Strain identifier

BacDive ID: 1888

Type strain: Yes

Species: Brucella intermedia

Strain history: <- CIP; CIP 105838 <- I. Moriyón, Univ. Navarra, Spain; CNS 2-75

NCBI tax ID(s): 641118 (strain), 94625 (species)

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General

@ref: 7318

BacDive-ID: 1888

DSM-Number: 17986

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, motile, rod-shaped

description: Brucella intermedia DSM 17986 is a mesophilic, motile, rod-shaped bacterium that was isolated from human blood.

NCBI tax id

NCBI tax idMatching level
94625species
641118strain

strain history

  • @ref: 7318
  • history: <- CIP; CIP 105838 <- I. Moriyón, Univ. Navarra, Spain; CNS 2-75

doi: 10.13145/bacdive1888.20230509.8.1

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 intermedia
  • full scientific name: Brucella intermedia (Velasco et al. 1998) Hördt et al. 2020

  • synonyms

    • @ref: 20215
    • synonym: Ochrobactrum intermedium

@ref: 7318

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Brucellaceae

genus: Brucella

species: Brucella intermedia

full scientific name: Brucella intermedia (Velasco et al. 1998) Hördt et al. 2020

type strain: yes

Morphology

cell morphology

  • @ref: 23338
  • cell shape: rod-shaped
  • motility: yes
  • flagellum arrangement: lophotrichous

colony morphology

@refincubation periodcolony sizecolony shapemedium used
73181-2 days
233381 day1 mmcircularNutrient agar

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7318COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://mediadive.dsmz.de/medium/693Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
7318TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: 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
7318TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
23338Nutrient agar (NA)yes
37230MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)

culture temp

@refgrowthtypetemperaturerange
7318positivegrowth30mesophilic
23338positivegrowth37mesophilic
23338positivegrowth18-22psychrophilic
37230positivegrowth30mesophilic

Physiology and metabolism

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
23338323734-coumarate-assimilation
2333817128adipate-assimilation
2333822599arabinose-assimilation
2333817234glucose-assimilation
2333817268myo-inositol-assimilation
2333817716lactose-assimilation
2333817306maltose-assimilation
2333829864mannitol-assimilation
2333828053melibiose-assimilation
2333818401phenylacetate-assimilation
2333816634raffinose-assimilation
2333826546rhamnose-assimilation
2333817992sucrose-assimilation
2333830911sorbitol-assimilation
233384-nitrophenyl beta-D-galactopyranoside hydrolysate-hydrolysis
23338901464-nitrophenyl beta-D-glucuronide-hydrolysis
23338901484-nitrophenyl beta-D-xylopyranoside-hydrolysis
233383122bis-4-nitrophenyl phosphate-hydrolysis
233384853esculin-hydrolysis
23338L-proline-4-nitroanilide-hydrolysis
23338O-nitrophenyl-beta-D-galactopyranosid-hydrolysis
2333855394p-nitrophenylphosphocholine-hydrolysis
2333827856acetamide-
2333815792malonate-
2333816947citrate+assimilation
2333817754glycerol+assimilation
2333817306maltose+assimilation
23338902594-nitrophenyl beta-D-glucopyranoside+hydrolysis
233383122bis-4-nitrophenyl phosphate+hydrolysis
2333817632nitrate+reduction
6836925115malate+assimilation
6836917128adipate-assimilation
6836927689decanoate+assimilation
6836917306maltose+assimilation
6836959640N-acetylglucosamine+assimilation
6836916899D-mannitol+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

  • @ref: 23338
  • ChEBI: 37943
  • metabolite: colistin
  • is antibiotic: yes
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
2333835581indoleno
2333816136hydrogen sulfideyes
6836935581indoleno

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
23338arginine dihydrolase-3.5.3.6
23338cytochrome oxidase+1.9.3.1
23338gelatinase-
23338lysine decarboxylase-4.1.1.18
23338ornithine decarboxylase-4.1.1.17
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 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
7318--------+++++++/-+-++-+

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
7318human bloodFranceFRAEurope
48013Human bloodFranceFRAEurope

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body Product#Fluids#Blood

taxonmaps

  • @ref: 69479
  • File name: preview.99_1515.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_45;97_47;98_51;99_1515&stattab=map
  • Last taxonomy: Brucella
  • 16S sequence: AM114411
  • Sequence Identity:
  • Total samples: 901
  • soil counts: 255
  • aquatic counts: 171
  • animal counts: 403
  • plant counts: 72

