","article-title":"A complete domain-to-species taxonomy for Bacteria and Archaea","volume":"38","author":"Parks","year":"2020","journal-title":"Nat. Biotechnol."},{"key":"ref32","doi-asserted-by":"publisher","first-page":"915","DOI":"10.2307\/4583299","article-title":"The determination of V factor in the urine and tissues of normal dogs and of dogs with black-tongue by the use of Haemophilus parainfluenzae","volume":"55","author":"Pittman","year":"1940","journal-title":"Public Health Rep."},{"key":"ref33","doi-asserted-by":"publisher","first-page":"2049","DOI":"10.1099\/13500872-140-8-2049","article-title":"Population structure of Actinobacillus actinomycetemcomitans: a framework for studies of disease-associated properties","volume":"140","author":"Poulsen","year":"1994","journal-title":"Microbiology"},{"key":"ref34","doi-asserted-by":"publisher","first-page":"e9490","DOI":"10.1371\/journal.pone.0009490","article-title":"FastTree 2--approximately maximum-likelihood trees for large alignments","volume":"5","author":"Price","year":"2010","journal-title":"PLoS One"},{"key":"ref35","doi-asserted-by":"publisher","first-page":"1124","DOI":"10.1016\/j.meegid.2010.07.011","article-title":"Phylogenetic variation of Aggregatibacter actinomycetemcomitans serotype e reveals an aberrant distinct evolutionary stable lineage","volume":"10","author":"van der Reijden","year":"2010","journal-title":"Infect. Genet. Evol."},{"key":"ref36","doi-asserted-by":"publisher","first-page":"433","DOI":"10.1016\/s0176-6724(88)80120-2","article-title":"International committee on systematic bacteriology: announcement of the report of the ad hoc committee on reconciliation of approaches to bacterial systematics","volume":"268","author":"Wayne","year":"1988","journal-title":"Zentralbl Bakteriol Mikrobiol Hyg A."},{"key":"ref37","doi-asserted-by":"publisher","first-page":"892","DOI":"10.1099\/jmm.0.070060-0","article-title":"Association between HACEK bacteraemia and endocarditis","volume":"63","author":"Yew","year":"2014","journal-title":"J. Med. Microbiol."},{"key":"ref38","doi-asserted-by":"publisher","first-page":"1281","DOI":"10.1007\/s10482-017-0844-","article-title":"A large-scale evaluation of algorithms to calculate average nucleotide identity","volume":"110","author":"Yoon","year":"2017","journal-title":"Antonie Van Leeuwenhoek"}],"container-title":["Frontiers in Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2026.1866808\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,7,29]],"date-time":"2026-07-29T05:58:21Z","timestamp":1785304701000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2026.1866808\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,7,29]]},"references-count":38,"alternative-id":["10.3389\/fmicb.2026.1866808"],"URL":"https:\/\/doi.org\/10.3389\/fmicb.2026.1866808","relation":{},"ISSN":["1664-302X"],"issn-type":[{"value":"1664-302X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,7,29]]},"article-number":"1866808"}}