Strain identifier
BacDive ID: 11754
Type strain: 
Species: Aggregatibacter actinomycetemcomitans
Strain Designation: Y4
Strain history: Tokyo Med. Dent. Univ. <-- ATCC 43718 <-- H. Reynolds Y4 <-- S. S. Socransky.
NCBI tax ID(s): 1035194 (strain), 714 (species)
version 8.1 (current version)
General
@ref: 4215
BacDive-ID: 11754
DSM-Number: 11123
keywords: genome sequence, 16S sequence, Bacteria, microaerophile, mesophilic, human pathogen
description: Aggregatibacter actinomycetemcomitans Y4 is a microaerophile, mesophilic human pathogen that was isolated from subgingival dental plaque.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 1035194 | strain |
| 714 | species |
strain history
| @ref | history |
|---|---|
| 4215 | <- ATCC; ATCC 43718 <- H. Reynold; Y4 <- S. S. Socransky; |
| 67770 | Tokyo Med. Dent. Univ. <-- ATCC 43718 <-- H. Reynolds Y4 <-- S. S. Socransky. |
doi: 10.13145/bacdive11754.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Pasteurellales
- family: Pasteurellaceae
- genus: Aggregatibacter
- species: Aggregatibacter actinomycetemcomitans
- full scientific name: Aggregatibacter actinomycetemcomitans (Klinger 1912) Nørskov-Lauritsen and Kilian 2006
synonyms
@ref synonym 20215 Bacterium actinomycetemcomitans 20215 Haemophilus actinomycetemcomitans 20215 Actinobacillus actinomycetemcomitans
@ref: 4215
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Pasteurellales
family: Pasteurellaceae
genus: Aggregatibacter
species: Aggregatibacter actinomycetemcomitans
full scientific name: Aggregatibacter actinomycetemcomitans (Klinger 1912) Nørskov-Lauritsen and Kilian 2006
strain designation: Y4
type strain: no
Morphology
colony morphology
- @ref: 4215
- incubation period: 1-2 days
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 4215 | BHI MEDIUM (DSMZ Medium 215) | yes | https://mediadive.dsmz.de/medium/215 | Name: BHI MEDIUM (DSMZ Medium 215) Composition: Brain heart infusion 37.0 g/l Distilled water |
| 4215 | COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) | yes | https://mediadive.dsmz.de/medium/693 | Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base |
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 4215 | positive | growth | 37 | mesophilic |
| 67770 | positive | growth | 37 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 4215
- oxygen tolerance: microaerophile
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 68377 | 17634 | D-glucose | + | builds acid from |
| 68377 | 18257 | ornithine | - | degradation |
| 68377 | 16199 | urea | - | hydrolysis |
| 68377 | 27897 | tryptophan | - | energy source |
metabolite production
- @ref: 68377
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
- @ref: 68377
- Chebi-ID: 35581
- metabolite: indole
- indole test: -
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 4215 | catalase | + | 1.11.1.6 |
| 4215 | cytochrome-c oxidase | + | 1.9.3.1 |
| 68377 | tryptophan deaminase | - | 4.1.99.1 |
| 68377 | beta-galactosidase | - | 3.2.1.23 |
| 68377 | urease | - | 3.5.1.5 |
| 68377 | ornithine decarboxylase | - | 4.1.1.17 |
API NH
| @ref | PEN | GLU | FRU | MAL | SAC | ODC | URE | LIP | PAL | beta GAL | ProA | GGT | IND |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 4215 | - | + | + | + | - | - | - | - | + | - | - | + | - |
| 4215 | + | + | - | - | - | - | - | + | - | - | + | - | - |
| 4215 | + | + | - | - | - | - | - | + | - | - | + | - | - |
| 4215 | + | + | + | - | - | - | - | + | - | - | + | - | - |
| 4215 | + | + | + | + | - | - | - | + | - | - | + | - | - |
| 4215 | - | + | + | + | +/- | - | - | - | + | - | - | + | - |
| 4215 | - | + | + | - | - | - | - | - | + | - | - | + | - |
| 4215 | - | + | + | - | - | - | - | - | + | - | - | + | - |
