Strain identifier

BacDive ID: 1890

Type strain: Yes

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)

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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

@refhistory
15442<- CECT; ESC1 {2007} <- E. Velázquez
118836CIP <- 2007, CECT <- 2006, E. Velazquez, Salamanca Univ., Salamanca, Spain <- J. A. Carrasco, CIFA, Sevilla, Spain: strain ESC1

doi: 10.13145/bacdive1890.20250331.9.3

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

@refgram stainmotilitycell shapeconfidence
23339negativeyes
118836negativeyesrod-shaped
125438negative100

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

@refnamegrowthlinkcomposition
15442VIBRIO NATRIEGENS MEDIUM (DSMZ Medium 115)yeshttps://mediadive.dsmz.de/medium/115Name: 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
23339YMAyes
37777MEDIUM 328- for nutrient agaryesDistilled water make up to (1000.000 ml);Agar (15.000 g);Peptone (5.000g);Beef extract (3.000 g)
118836CIP Medium 328yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=328

culture temp

@refgrowthtypetemperature
15442positivegrowth26
37777positivegrowth25
60279positivegrowth37

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
60279aerobe
118836obligate aerobe
125439obligate aerobe97.9

spore formation

@refspore formationconfidence
23339no
125439no95.5
125438no91.378

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2333917128adipate-assimilation
2333927613amygdalin-assimilation
2333927689decanoate-assimilation
2333916634raffinose-assimilation
2333928066gentiobiose-assimilation
2333928087glycogen-assimilation
2333915443inulin-assimilation
2333918403L-arabitol-assimilation
2333917266L-sorbose-assimilation
233396731melezitose-assimilation
2333943943methyl alpha-D-mannoside-assimilation
2333974863methyl beta-D-xylopyranoside-assimilation
2333917814salicin-assimilation
2333930911sorbitol-assimilation
2333928017starch-assimilation
2333917151xylitol-assimilation
23339168082-dehydro-D-gluconate+assimilation
23339174265-dehydro-D-gluconate+assimilation
2333915963ribitol+assimilation
2333922605arabinitol+assimilation
2333918305arbutin+assimilation
2333916947citrate+assimilation
2333917108D-arabinose+assimilation
2333915824D-fructose+assimilation
2333928847D-fucose+assimilation
2333917634D-glucose+assimilation
2333916024D-mannose+assimilation
2333916813galactitol+assimilation
2333917113erythritol+assimilation
2333930849L-arabinose+assimilation
2333918287L-fucose+assimilation
2333962345L-rhamnose+assimilation
2333925097lyxose+assimilation
2333917306maltose+assimilation
2333929864mannitol+assimilation
23339506227N-acetylglucosamine+assimilation
2333933942ribose+assimilation
2333917992sucrose+assimilation
2333933954tagatose+assimilation
2333932528turanose+assimilation
233394853esculin+hydrolysis
2333917632nitrate+reduction
2333917057cellobiose+/-assimilation
2333915824D-fructose+/-assimilation
2333965327D-xylose+/-assimilation
2333916813galactitol+/-assimilation
2333928260galactose+/-assimilation
2333924265gluconate+/-assimilation
2333917754glycerol+/-assimilation
2333917268myo-inositol+/-assimilation
2333965328L-xylose+/-assimilation
2333917716lactose+/-assimilation
2333928053melibiose+/-assimilation
23339320061methyl alpha-D-glucopyranoside+/-assimilation
2333927082trehalose+/-assimilation
11883617632nitrate+reduction
11883616301nitrite+reduction
6837028087glycogen-builds acid from
6837028017starch-builds acid from
6837016634raffinose-builds acid from
6837015443inulin-builds acid from
6837027082trehalose-builds acid from
6837017716lactose-builds acid from
6837017924D-sorbitol-builds acid from
6837016899D-mannitol-builds acid from
6837030849L-arabinose-builds acid from
6837016988D-ribose-builds acid from
6837029016arginine-hydrolysis
683704853esculin-hydrolysis
68370606565hippurate+hydrolysis
6836925115malate+assimilation
6836917128adipate-assimilation
6836917306maltose+assimilation
6836959640N-acetylglucosamine+assimilation
6836916024D-mannose+assimilation
6836930849L-arabinose+assimilation
6836917634D-glucose+assimilation
683695291gelatin-hydrolysis
683694853esculin-hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate+reduction

antibiotic resistance

@refChEBImetaboliteis antibioticis resistantis intermediateis sensitive
2333928971ampicillinyesyes
233393515cefuroximeyesyes
2333917698chloramphenicolyesyes
2333949566cloxacillinyesyes
2333948923erythromycinyesyes
233397507neomycinyesyes
2333927701oxytetracyclineyesyes
2333917334penicillinyesyes
233398309polymyxin byesyes
2333917833gentamicinyesyes
23339100241ciprofloxacinyesyes

metabolite production

@refChebi-IDmetaboliteproduction
2333935581indoleyes
2333915688acetoinyes
6837015688acetoinyes
6836935581indoleno
11883635581indoleyes