Safety information

risk assessment

  • @ref: 7318
  • biosafety level: 2
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Ochrobactrum intermedium 16S rRNA gene (partial), 23S rRNA gene (partial), tRNA-Ile gene, tRNA-Ala gene and ITS1, type strain LMG 3301, allele AAJ867340913ena94625
20218Ochrobactrum intermedium 16S rRNA gene (partial), 23S rRNA gene (partial), tRNA-Ile gene, tRNA-Ala gene and ITS1, type strain LMG 3301, allele BAJ867341915ena94625
20218Ochrobactrum intermedium 16S rRNA gene (partial), 23S rRNA gene (partial), tRNA-Ile gene, tRNA-Ala gene and ITS1, type strain LMG 3301, allele CAJ867342915ena94625
20218Ochrobactrum intermedium 16S rRNA gene (partial), 23S rRNA gene (partial), tRNA-Ile gene, tRNA-Ala gene and ITS1, type strain LMG 3301, allele DAJ867343936ena94625
20218Ochrobactrum intermedium 16S rRNA gene (partial), 23S rRNA gene (partial), tRNA-Ile gene, tRNA-Ala gene and ITS1, type strain LMG 3301, allele EAJ867344985ena94625
20218Ochrobactrum intermedium partial 16S rRNA gene, strain LMG 3301TAM4906231390ena641118
23338Ochrobactrum intermedium LMG 3301 16S ribosomal RNA gene, partial sequenceU709781454nuccore641118
7318Ochrobactrum intermedium gene for 16S rRNA, partial sequence, strain: NBRC 15820AB6809671410ena94625
7318Ochrobactrum intermedium partial 16S rRNA gene, type strain CCUG 24694TAM1144111390ena94625

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Brucella intermedia NCTC12171GCA_900454225contigncbi94625
66792Brucella intermedia LMG 3301GCA_000182645scaffoldncbi641118
66792Brucella intermedia CIP 105838GCA_012103055contigncbi94625
66792Ochrobactrum intermedium LMG 3301641118.3wgspatric641118
66792Ochrobactrum intermedium strain CIP 10583894625.26wgspatric94625
66792Ochrobactrum intermedium strain NCTC1217194625.13wgspatric94625
66792Ochrobactrum intermedium LMG 3301645058765draftimg641118

GC content

  • @ref: 23338
  • GC-content: 57.7-58.3

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes81.775yes
flagellatedno85.664yes
gram-positiveno98.293no
anaerobicno97.759no
aerobicyes94.057no
halophileno93.299no
spore-formingno95.926no
thermophileno98.421no
glucose-utilyes92.206no
glucose-fermentno91.194no

External links

@ref: 7318

culture collection no.: DSM 17986, CIP 105838, LMG 3301, NCTC 12171, CCUG 24694, CNS 2-75