| 4215 | - | + | + | + | + | - | - | - | + | - | - | + | - |
| 4215 | - | + | + | + | - | - | - | - | + | - | - | + | - |
Isolation, sampling and environmental information
isolation
- @ref: 4215
- sample type: subgingival dental plaque
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host Body-Site | #Oral cavity and airways | #Subgingival plaque |
| #Host Body-Site | #Oral cavity and airways | #Tooth |
taxonmaps
- @ref: 69479
- File name: preview.99_570.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_18;96_321;97_406;98_465;99_570&stattab=map
- Last taxonomy: Aggregatibacter actinomycetemcomitans subclade
- 16S sequence: AB595137
- Sequence Identity:
- Total samples: 8336
- soil counts: 46
- aquatic counts: 279
- animal counts: 7969
- plant counts: 42
Safety information
risk assessment
- @ref: 4215
- pathogenicity human: yes
- pathogenicity animal: yes
- biosafety level: 2
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Actinobacillus actinomycetemcomitans strain ATCC 43718 16S ribosomal RNA gene, partial sequence | AY362884 | 1362 | ena | 1035194 |
| 67770 | Aggregatibacter actinomycetemcomitans gene for 16S ribosomal RNA, partial sequence, strain: JCM 8578 | AB595137 | 1501 | ena | 714 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Aggregatibacter actinomycetemcomitans Y4 | GCA_000318155 | scaffold | ncbi | 1035194 |
| 66792 | Aggregatibacter actinomycetemcomitans Y4 | 1035194.3 | wgs | patric | 1035194 |
| 66792 | Aggregatibacter actinomycetemcomitans Y4 | 2537561947 | draft | img | 1035194 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| motile | no | 88.927 | no |
| flagellated | no | 96.933 | no |
| gram-positive | no | 98.536 | no |
| anaerobic | no | 93.925 | yes |
| aerobic | no | 96.166 | yes |
| halophile | no | 50 | no |
| spore-forming | no | 98.591 | no |
| thermophile | no | 96.516 | no |
| glucose-util | no | 51.447 | no |
| glucose-ferment | no | 52.109 | no |
External links
@ref: 4215
culture collection no.: DSM 11123, ATCC 43718, JCM 8578
straininfo link
- @ref: 80972
- straininfo: 42003
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Enzymology | 1381732 | Identification and analysis of the gap region in the 23S ribosomal RNA from Actinobacillus actinomycetemcomitans. | Haraszthy VI, Sunday GJ, Bobek LA, Motley TS, Preus H, Zambon JJ | J Dent Res | 10.1177/00220345920710090401 | 1992 | Aggregatibacter actinomycetemcomitans/*genetics, Base Sequence, Cloning, Molecular, DNA, Bacterial/genetics, DNA, Ribosomal/*genetics, DNA, Single-Stranded/genetics, Electrophoresis, Agar Gel, *Genes, Bacterial, Molecular Sequence Data, Polymerase Chain Reaction, *RNA Processing, Post-Transcriptional, RNA, Bacterial/genetics, RNA, Ribosomal, 23S/*genetics, Restriction Mapping, Single-Strand Specific DNA and RNA Endonucleases | Genetics |
| Pathogenicity | 1706323 | Evidence that the serotype b antigenic determinant of Actinobacillus actinomycetemcomitans Y4 resides in the polysaccharide moiety of lipopolysaccharide. | Wilson ME, Schifferle RE | Infect Immun | 10.1128/iai.59.4.1544-1551.1991 | 1991 | Actinobacillus/*immunology, Adolescent, Adult, Age Factors, Antibodies, Bacterial/analysis, Antigens, Bacterial/analysis/*immunology, Child, Epitopes/*analysis, Humans, Immunodiffusion, Immunoglobulin G/analysis, Lipopolysaccharides/analysis/*immunology, Periodontitis/immunology/microbiology, Polysaccharides, Bacterial/analysis/*immunology | |
| Metabolism | 7927715 | Identification of an immunoglobulin Fc receptor of Actinobacillus actinomycetemcomitans. | Mintz KP, Fives-Taylor PM | Infect Immun | 10.1128/iai.62.10.4500-4505.1994 | 1994 | Aggregatibacter actinomycetemcomitans/*immunology, Amino Acid Sequence, Avidin/metabolism, Bacterial Outer Membrane Proteins/*analysis, Humans, Immunoglobulin Fc Fragments/metabolism, Molecular Sequence Data, Receptors, Fc/*analysis/chemistry/physiology | Pathogenicity |