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
2333915688acetoin+
6837015688acetoin+
6836935581indole-

enzymes

@refvalueactivityec
23339Acid phosphatase+3.1.3.2
23339Alkaline phosphatase+3.1.3.1
23339alpha-chymotrypsin+3.4.21.1
23339alpha-fucosidase-3.2.1.51
23339alpha-galactosidase-3.2.1.22
23339alpha-glucosidase+3.2.1.20
23339alpha-mannosidase-3.2.1.24
23339arginine dihydrolase-3.5.3.6
23339beta-galactosidase+/-3.2.1.23
23339beta-galactosidase+3.2.1.23
23339beta-glucosidase-3.2.1.21
23339beta-glucuronidase-3.2.1.31
23339cystine arylamidase+3.4.11.3
23339esterase (C 4)+
23339esterase lipase (C 8)+
23339gelatinase-
23339leucine arylamidase+3.4.11.1
23339lipase (C 14)+
23339lysine decarboxylase-4.1.1.18
23339N-acetyl-beta-glucosaminidase-3.2.1.52
23339naphthol-AS-BI-phosphohydrolase+
23339ornithine decarboxylase-4.1.1.17
23339trypsin+3.4.21.4
23339urease-3.5.1.5
23339valine arylamidase+
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase-3.2.1.21
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382cystine arylamidase+3.4.11.3
68382trypsin-3.4.21.4
68382valine arylamidase-
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382esterase lipase (C 8)-
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
118836oxidase+
118836catalase+1.11.1.6
118836urease+3.5.1.5
68370alkaline phosphatase-3.1.3.1
68370beta-galactosidase-3.2.1.23
68370beta-glucuronidase-3.2.1.31
68370arginine dihydrolase-3.5.3.6
68370leucine arylamidase+3.4.11.1
68370alpha-galactosidase-3.2.1.22
68370pyrrolidonyl arylamidase+3.4.19.3
68370beta-glucosidase-3.2.1.21
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
118836-++--+-+--++--------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
15442+-------++++/-+++/-+/--++-+

API 20STR

@refVPHIPESCPYRAalpha GALbeta GURbeta GALPALLAPADHRIBARAMANSORLACTREINURAFAMDGLYG
15442++-+----+-----------

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinent
15442root nodules of Cytisus scopariusCytisus scopariusSpainESPEurope
60279Nodules from Cytisus scopariusSpainESPEurope
118836Legume Cystisus scoparius, nodulesSpainESPEurope

isolation source categories

Cat1Cat2Cat3
#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

@refbiosafety levelbiosafety level comment
154421Risk group (German classification)
1188361Risk 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: nuccore
  • NCBI tax ID: 407152

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Brucella cytisi LMG 22713GCA_012103075contigncbi407152
66792Ochrobactrum cytisi strain LMG 22713407152.6wgspatric407152

GC content

  • @ref: 15442
  • GC-content: 56.4
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno100yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no95.895yes
125438spore-formingspore-formingAbility to form endo- or exosporesno91.378yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes86.009yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno98.988yes
125438motile2+flagellatedAbility to perform flagellated movementyes58.887no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno95.5
125439BacteriaNetmotilityAbility to perform movementyes60.2
125439BacteriaNetgram_stainReaction to gram-stainingnegative89.6
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe97.9

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

@idauthorscataloguedoi/urltitlejournalpubmed
15442Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19778)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19778
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
23339José Luis Zurdo-Pineiro, Raúl Rivas, Martha E. Trujillo, Nieves Vizcaíno, José Antonio Carrasco, Manuel Chamber, Antonio Palomares, Pedro F. Mateos, Eustoquio Martínez-Molina, Encarna Velázquez10.1099/ijs.0.64613-0Ochrobactrum cytisi sp. nov., isolated from nodules of Cytisus scoparius in SpainIJSEM 57: 784-788 200717392207
37777Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7351
60279Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 54646)https://www.ccug.se/strain?id=54646
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
68369Automatically annotated from API 20NE
68370Automatically annotated from API 20STR
68382Automatically annotated from API zym
69479João 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
71534Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID292882.1StrainInfo: A central database for resolving microbial strain identifiers
118836Curators of the CIPCollection of Institut Pasteur (CIP 109590)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109590
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1