Strain identifier
BacDive ID: 7591
Type strain:
Species: Arthrobacter gandavensis
Strain Designation: R 5812, R5812
Strain history: CIP <- 2004, DSMZ <- V. Storms, RUG <- L. A. Devriese, Ghent Univ., Ghent, Belgium: strain R5812
NCBI tax ID(s): 169960 (species)
General
@ref: 5684
BacDive-ID: 7591
DSM-Number: 15046
keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, Gram-positive, animal pathogen
description: Arthrobacter gandavensis R 5812 is an obligate aerobe, mesophilic, Gram-positive animal pathogen that was isolated from caw, mastitic milk.
NCBI tax id
- NCBI tax id: 169960
- Matching level: species
strain history
@ref | history |
---|---|
5684 | <- V. Storms, RUG <- L. A. Devriese; R 5812 |
67770 | LMG 21285 <-- V. Storms R-5812 <-- L. A. Devriese 266/2537. |
119527 | CIP <- 2004, DSMZ <- V. Storms, RUG <- L. A. Devriese, Ghent Univ., Ghent, Belgium: strain R5812 |
doi: 10.13145/bacdive7591.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Micrococcales
- family: Micrococcaceae
- genus: Arthrobacter
- species: Arthrobacter gandavensis
- full scientific name: Arthrobacter gandavensis Storms et al. 2003
@ref: 5684
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Micrococcaceae
genus: Arthrobacter
species: Arthrobacter gandavensis
full scientific name: Arthrobacter gandavensis Storms et al. 2003
strain designation: R 5812, R5812
type strain: yes
Morphology
cell morphology
@ref | gram stain | confidence | cell shape | motility |
---|---|---|---|---|
69480 | positive | 100 | ||
119527 | positive | rod-shaped | no |
colony morphology
@ref | colony color | incubation period | medium used |
---|---|---|---|
18389 | Zinc yellow (1018) | 10-14 days | ISP 2 |
18389 | Zinc yellow (1018) | 10-14 days | ISP 3 |
18389 | Zinc yellow (1018) | 10-14 days | ISP 4 |
18389 | Zinc yellow (1018) | 10-14 days | ISP 5 |
18389 | Zinc yellow (1018) | 10-14 days | ISP 6 |
18389 | Zinc yellow (1018) | 10-14 days | ISP 7 |
119527 |
multicellular morphology
@ref | forms multicellular complex | medium name |
---|---|---|
18389 | no | ISP 2 |
18389 | no | ISP 3 |
18389 | no | ISP 4 |
18389 | no | ISP 5 |
18389 | no | ISP 6 |
18389 | no | ISP 7 |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
5684 | 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 |
5684 | TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) | yes | https://mediadive.dsmz.de/medium/92 | Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water |
18389 | ISP 2 | yes | Name: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes | |
18389 | ISP 4 | yes | Name: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml | |
18389 | ISP 3 | yes | Name: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms: | |
18389 | ISP 5 | yes | Name: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes | |
18389 | ISP 6 | yes | Name: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes | |
18389 | ISP 7 | yes | Name: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes | |
37396 | MEDIUM 72- for trypto casein soja agar | yes | Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g) | |
119527 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
18389 | positive | optimum | 28 | mesophilic |
5684 | positive | growth | 30 | mesophilic |
37396 | positive | growth | 30 | mesophilic |
67770 | positive | growth | 30 | mesophilic |
119527 | positive | growth | 10-37 | |
119527 | no | growth | 41 | thermophilic |
119527 | no | growth | 45 | thermophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 119527
- oxygen tolerance: obligate aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 99 |
69480 | no | 99.947 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
119527 | NaCl | positive | growth | 0-8 % |
119527 | NaCl | no | growth | 10 % |
observation
- @ref: 67770
- observation: quinones: MK-9(H2)
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
18389 | 17234 | glucose | + | |
18389 | 22599 | arabinose | - | |
18389 | 17992 | sucrose | + | |
18389 | 18222 | xylose | - | |
18389 | 17268 | myo-inositol | - | |
18389 | 29864 | mannitol | - | |
18389 | 28757 | fructose | - | |
18389 | 26546 | rhamnose | - | |
18389 | 16634 | raffinose | - | |