| Enzymology | 8837475 | Isolation and characterization of hemolytic genes from Actinobacillus actinomycetemcomitans. | Kato T, Kimizuka R, Okuda K | FEMS Microbiol Lett | 10.1111/j.1574-6968.1996.tb08483.x | 1996 | Aggregatibacter actinomycetemcomitans/*genetics/*pathogenicity, Animals, Cloning, Molecular, DNA, Bacterial/genetics, Escherichia coli/genetics, *Genes, Bacterial, Hemolysin Proteins/genetics, Hemolysis/*genetics, Horses, Humans, In Vitro Techniques, Rabbits, Restriction Mapping, Sheep | Pathogenicity |
| Enzymology | 9916112 | Cloning of the gene encoding the Actinobacillus actinomycetemcomitans serotype b OmpA-like outer membrane protein. | Komatsuzawa H, Kawai T, Wilson ME, Taubman MA, Sugai M, Suginaka H | Infect Immun | 10.1128/IAI.67.2.942-945.1999 | 1999 | Aggregatibacter actinomycetemcomitans/*genetics, Amino Acid Sequence, Animals, Bacterial Outer Membrane Proteins/*genetics, Base Sequence, Cloning, Molecular, DNA, Bacterial, Escherichia coli, Gene Expression, Genes, Bacterial, Mice, Mice, Inbred BALB C, Molecular Sequence Data | Genetics |
| Pathogenicity | 10093529 | Antigenic components of Actinobacillus actinomycetemcomitans lipopolysaccharide recognized by sera from patients with localized juvenile periodontitis. | Gu K, Bainbridge B, Darveau RP, Page RC | Oral Microbiol Immunol | 10.1111/j.1399-302x.1998.tb00726.x | 1998 | Adolescent, Aggregatibacter actinomycetemcomitans/*immunology, Aggressive Periodontitis/blood/*immunology, Antibodies, Bacterial/biosynthesis/blood, Antibody Formation, Antigens, Bacterial/chemistry, Child, Enzyme-Linked Immunosorbent Assay, Humans, Immunoglobulin G/biosynthesis/blood, Lipid A/immunology, Lipopolysaccharides/*chemistry/*immunology, O Antigens/immunology, Oligosaccharides/immunology | |
| Phylogeny | 10588502 | Bacterial adhesion of Actinobacillus actinomycetemcomitans serotypes to titanium implants: SEM evaluation. A preliminary report. | Okte E, Sultan N, Dogan B, Asikainen S | J Periodontol | 10.1902/jop.1999.70.11.1376 | 1999 | Aggregatibacter actinomycetemcomitans/classification/*physiology, *Bacterial Adhesion, Blade Implantation, Dental Implants/*microbiology, Microscopy, Electron, Scanning, Species Specificity | |
| Phylogeny | 10767609 | Heterogeneity in the immune response to serotype b LPS of Actinobacillus actinomycetemcomitans in inbred strains of mice. | Kato T, Honma K, Yamanaka A, Miura T, Okuda K | FEMS Immunol Med Microbiol | 10.1111/j.1574-695X.2000.tb01458.x | 2000 | Actinobacillus Infections/immunology/microbiology, Aggregatibacter actinomycetemcomitans/classification/*immunology, Animals, Antibodies, Bacterial/*blood, Cytokines/metabolism, Enzyme-Linked Immunosorbent Assay, Female, Immunization, Lipopolysaccharides/*immunology, Mice, Mice, Inbred Strains, Serotyping | Metabolism |
| Pathogenicity | 10899863 | Novel apoptosis-inducing activity in Bacteroides forsythus: a comparative study with three serotypes of Actinobacillus actinomycetemcomitans. | Arakawa S, Nakajima T, Ishikura H, Ichinose S, Ishikawa I, Tsuchida N | Infect Immun | 10.1128/IAI.68.8.4611-4615.2000 | 2000 | Aggregatibacter actinomycetemcomitans/classification/*pathogenicity, *Apoptosis, Bacterial Proteins/*toxicity, Bacteroides/*pathogenicity, Caspase 3, Caspases/metabolism, DNA Fragmentation, Enzyme Activation, HL-60 Cells, Humans, Jurkat Cells, Leukocytes/pathology, Serotyping | Phylogeny |
