Strain identifier
BacDive ID: 1890
Type strain:
Species: Brucella cytisi
Strain history: CIP <- 2007, CECT <- 2006, E. Velazquez, Salamanca Univ., Salamanca, Spain <- J. A. Carrasco, CIFA, Sevilla, Spain: strain ESC1
NCBI tax ID(s): 407152 (species)
General
@ref: 15442
BacDive-ID: 1890
DSM-Number: 19778
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, colony-forming
description: Brucella cytisi DSM 19778 is an aerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from root nodules of Cytisus scoparius.
NCBI tax id
- NCBI tax id: 407152
- Matching level: species
strain history
@ref | history |
---|---|
15442 | <- CECT; ESC1 {2007} <- E. Velázquez |
118836 | CIP <- 2007, CECT <- 2006, E. Velazquez, Salamanca Univ., Salamanca, Spain <- J. A. Carrasco, CIFA, Sevilla, Spain: strain ESC1 |
doi: 10.13145/bacdive1890.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Hyphomicrobiales
- family: Brucellaceae
- genus: Brucella
- species: Brucella cytisi
- full scientific name: Brucella cytisi (Zurdo-Piñeiro et al. 2007) Hördt et al. 2020
synonyms
- @ref: 20215
- synonym: Ochrobactrum cytisi
@ref: 15442
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhizobiales
family: Brucellaceae
genus: Ochrobactrum
species: Ochrobactrum cytisi
full scientific name: Ochrobactrum cytisi Zurdo-Piñeiro et al. 2007
type strain: yes
Morphology
cell morphology
@ref | gram stain | motility | cell shape |
---|---|---|---|
23339 | negative | yes | |
118836 | negative | yes | rod-shaped |
colony morphology
- @ref: 23339
- colony size: 2-3 mm
- colony color: white to beige
- colony shape: circular
- incubation period: 1 day
- medium used: YMA
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
15442 | VIBRIO NATRIEGENS MEDIUM (DSMZ Medium 115) | yes | https://mediadive.dsmz.de/medium/115 | Name: VIBRIO NATRIEGENS MEDIUM (DSMZ Medium 115) Composition: NaCl 15.0 g/l Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water |
23339 | YMA | yes | ||
37777 | MEDIUM 328- for nutrient agar | yes | Distilled water make up to (1000.000 ml);Agar (15.000 g);Peptone (5.000g);Beef extract (3.000 g) | |
118836 | CIP Medium 328 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=328 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
15442 | positive | growth | 26 | mesophilic |
37777 | positive | growth | 25 | mesophilic |
60279 | positive | growth | 37 | mesophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
60279 | aerobe |
118836 | obligate aerobe |
spore formation
- @ref: 23339
- spore formation: no
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
23339 | 17128 | adipate | - | assimilation |
23339 | 27613 | amygdalin | - | assimilation |
23339 | 27689 | decanoate | - | assimilation |
23339 | 16634 | raffinose | - | assimilation |
23339 | 28066 | gentiobiose | - | assimilation |
23339 | 28087 | glycogen | - | assimilation |
23339 | 15443 | inulin | - | assimilation |
23339 | 18403 | L-arabitol | - | assimilation |
23339 | 17266 | L-sorbose | - | assimilation |
23339 | 6731 | melezitose | - | assimilation |
23339 | 43943 | methyl alpha-D-mannoside | - | assimilation |
23339 | 74863 | methyl beta-D-xylopyranoside | - | assimilation |
23339 | 17814 | salicin | - | assimilation |
23339 | 30911 | sorbitol | - | assimilation |
23339 | 28017 | starch | - | assimilation |
23339 | 17151 | xylitol | - | assimilation |
23339 | 16808 | 2-dehydro-D-gluconate | + | assimilation |
