Strain identifier
BacDive ID: 24116
Type strain:
Species: Oribacterium asaccharolyticum
Strain Designation: ACB7, HM-482
Strain history: <- DSM <- M. Sizova, Northeastern Univ., Boston, USA
NCBI tax ID(s): 1501332 (species)
General
@ref: 20700
BacDive-ID: 24116
DSM-Number: 24638
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, motile, rod-shaped
description: Oribacterium asaccharolyticum ACB7 is an anaerobe, mesophilic, motile bacterium that was isolated from subgingival plaque, healthy 25-year-old African American female.
NCBI tax id
- NCBI tax id: 1501332
- Matching level: species
strain history
@ref | history |
---|---|
20700 | <- M. Sizova, Northeastern Univ., Boston, USA |
67771 | <- DSM <- M. Sizova, Northeastern Univ., Boston, USA |
doi: 10.13145/bacdive24116.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Clostridia
- order: Eubacteriales
- family: Lachnospiraceae
- genus: Oribacterium
- species: Oribacterium asaccharolyticum
- full scientific name: Oribacterium asaccharolyticum Sizova et al. 2014
@ref: 20700
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Clostridiales
family: Lachnospiraceae
genus: Oribacterium
species: Oribacterium asaccharolyticum
full scientific name: Oribacterium asaccharolyticum Sizova et al. 2014
strain designation: ACB7, HM-482
type strain: yes
Morphology
cell morphology
@ref | cell shape | motility | gram stain |
---|---|---|---|
67771 | rod-shaped | yes | |
67771 | variable |
Culture and growth conditions
culture medium
- @ref: 20700
- name: WILKINS-CHALGREN ANAEROBE BROTH (DSMZ Medium 339)
- growth: yes
- link: https://mediadive.dsmz.de/medium/339
- composition: Name: WILKINS-CHALGREN ANAEROBE BROTH (DSMZ Medium 339) Composition: dehydrated Wilkins-Chalgren medium 33.0 g/l L-Cysteine HCl 0.3 g/l Sodium resazurin 0.0005 g/l Distilled water
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
20700 | positive | growth | 37 | mesophilic |
67771 | positive | growth | 37 | mesophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
20700 | anaerobe |
67771 | anaerobe |
spore formation
- @ref: 67771
- spore formation: no
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
68380 | 16199 | urea | - | hydrolysis |
68380 | 29016 | arginine | + | hydrolysis |
68380 | 16024 | D-mannose | - | fermentation |
68380 | 16634 | raffinose | - | fermentation |
68380 | 29985 | L-glutamate | - | degradation |
68380 | 17632 | nitrate | - | reduction |
68380 | 27897 | tryptophan | - | energy source |
metabolite production
- @ref: 68380
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
- @ref: 68380
- Chebi-ID: 35581
- metabolite: indole
- indole test: -
enzymes
@ref | value | activity | ec |
---|---|---|---|
68380 | serine arylamidase | - | |
68380 | glutamyl-glutamate arylamidase | - | |
68380 | histidine arylamidase | - | |
68380 | alanine arylamidase | - | 3.4.11.2 |
68380 | tyrosine arylamidase | - | |
68380 | pyrrolidonyl arylamidase | - | 3.4.19.3 |
68380 | leucine arylamidase | + | 3.4.11.1 |
68380 | phenylalanine arylamidase | - | |
68380 | leucyl glycin arylamidase | - | 3.4.11.1 |
68380 | proline-arylamidase | + | 3.4.11.5 |
68380 | L-arginine arylamidase | + | |
68380 | alkaline phosphatase | - | 3.1.3.1 |
68380 | tryptophan deaminase | - | 4.1.99.1 |
68380 | alpha-fucosidase | - | 3.2.1.51 |
68380 | glutamate decarboxylase | - | 4.1.1.15 |
68380 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68380 | beta-glucuronidase | - | 3.2.1.31 |
68380 | alpha-arabinosidase | - | 3.2.1.55 |
68380 | beta-glucosidase | + | 3.2.1.21 |
68380 | alpha-glucosidase | + | 3.2.1.20 |
68380 | beta-Galactosidase 6-phosphate | - | |
68380 | beta-galactosidase | + | 3.2.1.23 |
68380 | alpha-galactosidase | - | 3.2.1.22 |
68380 | arginine dihydrolase | + | 3.5.3.6 |
68380 | urease | - | 3.5.1.5 |
API rID32A