| Pathogenicity | 10951380 | Influence of surface modifications to titanium on oral bacterial adhesion in vitro. | Yoshinari M, Oda Y, Kato T, Okuda K, Hirayama A | J Biomed Mater Res | 10.1002/1097-4636(200011)52:2<388::aid-jbm20>3.0.co;2-e | 2000 | Aggregatibacter actinomycetemcomitans, *Bacterial Adhesion, *Dental Materials, Humans, Oral Health, Porphyromonas gingivalis, Surface Properties, *Titanium | |
| Pathogenicity | 11426884 | Influence of surface modifications to titanium on antibacterial activity in vitro. | Yoshinari M, Oda Y, Kato T, Okuda K | Biomaterials | 10.1016/s0142-9612(00)00392-6 | 2001 | Aggregatibacter actinomycetemcomitans/*drug effects/growth & development/physiology, Animals, Bacterial Adhesion/*drug effects, Biocompatible Materials/*chemistry/pharmacology/toxicity, Calcium/pharmacology, Coated Materials, Biocompatible/chemistry/pharmacology/toxicity, Fluorine/pharmacology, L Cells/drug effects, Materials Testing, Mice, Mouth/microbiology, Nitrogen/pharmacology, Oxidation-Reduction, Porphyromonas gingivalis/*drug effects/growth & development/physiology, Surface Properties, Titanium/analysis/*chemistry/pharmacology/toxicity | |
| Pathogenicity | 12019120 | Effect of ciprofloxacin on killing of Actinobacillus actinomycetemcomitans by polymorphonuclear leukocytes. | Cacchillo DA, Walters JD | Antimicrob Agents Chemother | 10.1128/AAC.46.6.1980-1984.2002 | 2002 | Aggregatibacter actinomycetemcomitans/*drug effects/*immunology, Anti-Infective Agents/*pharmacology, Ciprofloxacin/*pharmacology, Colony Count, Microbial, Humans, Immunity, Cellular/*drug effects, In Vitro Techniques, Neutrophils/*drug effects/*immunology, Oxidation-Reduction, Phagocytosis/*drug effects, Respiratory Burst/drug effects | |
| 16904783 | A simple viability-maintaining method produces homogenic cell suspensions of autoaggregating wild-type Actinobacillus actinomycetemcomitans. | Karched M, Paul-Satyaseela M, Asikainen S | J Microbiol Methods | 10.1016/j.mimet.2006.06.004 | 2006 | Aggregatibacter actinomycetemcomitans/growth & development/*physiology/ultrastructure, Colony Count, Microbial, Microscopy, Electron, Statistics, Nonparametric | ||
| Pathogenicity | 18173797 | Reduction of periodontal pathogens adhesion by antagonistic strains. | Van Hoogmoed CG, Geertsema-Doornbusch GI, Teughels W, Quirynen M, Busscher HJ, Van der Mei HC | Oral Microbiol Immunol | 10.1111/j.1399-302X.2007.00388.x | 2008 | Actinomyces/physiology, Aggregatibacter actinomycetemcomitans/*physiology, Antibiosis/*physiology, Bacterial Adhesion/*physiology, Bacteriological Techniques, Colony Count, Microbial, Haemophilus parainfluenzae/physiology, Humans, Periodontitis/microbiology, Porphyromonas gingivalis/*physiology, Prevotella intermedia/*physiology, Streptococcus/classification/physiology, Streptococcus mitis/physiology, Streptococcus sanguis/physiology | Phylogeny |
| Metabolism | 18954350 | Differential effects of five Aggregatibacter actinomycetemcomitans strains on gingival epithelial cells. | Shimada T, Sugano N, Nishihara R, Suzuki K, Tanaka H, Ito K | Oral Microbiol Immunol | 10.1111/j.1399-302X.2008.00449.x | 2008 | Actinobacillus Infections/*microbiology, Aggregatibacter actinomycetemcomitans/*pathogenicity, Cell Proliferation, Cells, Cultured, Epithelial Cells/metabolism/*microbiology, Gingiva/metabolism/*microbiology, Humans, Intercellular Adhesion Molecule-1/metabolism, Interleukin-8/metabolism, RNA, Messenger/metabolism, Species Specificity | Pathogenicity |
| Metabolism | 20716951 | Differential epithelial cell response upon stimulation with the Aggregatibacter actinomycetemcomitans strains VT 1169, VT 1560 DAM(-) and ATCC 4318. | Eberhard J, Banasch T, Jepsen S, Dommisch H | Epigenetics | 10.4161/epi.5.8.13106 | 2010 | Adult, Bacterial Proteins/genetics/immunology/*metabolism, Epithelial Cells/immunology/*metabolism/microbiology, Female, *Gene Expression Regulation, Humans, Male, Mouth Diseases/genetics/immunology/*metabolism/microbiology, Pasteurellaceae/genetics/immunology/*metabolism, RNA, Messenger/biosynthesis/immunology, Site-Specific DNA-Methyltransferase (Adenine-Specific) | Pathogenicity |
