Strain identifier

BacDive ID: 1900

Type strain: Yes

Species: Pseudochrobactrum saccharolyticum

Strain history: CIP <- 2005, CCUG

NCBI tax ID(s): 354352 (species)

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General

@ref: 18066

BacDive-ID: 1900

DSM-Number: 25620

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, Gram-negative, rod-shaped

description: Pseudochrobactrum saccharolyticum DSM 25620 is an obligate aerobe, mesophilic, Gram-negative bacterium that was isolated from industrial glue.

NCBI tax id

  • NCBI tax id: 354352
  • Matching level: species

strain history

@refhistory
18066<- CIP <- CCUG <- A. Möller and A.B. Mölnlycke
340162005, CCUG
122334CIP <- 2005, CCUG

doi: 10.13145/bacdive1900.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Brucellaceae
  • genus: Pseudochrobactrum
  • species: Pseudochrobactrum saccharolyticum
  • full scientific name: Pseudochrobactrum saccharolyticum Kämpfer et al. 2006

@ref: 18066

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Brucellaceae

genus: Pseudochrobactrum

species: Pseudochrobactrum saccharolyticum

full scientific name: Pseudochrobactrum saccharolyticum Kämpfer et al. 2006

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
23346negativerod-shapedno
69480negative99.946
122334negativerod-shapedno

colony morphology

@refincubation periodcolony sizecolony colorcolony shapehemolysis ability
180661-2 days
233461 day2 mmbeige, translucentcircular
1223341

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
18066CASO AGAR (MERCK 105458) (DSMZ Medium 220)yeshttps://mediadive.dsmz.de/medium/220Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water
23346MacConkeyyes
23346Nutrient agar (NA)yes
23346Reasoner's 2A agar (R2A)yes
23346Trypticase Soy Agar (TSA)yes
34016MEDIUM 6 - Columbia agar with 10 % horse bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
122334CIP Medium 6yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6
122334CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
18066positivegrowth30mesophilic
23346positivegrowth25-30mesophilic
34016positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 122334
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
23346no
69481no100
69480no99.998

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
23346178794-hydroxybenzoate-assimilation
2334615963ribitol-assimilation
2334616947citrate-assimilation
2334617057cellobiose-assimilation
2334617306maltose-assimilation
2334616899D-mannitol-assimilation
2334617924D-sorbitol-assimilation
2334624265gluconate-assimilation
2334617268myo-inositol-assimilation
2334615603L-leucine-assimilation
2334662345L-rhamnose-assimilation
2334668428maltitol-assimilation
2334628037N-acetylgalactosamine-assimilation
233469300suberic acid-assimilation
2334617992sucrose-assimilation
2334615708trans-aconitate-assimilation
23346gamma-L-glutamate-4-nitroanilide-hydrolysis
2334691050p-nitrophenyl phenyl phosphonate-hydrolysis
2334616865gamma-aminobutyric acid+assimilation
2334616958beta-alanine+assimilation
2334616383cis-aconitate+assimilation
2334615824D-fructose+assimilation
2334612936D-galactose+assimilation
2334617634D-glucose+assimilation
2334616024D-mannose+assimilation
2334616988D-ribose+assimilation
2334616551D-trehalose+assimilation
2334665327D-xylose+assimilation
23346370543-hydroxybutyrate+assimilation
2334624996lactate+assimilation
2334629806fumarate+assimilation
2334617859glutaric acid+assimilation
2334630849L-arabinose+assimilation
2334629991L-aspartate+assimilation
2334615971L-histidine+assimilation
2334615589L-malate+assimilation
23346506227N-acetylglucosamine+assimilation
2334618257ornithine+assimilation
2334617272propionate+assimilation
23346L-proline-4-nitroanilide+hydrolysis
2334615361pyruvate+
6836925115malate+assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-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
12233417632nitrate-reduction
12233416301nitrite-reduction
6837717634D-glucose+builds acid from
6837715824D-fructose-builds acid from
6837717306maltose-builds acid from
6837717992sucrose-builds acid from
6837718257ornithine-degradation
6837716199urea-hydrolysis
6837727897tryptophan-energy source

metabolite production

@refChebi-IDmetaboliteproduction
6837735581indoleno
6836935581indoleno
12233435581indoleno