23339 | 17426 | 5-dehydro-D-gluconate | + | assimilation |
23339 | 15963 | ribitol | + | assimilation |
23339 | 22605 | arabinitol | + | assimilation |
23339 | 18305 | arbutin | + | assimilation |
23339 | 16947 | citrate | + | assimilation |
23339 | 17108 | D-arabinose | + | assimilation |
23339 | 15824 | D-fructose | + | assimilation |
23339 | 28847 | D-fucose | + | assimilation |
23339 | 17634 | D-glucose | + | assimilation |
23339 | 16024 | D-mannose | + | assimilation |
23339 | 16813 | galactitol | + | assimilation |
23339 | 17113 | erythritol | + | assimilation |
23339 | 30849 | L-arabinose | + | assimilation |
23339 | 18287 | L-fucose | + | assimilation |
23339 | 62345 | L-rhamnose | + | assimilation |
23339 | 25097 | lyxose | + | assimilation |
23339 | 17306 | maltose | + | assimilation |
23339 | 29864 | mannitol | + | assimilation |
23339 | 506227 | N-acetylglucosamine | + | assimilation |
23339 | 33942 | ribose | + | assimilation |
23339 | 17992 | sucrose | + | assimilation |
23339 | 33954 | tagatose | + | assimilation |
23339 | 32528 | turanose | + | assimilation |
23339 | 4853 | esculin | + | hydrolysis |
23339 | 17632 | nitrate | + | reduction |
23339 | 17057 | cellobiose | +/- | assimilation |
23339 | 15824 | D-fructose | +/- | assimilation |
23339 | 65327 | D-xylose | +/- | assimilation |
23339 | 16813 | galactitol | +/- | assimilation |
23339 | 28260 | galactose | +/- | assimilation |
23339 | 24265 | gluconate | +/- | assimilation |
23339 | 17754 | glycerol | +/- | assimilation |
23339 | 17268 | myo-inositol | +/- | assimilation |
23339 | 65328 | L-xylose | +/- | assimilation |
23339 | 17716 | lactose | +/- | assimilation |
23339 | 28053 | melibiose | +/- | assimilation |
23339 | 320061 | methyl alpha-D-glucopyranoside | +/- | assimilation |
23339 | 27082 | trehalose | +/- | assimilation |
68370 | 28087 | glycogen | - | builds acid from |
68370 | 28017 | starch | - | builds acid from |
68370 | 16634 | raffinose | - | builds acid from |
68370 | 15443 | inulin | - | builds acid from |
68370 | 27082 | trehalose | - | builds acid from |
68370 | 17716 | lactose | - | builds acid from |
68370 | 17924 | D-sorbitol | - | builds acid from |
68370 | 16899 | D-mannitol | - | builds acid from |
68370 | 30849 | L-arabinose | - | builds acid from |
68370 | 16988 | D-ribose | - | builds acid from |
68370 | 29016 | arginine | - | hydrolysis |
68370 | 4853 | esculin | - | hydrolysis |
68370 | 606565 | hippurate | + | hydrolysis |
68369 | 25115 | malate | + | assimilation |
68369 | 17128 | adipate | - | assimilation |
68369 | 17306 | maltose | + | assimilation |
68369 | 59640 | N-acetylglucosamine | + | assimilation |
68369 | 16024 | D-mannose | + | assimilation |
68369 | 30849 | L-arabinose | + | assimilation |
68369 | 17634 | D-glucose | + | assimilation |
68369 | 5291 | gelatin | - | hydrolysis |
68369 | 4853 | esculin | - | hydrolysis |
68369 | 16199 | urea | - | hydrolysis |
68369 | 29016 | arginine | - | hydrolysis |
68369 | 17634 | D-glucose | - | fermentation |
68369 | 27897 | tryptophan | - | energy source |
68369 | 17632 | nitrate | + | reduction |
118836 | 17632 | nitrate | + | reduction |
118836 | 16301 | nitrite | + | reduction |
antibiotic resistance
@ref | ChEBI | metabolite | is antibiotic | is resistant | is intermediate | is sensitive |
---|---|---|---|---|---|---|
23339 | 28971 | ampicillin | yes | yes | ||
23339 | 3515 | cefuroxime | yes | yes | ||