straininfo link

  • @ref: 71532
  • straininfo: 3682

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny9734029Evaluation of the relatedness of Brucella spp. and Ochrobactrum anthropi and description of Ochrobactrum intermedium sp. nov., a new species with a closer relationship to Brucella spp.Velasco J, Romero C, Lopez-Goni I, Leiva J, Diaz R, Moriyon IInt J Syst Bacteriol10.1099/00207713-48-3-7591998Animals, Bacterial Proteins/analysis, Base Sequence, Brucella/*classification/genetics/immunology, Cross Reactions, Humans, Molecular Sequence Data, Phenotype, RNA, Ribosomal, 16S/genetics, RabbitsPathogenicity
Phylogeny16352412Comparative sequence analysis of the internal transcribed spacer 1 of Ochrobactrum species.Lebuhn M, Bathe S, Achouak W, Hartmann A, Heulin T, Schloter MSyst Appl Microbiol10.1016/j.syapm.2005.11.0032005Alleles, DNA, Bacterial/chemistry/genetics, DNA, Intergenic/*chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Gene Transfer, Horizontal, *Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Ochrobactrum/classification/*genetics, Phylogeny, Polymorphism, Genetic, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Statistics as TopicTranscriptome
Phylogeny18473108Isolation of urease-positive Ochrobactrum intermedium in the stomach of a non-ulcer dyspeptic patient from north India.Dharne MS, Misra SP, Misra V, Dwivedi M, Patole MS, Shouche YSJ Microbiol Immunol Infect2008Adult, Bacterial Proteins/genetics/*metabolism, Dyspepsia/*microbiology/pathology, Gram-Negative Aerobic Rods and Cocci/classification/genetics/isolation & purification, Gram-Negative Bacterial Infections/*microbiology/pathology, Helicobacter pylori/genetics/isolation & purification, Humans, India, Male, Molecular Sequence Data, Ochrobactrum/enzymology/genetics/*isolation & purification, Phylogeny, Stomach/*microbiology/pathology, Urease/genetics/*metabolismEnzymology
Phylogeny19684324Ochrobactrum ciceri sp. nov., isolated from nodules of Cicer arietinum.Imran A, Hafeez FY, Fruhling A, Schumann P, Malik KA, Stackebrandt EInt J Syst Evol Microbiol10.1099/ijs.0.013987-02009Base Sequence, Cicer/*microbiology, Fatty Acids/analysis, Molecular Sequence Data, Ochrobactrum/*classification/genetics/isolation & purification, Phylogeny, RNA, Ribosomal, 16S/genetics, Spectrometry, Mass, Matrix-Assisted Laser Desorption-IonizationGenetics
Phylogeny20952542Ochrobactrum pecoris sp. nov., isolated from farm animals.Kampfer P, Huber B, Busse HJ, Scholz HC, Tomaso H, Hotzel H, Melzer FInt J Syst Evol Microbiol10.1099/ijs.0.027631-02010Animals, Animals, Domestic/microbiology, Bacterial Typing Techniques, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Ochrobactrum/*classification/genetics/*isolation & purification, Phospholipids/analysis, Phylogeny, Polyamines/analysis, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Rec A Recombinases/genetics, Sequence Analysis, DNA, Sheep/*microbiology, Sus scrofa/*microbiologyGenetics
23557353Draft genome of Ochrobactrum intermedium strain M86 isolated from non-ulcer dyspeptic individual from India.Kulkarni G, Dhotre D, Dharne M, Shetty S, Chowdhury S, Misra V, Misra S, Patole M, Shouche YGut Pathog10.1186/1757-4749-5-72013
Biotechnology24038701Acquired genetic mechanisms of a multiresistant bacterium isolated from a treatment plant receiving wastewater from antibiotic production.Johnning A, Moore ER, Svensson-Stadler L, Shouche YS, Larsson DG, Kristiansson EAppl Environ Microbiol10.1128/AEM.02141-132013Anti-Bacterial Agents/*pharmacology, DNA Mutational Analysis, DNA Transposable Elements, *Drug Resistance, Bacterial, Gene Transfer, Horizontal, Genome, Bacterial, India, *Industrial Waste, Microbial Sensitivity Tests, Mutation, Missense, Ochrobactrum/*drug effects/*genetics/isolation & purification, Sequence Analysis, DNA, Waste Water/*microbiologyGenetics
Phylogeny26465134Isolation and characterization of a crude oil degrading bacteria from formation water: comparative genomic analysis of environmental Ochrobactrum intermedium isolate versus clinical strains.Chai LJ, Jiang XW, Zhang F, Zheng BW, Shu FC, Wang ZL, Cui QF, Dong HP, Zhang ZZ, Hou DJ, She YHJ Zhejiang Univ Sci B10.1631/jzus.B15000292015Bacterial Proteins/*genetics, Ochrobactrum/classification/*genetics/*isolation & purification, Petroleum/*microbiology, Species Specificity, *Water MicrobiologyEnzymology
Pathogenicity28713341Prevalence, Host Range, and Comparative Genomic Analysis of Temperate Ochrobactrum Phages.Jackel C, Hertwig S, Scholz HC, Nockler K, Reetz J, Hammerl JAFront Microbiol10.3389/fmicb.2017.012072017

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
7318Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17986)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17986
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
23338Julián Velasco, Conchi Romero, Ignacio López-Goni, José Leiva, Ramón Díaz, Ignacio Moriyón10.1099/00207713-48-3-759Evaluation of the relatedness of Brucella spp. and Ochrobactrum anthropi and description of Ochrobactrum intermedium sp. nov., a new species with a closer relationship to Brucella spp.IJSEM 48: 759-768 19989734029
37230Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17902
48013Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 24694)https://www.ccug.se/strain?id=24694
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
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
71532Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID3682.1StrainInfo: A central database for resolving microbial strain identifiers