| Pathogenicity | 21420071 | Influence of different biomaterials on the viability of Aggregatibacter actinomycetemcomitans. | Kasaj A, Willershausen B, Junker R, Callaway A, Krahn U, Kraft B, Pietsch M | Arch Oral Biol | 10.1016/j.archoralbio.2011.02.013 | 2011 | Aggregatibacter actinomycetemcomitans/*drug effects, Animals, Biocompatible Materials/*pharmacology, Bone Matrix/physiology, Calcium Hydroxide/pharmacology, Calcium Phosphates/pharmacology, Cattle, Dental Enamel Proteins/pharmacology, Durapatite/pharmacology, Least-Squares Analysis, Linear Models, Materials Testing, Microbial Viability/drug effects, Nanostructures, Regenerative Medicine/methods | |
| Pathogenicity | 25327222 | Antimicrobial effect of lemongrass oil against oral malodour micro-organisms and the pilot study of safety and efficacy of lemongrass mouthrinse on oral malodour. | Satthanakul P, Taweechaisupapong S, Paphangkorakit J, Pesee M, Timabut P, Khunkitti W | J Appl Microbiol | 10.1111/jam.12667 | 2014 | Adult, Aggregatibacter actinomycetemcomitans/drug effects, Anti-Bacterial Agents/adverse effects/pharmacology/*therapeutic use, Double-Blind Method, Female, Halitosis/*drug therapy/microbiology, Humans, Male, Mouthwashes/adverse effects/pharmacology/*therapeutic use, Pilot Projects, Plant Oils/adverse effects/chemistry/pharmacology/*therapeutic use, Porphyromonas gingivalis/drug effects, Streptococcus mutans/drug effects, Terpenes/adverse effects/chemistry/pharmacology/*therapeutic use, Young Adult | |
| Pathogenicity | 28823045 | Killing activity of LFchimera on periodontopathic bacteria and multispecies oral biofilm formation in vitro. | Ruangcharoen S, Suwannarong W, Lachica MRCT, Bolscher JGM, Nazmi K, Khunkitti W, Taweechaisupapong S | World J Microbiol Biotechnol | 10.1007/s11274-017-2334-2 | 2017 | Aggregatibacter actinomycetemcomitans/drug effects/physiology, Anti-Bacterial Agents/*pharmacology, Antimicrobial Cationic Peptides/*pharmacology, Biofilms/*drug effects, Humans, In Vitro Techniques, Microbial Sensitivity Tests, Microbial Viability/drug effects, Periodontitis/*microbiology, Plankton/drug effects | |
| Pathogenicity | 31329599 | Synergistic effects of LFchimera and antibiotic against planktonic and biofilm form of Aggregatibacter actinomycetemcomitans. | Lachica MRCT, Anutrakunchai C, Prajaneh S, Nazmi K, Bolscher JGM, Taweechaisupapong S | PLoS One | 10.1371/journal.pone.0217205 | 2019 | Aggregatibacter actinomycetemcomitans/*physiology, Anti-Bacterial Agents/chemistry/*pharmacology, Antimicrobial Cationic Peptides/agonists/chemistry/genetics/*pharmacology, Biofilms/*drug effects/growth & development, Drug Synergism, Humans, Lactoferrin/agonists/chemistry/genetics/*pharmacology, Periodontitis/drug therapy/microbiology, Plankton/*growth & development, Recombinant Fusion Proteins/chemistry/genetics/pharmacology |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 4215 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11123) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-11123 | |||
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
| 20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
| 68377 | Automatically annotated from API NH | |||||
| 69479 | João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |||
| 80972 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID42003.1 | StrainInfo: A central database for resolving microbial strain identifiers |