18389 | 62968 | cellulose | - | |
119527 | 16947 | citrate | - | carbon source |
119527 | 4853 | esculin | + | hydrolysis |
119527 | 606565 | hippurate | - | hydrolysis |
119527 | 17632 | nitrate | + | reduction |
119527 | 16301 | nitrite | - | reduction |
119527 | 17632 | nitrate | - | respiration |
68379 | 17632 | nitrate | + | reduction |
68379 | 4853 | esculin | + | hydrolysis |
68379 | 17634 | D-glucose | - | fermentation |
68379 | 16988 | D-ribose | - | fermentation |
68379 | 65327 | D-xylose | - | fermentation |
68379 | 16899 | D-mannitol | - | fermentation |
68379 | 17306 | maltose | - | fermentation |
68379 | 17716 | lactose | - | fermentation |
68379 | 28087 | glycogen | - | fermentation |
antibiotic resistance
- @ref: 119527
- metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
- is antibiotic: yes
- is sensitive: no
- is resistant: yes
metabolite production
- @ref: 119527
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
@ref | Chebi-ID | metabolite | voges-proskauer-test | methylred-test |
---|---|---|---|---|
119527 | 15688 | acetoin | - | |
119527 | 17234 | glucose | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
68382 | alpha-fucosidase | - | 3.2.1.51 |
68382 | alpha-mannosidase | + | 3.2.1.24 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | beta-glucosidase | + | 3.2.1.21 |
68382 | alpha-glucosidase | + | 3.2.1.20 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | beta-galactosidase | + | 3.2.1.23 |
68382 | alpha-galactosidase | + | 3.2.1.22 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | trypsin | + | 3.4.21.4 |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | esterase lipase (C 8) | + | |
68382 | alkaline phosphatase | + | 3.1.3.1 |
68379 | catalase | + | 1.11.1.6 |
68379 | beta-glucosidase | + | 3.2.1.21 |
68379 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68379 | beta-galactosidase | + | 3.2.1.23 |
68379 | beta-glucuronidase | - | 3.2.1.31 |
68379 | pyrrolidonyl arylamidase | - | 3.4.19.3 |
68379 | pyrazinamidase | + | 3.5.1.B15 |
119527 | oxidase | - | |
119527 | beta-galactosidase | + | 3.2.1.23 |
119527 | alcohol dehydrogenase | - | 1.1.1.1 |
119527 | gelatinase | +/- | |
119527 | amylase | + | |
119527 | DNase | + | |
119527 | caseinase | - | 3.4.21.50 |
119527 | catalase | + | 1.11.1.6 |
119527 | tween esterase | - | |
119527 | gamma-glutamyltransferase | - | 2.3.2.2 |
119527 | lecithinase | - | |
119527 | lipase | - | |
119527 | lysine decarboxylase | - | 4.1.1.18 |
119527 | ornithine decarboxylase | - | 4.1.1.17 |
119527 | phenylalanine ammonia-lyase | - | 4.3.1.24 |
119527 | tryptophan deaminase | - | |
119527 | urease | - | 3.5.1.5 |
API coryne
@ref | PYZ | PYRA | PAL | beta GUR | beta GAL | alpha GLU | beta NAG | ESC | URE | GEL | SAC | NIT | Control | GLU | RIB | XYL | MAN | MAL | LAC | GLYG | CAT |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
18389 | + | - | + | - | + | + | - | + | + | - | + | ||||||||||
5684 | + | - | +/- | - | + | - | - | + | - | + | - | + | - | - | - | - | - | - | - | - | + |
API zym
@ref | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase | Control |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
18389 | + | - | + | + | + | + | + | + | - | + | + | + | + | - | + | + | - | + | - | |
119527 | + | + | + | - | + | - | - | + | - | + | + | + | + | - | + | + | - | + | - | - |
API biotype100
@ref | GLU | FRU | GAL | TRE | MNE | SBE | MEL | SAC | RAF | MTE | MAL | LAC | LTE | MbGa | MaGa | CEL | GEN | MbGu | ESC | RIB | ARA | XYL | PLE | RHA | FUC | MLZ | DARL | LARL | XLT | DUL | TAG | GLY | INO | MAN | MTL | TUR | SOR | ADO | HBG | LYX | ERY | MDG | 3MDG | SAT | MUC | LTAT | DTAT | MTAT | DMLT | LMLT | CATE | TATE | TTE | CIT | GRT | GAT | 2KG | 5KG | TRY | NAG | GNT | PAC | PAT | pOBE | QAT | GTE | mOBE | BAT | PPAT | CMT | TGE | BET | PCE | ABT | HIN | LAT | CAP | CYT | HIS | SUC | FUM | GRE | GYT | AVT | ETN | TTN | GLN | ITA | 3OBU | APT | GTT | PRO | DALA | LALA | SER | MNT | PROP | TYR | 2KT |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