23339 | 17698 | chloramphenicol | yes | yes | ||
23339 | 49566 | cloxacillin | yes | yes | ||
23339 | 48923 | erythromycin | yes | yes | ||
23339 | 7507 | neomycin | yes | yes | ||
23339 | 27701 | oxytetracycline | yes | yes | ||
23339 | 17334 | penicillin | yes | yes | ||
23339 | 8309 | polymyxin b | yes | yes | ||
23339 | 17833 | gentamicin | yes | yes | ||
23339 | 100241 | ciprofloxacin | yes | yes |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
23339 | 35581 | indole | yes |
23339 | 15688 | acetoin | yes |
68370 | 15688 | acetoin | yes |
68369 | 35581 | indole | no |
118836 | 35581 | indole | yes |
metabolite tests
@ref | Chebi-ID | metabolite | voges-proskauer-test | indole test |
---|---|---|---|---|
23339 | 15688 | acetoin | + | |
68370 | 15688 | acetoin | + | |
68369 | 35581 | indole | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
23339 | Acid phosphatase | + | 3.1.3.2 |
23339 | Alkaline phosphatase | + | 3.1.3.1 |
23339 | alpha-chymotrypsin | + | 3.4.21.1 |
23339 | alpha-fucosidase | - | 3.2.1.51 |
23339 | alpha-galactosidase | - | 3.2.1.22 |
23339 | alpha-glucosidase | + | 3.2.1.20 |
23339 | alpha-mannosidase | - | 3.2.1.24 |
23339 | arginine dihydrolase | - | 3.5.3.6 |
23339 | beta-galactosidase | +/- | 3.2.1.23 |
23339 | beta-galactosidase | + | 3.2.1.23 |
23339 | beta-glucosidase | - | 3.2.1.21 |
23339 | beta-glucuronidase | - | 3.2.1.31 |
23339 | cystine arylamidase | + | 3.4.11.3 |
23339 | esterase (C 4) | + | |
23339 | esterase lipase (C 8) | + | |
23339 | gelatinase | - | |
23339 | leucine arylamidase | + | 3.4.11.1 |
23339 | lipase (C 14) | + | |
23339 | lysine decarboxylase | - | 4.1.1.18 |
23339 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
23339 | naphthol-AS-BI-phosphohydrolase | + | |
23339 | ornithine decarboxylase | - | 4.1.1.17 |
23339 | trypsin | + | 3.4.21.4 |
23339 | urease | - | 3.5.1.5 |
23339 | valine arylamidase | + | |
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 | cystine arylamidase | + | 3.4.11.3 |
68382 | valine arylamidase | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | lipase (C 14) | - | |
68382 | esterase lipase (C 8) | - | |
68382 | esterase (C 4) | + | |
68382 | alkaline phosphatase | + | 3.1.3.1 |
68370 | arginine dihydrolase | - | 3.5.3.6 |
68370 | leucine arylamidase | + | 3.4.11.1 |
68370 | alkaline phosphatase | - | 3.1.3.1 |
68370 | beta-galactosidase | - | 3.2.1.23 |
68370 | beta-glucuronidase | - | 3.2.1.31 |
68370 | alpha-galactosidase | - | 3.2.1.22 |
68370 | pyrrolidonyl arylamidase | + | 3.4.19.3 |
68370 | beta-glucosidase | - | 3.2.1.21 |
68369 | cytochrome oxidase | + | 1.9.3.1 |
68369 | gelatinase | - | |
68369 | beta-glucosidase | - | 3.2.1.21 |
68369 | urease | - | 3.5.1.5 |
68369 | arginine dihydrolase | - | 3.5.3.6 |
118836 | oxidase | + | |
118836 | catalase | + | 1.11.1.6 |
118836 | urease | + | 3.5.1.5 |
API zym
@ref | Control | 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
118836 | - | + | + | - | - | + | - | + | - | - | + | + | - | - | - | - | - | - | - | - |
API 20NE
@ref | NO3 | TRP | GLU_ Ferm | ADH Arg | URE | ESC | GEL | PNPG | GLU_ Assim | ARA | MNE | MAN | NAG | MAL | GNT | CAP | ADI | MLT | CIT | PAC | OX |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
15442 | + | - | - | - | - | - | - | - | + | + | + | +/- | + | + | +/- | +/- | - | + | + | - | + |
API 20STR