@ref | URE | ADH Arg | alpha GAL | beta GAL | beta GP | alpha GLU | beta GLU | alpha ARA | beta GUR | beta NAG | MNE | RAF | GDC | alpha FUC | NIT | IND | PAL | ArgA | ProA | LGA | PheA | LeuA | PyrA | TyrA | AlaA | GlyA | HisA | GGA | SerA |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
20700 | - | + | - | + | - | + | + | - | - | - | - | - | - | - | - | - | - | + | + | - | - | + | - | - | - | +/- | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
20700 | subgingival plaque, healthy 25-year-old African American female | MA, Boston | USA | USA | North America |
67771 | From subgingival plaque, healthy 25-year-old African American female | Boston | USA | USA | North America |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Infection | #Patient | |
#Host Body-Site | #Oral cavity and airways | #Subgingival plaque |
#Host | #Human | #Female |
taxonmaps
- @ref: 69479
- File name: preview.99_4525.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_112;96_314;97_350;98_3401;99_4525&stattab=map
- Last taxonomy: Oribacterium
- 16S sequence: HM120211
- Sequence Identity:
- Total samples: 8583
- soil counts: 59
- aquatic counts: 56
- animal counts: 8384
- plant counts: 84
Safety information
risk assessment
- @ref: 20700
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 20700
- description: Oribacterium asaccharolyticum ACB7 16S ribosomal RNA gene, partial sequence
- accession: HM120211
- length: 1436
- database: ena
- NCBI tax ID: 796944
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Oribacterium asaccharolyticum ACB7 | GCA_000238075 | scaffold | ncbi | 796944 |
66792 | Oribacterium asaccharolyticum ACB7 | 2513237306 | draft | img | 796944 |
GC content
@ref | GC-content | method |
---|---|---|
20700 | 43.3 | sequence analysis |
67771 | 43.3 | genome sequence analysis |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | yes | 79.736 | yes |
flagellated | no | 75.343 | no |
gram-positive | yes | 64.456 | yes |
anaerobic | yes | 99.05 | yes |
aerobic | no | 98.769 | yes |
halophile | no | 70.65 | no |
spore-forming | no | 85.187 | yes |
thermophile | no | 98.218 | yes |
glucose-util | yes | 83.935 | no |
glucose-ferment | yes | 75.068 | no |
External links
@ref: 20700
culture collection no.: DSM 24638, ATCC BAA 2639, KCTC 15511
straininfo link
- @ref: 88076
- straininfo: 399846
literature
- topic: Phylogeny
- Pubmed-ID: 24824639
- title: Oribacterium parvum sp. nov. and Oribacterium asaccharolyticum sp. nov., obligately anaerobic bacteria from the human oral cavity, and emended description of the genus Oribacterium.
- authors: Sizova MV, Muller PA, Stancyk D, Panikov NS, Mandalakis M, Hazen A, Hohmann T, Doerfert SN, Fowle W, Earl AM, Nelson KE, Epstein SS
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.060988-0
- year: 2014
- mesh: Adult, Bacteria, Anaerobic/classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Dental Plaque/*microbiology, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Female, Gram-Positive Asporogenous Rods/*classification/genetics/isolation & purification, Humans, Molecular Sequence Data, Mouth/*microbiology, Nucleic Acid Hybridization, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
- topic2: Enzymology
Reference
@id | authors | title | doi/url | catalogue |
---|---|---|---|---|
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | 10.1099/ijsem.0.004332 | |
20700 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-24638 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24638) | |
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |
67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | ||
68380 | Automatically annotated from API rID32A | |||
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. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ | |
88076 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | StrainInfo: A central database for resolving microbial strain identifiers | 10.60712/SI-ID399846.1 |