119527 | + | + | + | + | + | - | + | + | - | + | + | + | + | + | + | + | + | + | + | + | + | + | + | + | + | + | + | + | + | - | - | + | + | + | + | + | + | - | - | - | - | + | + | + | + | + | - | - | + | + | + | - | - | + | - | + | + | + | - | - | + | + | + | + | + | - | + | + | - | + | + | - | + | - | + | + | - | - | - | + | - | + | + | + | + | - | + | - | + | - | + | + | - | - | - | + | + | + | + |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
5684 | caw, mastitic milk | Ghent | Belgium | BEL | Europe |
60834 | Cow,mastitic milk | Belgium | BEL | Europe | |
67770 | Mastitic milk | Belgium | BEL | Europe | |
119527 | Food, Caw, mastitic milk | Belgium | BEL | Europe |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Host | #Mammals | #Bovinae (Cow, Cattle) |
#Host Body Product | #Fluids | #Milk |
taxonmaps
- @ref: 69479
- File name: preview.99_6941.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_458;97_525;98_603;99_6941&stattab=map
- Last taxonomy: Arthrobacter
- 16S sequence: AJ316140
- Sequence Identity:
- Total samples: 25
- soil counts: 8
- aquatic counts: 2
- animal counts: 15
Safety information
risk assessment
@ref | pathogenicity animal | biosafety level | biosafety level comment |
---|---|---|---|
5684 | yes | 2 | Risk group (German classification) |
18389 | 2 | ||
119527 | 1 | Risk group (French classification) |
Sequence information
16S sequences
- @ref: 5684
- description: Arthrobacter gandensis 16S rRNA gene, type strain R5812T
- accession: AJ316140
- length: 1445
- database: ena
- NCBI tax ID: 169960
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Arthrobacter gandavensis strain JCM 13316 | 169960.3 | wgs | patric | 169960 |
67770 | Arthrobacter gandavensis JCM 13316 | GCA_009192735 | contig | ncbi | 169960 |
66792 | Arthrobacter citreus DSM 15046 | GCA_029023805 | complete | ncbi | 1670 |
GC content
@ref | GC-content | method |
---|---|---|
5684 | 65 | |
67770 | 65 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 99 | no |
motile | no | 62.991 | no |
flagellated | no | 95.484 | no |
gram-positive | yes | 91.839 | no |
anaerobic | no | 99.23 | no |
aerobic | yes | 91.567 | no |
halophile | no | 65.454 | no |
spore-forming | no | 87.399 | no |
glucose-ferment | no | 86.067 | yes |
thermophile | no | 98.814 | yes |
glucose-util | yes | 86.994 | yes |
External links
@ref: 5684
culture collection no.: DSM 15046, CIP 108364, LMG 21285, CCUG 56033, JCM 13316
straininfo link
@ref | straininfo |
---|---|
77035 | 127284 |
77036 | 410886 |
literature
- topic: Phylogeny
- Pubmed-ID: 14657117
- title: Arthrobacter gandavensis sp. nov., for strains of veterinary origin.
- authors: Storms V, Devriese LA, Coopman R, Schumann P, Vyncke F, Gillis M
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.02353-0
- year: 2003
- mesh: Animals, Arthrobacter/*classification/genetics/isolation & purification, Cattle/*microbiology, DNA, Bacterial/genetics, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny
- topic2: Genetics
Reference
@id | authors | catalogue | doi/url | title |
---|---|---|---|---|
5684 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15046) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-15046 | |
18389 | Wink, J. | http://www.dsmz.de/microorganisms/wink_pdf/DSM15046.pdf | Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig | |
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 | |
37396 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/5978 | ||
60834 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 56033) | https://www.ccug.se/strain?id=56033 | |
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/ | ||
68379 | Automatically annotated from API Coryne | |||
68382 | Automatically annotated from API zym | |||
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 | |
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |
77035 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID127284.1 | StrainInfo: A central database for resolving microbial strain identifiers | |
77036 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID410886.1 | StrainInfo: A central database for resolving microbial strain identifiers | |
119527 | Curators of the CIP | Collection of Institut Pasteur (CIP 108364) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108364 |