metabolite tests

@refChebi-IDmetaboliteindole test
6837735581indole-
6836935581indole-

enzymes

@refvalueactivityec
18066catalase+1.11.1.6
18066cytochrome-c oxidase+1.9.3.1
23346cytochrome oxidase+1.9.3.1
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin+3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68377tryptophan deaminase-4.1.99.1
68377gamma-glutamyltransferase-2.3.2.2
68377proline-arylamidase+3.4.11.5
68377beta-galactosidase-3.2.1.23
68377alkaline phosphatase-3.1.3.1
68377lipase-
68377urease-3.5.1.5
68377ornithine decarboxylase-4.1.1.17
68377beta-lactamase-3.5.2.6
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
122334oxidase+
122334alcohol dehydrogenase-1.1.1.1
122334catalase+1.11.1.6
122334lysine decarboxylase-4.1.1.18
122334ornithine decarboxylase-4.1.1.17
122334urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
51784-+++-+--+-+---------
122334--++-+--+-++--------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
18066--------+-+-+----++-+

API NH

@refPENGLUFRUMALSACODCURELIPPALbeta GALProAGGTIND
51784-+--------+--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentenrichment culture
18066industrial glueGöteborgSwedenSWEEurope
23346blood agar
51784Industrial glueGöteborgSwedenSWEEurope
122334Environment, Industrial glueGöteborgSwedenSWEEurope

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Industrial
  • Cat3: #Engineered product

taxonmaps

  • @ref: 69479
  • File name: preview.99_3029.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_1591;97_1899;98_2331;99_3029&stattab=map
  • Last taxonomy: Pseudochrobactrum
  • 16S sequence: AM180484
  • Sequence Identity:
  • Total samples: 1773
  • soil counts: 281
  • aquatic counts: 437
  • animal counts: 988
  • plant counts: 67

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
180661Risk group (German classification)
1223341Risk group (French classification)

Sequence information

16S sequences

  • @ref: 18066
  • description: Pseudochrobactrum saccharolyticum partial 16S rRNA gene, type strain CCUG 33852
  • accession: AM180484
  • length: 1401
  • database: ena
  • NCBI tax ID: 354352

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudochrobactrum saccharolyticum CCUG 33852GCA_008801715contigncbi354352
66792Pseudochrobactrum saccharolyticum DSM 25620GCA_014203195scaffoldncbi354352
66792Pseudochrobactrum saccharolyticum strain CCUG 33852354352.3wgspatric354352
66792Pseudochrobactrum saccharolyticum strain DSM 25620354352.4wgspatric354352
66792Pseudochrobactrum saccharolyticum DSM 256202861726604draftimg354352

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno93.97no
gram-positiveno98.355yes
anaerobicno99.088no
aerobicyes87.472no
halophileno63.936no
spore-formingno97.576yes
glucose-utilyes86.076yes
thermophileno97.122yes
motileno85.683yes
glucose-fermentno88.894yes

External links

@ref: 18066

culture collection no.: DSM 25620, CCUG 33852, CIP 108976

straininfo link

  • @ref: 71544
  • straininfo: 56742

literature

  • topic: Phylogeny
  • Pubmed-ID: 16902015
  • title: Description of Pseudochrobactrum gen. nov., with the two species Pseudochrobactrum asaccharolyticum sp. nov. and Pseudochrobactrum saccharolyticum sp. nov.
  • authors: Kampfer P, Rossello-Mora R, Scholz HC, Welinder-Olsson C, Falsen E, Busse HJ
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.64256-0
  • year: 2006
  • mesh: Adhesives, Aged, Bacterial Proteins/genetics, DNA, Bacterial/genetics, Environmental Microbiology, Fatty Acids/analysis, Gram-Negative Bacterial Infections/microbiology, Humans, Lipids/analysis, Male, Molecular Sequence Data, Nucleic Acid Hybridization, Ochrobactrum/chemistry/*classification/isolation & purification/physiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Rec A Recombinases/genetics, Sequence Homology, Nucleic Acid, Species Specificity
  • topic2: Pathogenicity

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
18066Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25620)https://www.dsmz.de/collection/catalogue/details/culture/DSM-25620
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
23346Peter Kämpfer, Ramon Rosselló-Mora, Holger C. Scholz, Christina Welinder-Olsson, Enevold Falsen, Hans-Jürgen Busse10.1099/ijs.0.64256-0Description of Pseudochrobactrum gen. nov., with the two species Pseudochrobactrum asaccharolyticum sp. nov. and Pseudochrobactrum saccharolyticum sp. nov.IJSEM 56: 1823-1829 200616902015
34016Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6665
51784Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 33852)https://www.ccug.se/strain?id=33852
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
68377Automatically annotated from API NH
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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
71544Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID56742.1StrainInfo: A central database for resolving microbial strain identifiers
122334Curators of the CIPCollection of Institut Pasteur (CIP 108976)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108976