@ref | VP | HIP | ESC | PYRA | alpha GAL | beta GUR | beta GAL | PAL | LAP | ADH | RIB | ARA | MAN | SOR | LAC | TRE | INU | RAF | AMD | GLYG |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
15442 | + | + | - | + | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | host species | country | origin.country | continent |
---|---|---|---|---|---|
15442 | root nodules of Cytisus scoparius | Cytisus scoparius | Spain | ESP | Europe |
60279 | Nodules from Cytisus scoparius | Spain | ESP | Europe | |
118836 | Legume Cystisus scoparius, nodules | Spain | ESP | Europe |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Host | #Plants | #Shrub (Scrub) |
#Host Body-Site | #Plant | #Root nodule |
taxonmaps
- @ref: 69479
- File name: preview.99_2226.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_45;97_1426;98_1736;99_2226&stattab=map
- Last taxonomy: Ochrobactrum
- 16S sequence: AY776289
- Sequence Identity:
- Total samples: 2394
- soil counts: 432
- aquatic counts: 339
- animal counts: 1469
- plant counts: 154
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
15442 | 1 | Risk group (German classification) |
118836 | 1 | Risk group (French classification) |
Sequence information
16S sequences
- @ref: 15442
- description: Ochrobactrum cytisi strain ESC1 16S ribosomal RNA gene, partial sequence
- accession: AY776289
- length: 1476
- database: ena
- NCBI tax ID: 407152
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Brucella cytisi LMG 22713 | GCA_012103075 | contig | ncbi | 407152 |
66792 | Ochrobactrum cytisi strain LMG 22713 | 407152.6 | wgs | patric | 407152 |
GC content
- @ref: 15442
- GC-content: 56.4
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
gram-positive | no | 98.521 | no |
anaerobic | no | 97.876 | yes |
halophile | no | 91.975 | no |
spore-forming | no | 96.746 | yes |
glucose-util | yes | 92.909 | yes |
aerobic | yes | 92.098 | no |
flagellated | no | 89.696 | no |
thermophile | no | 98.914 | yes |
motile | yes | 77.848 | yes |
glucose-ferment | no | 90.879 | yes |
External links
@ref: 15442
culture collection no.: DSM 19778, CECT 7172, CIP 109590, LMG 22713, CCUG 54646, ESC 1
straininfo link
- @ref: 71534
- straininfo: 292882
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
15442 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19778) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-19778 | |||
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 | |||
23339 | José Luis Zurdo-Pineiro, Raúl Rivas, Martha E. Trujillo, Nieves Vizcaíno, José Antonio Carrasco, Manuel Chamber, Antonio Palomares, Pedro F. Mateos, Eustoquio Martínez-Molina, Encarna Velázquez | 10.1099/ijs.0.64613-0 | Ochrobactrum cytisi sp. nov., isolated from nodules of Cytisus scoparius in Spain | IJSEM 57: 784-788 2007 | 17392207 | |
37777 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/7351 | ||||
60279 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 54646) | https://www.ccug.se/strain?id=54646 | |||
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) | |||
68369 | Automatically annotated from API 20NE | |||||
68370 | Automatically annotated from API 20STR | |||||
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 | |||
71534 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID292882.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
118836 | Curators of the CIP | Collection of Institut Pasteur (CIP 109590) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109590 |