Strain identifier

BacDive ID: 1901

Type strain: Yes

Species: Pseudochrobactrum asaccharolyticum

Strain history: CIP <- 2005, CCUG

NCBI tax ID(s): 354351 (species)

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General

@ref: 18065

BacDive-ID: 1901

DSM-Number: 25619

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

description: Pseudochrobactrum asaccharolyticum DSM 25619 is an obligate aerobe, mesophilic, Gram-negative human pathogen that was isolated from knee aspirate of human.

NCBI tax id

  • NCBI tax id: 354351
  • Matching level: species

strain history

@refhistory
18065<- CIP <- CCUG <- PHLS, Göteborg, Sweden
400752005, CCUG
116518CIP <- 2005, CCUG

doi: 10.13145/bacdive1901.20230509.8.1

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 asaccharolyticum
  • full scientific name: Pseudochrobactrum asaccharolyticum Kämpfer et al. 2006

@ref: 18065

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Brucellaceae

genus: Pseudochrobactrum

species: Pseudochrobactrum asaccharolyticum

full scientific name: Pseudochrobactrum asaccharolyticum Kämpfer et al. 2006

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell shapemotilityconfidence
23346negative2 µmrod-shapedno
69480negative99.848
116518negativerod-shapedno

colony morphology

@refincubation periodcolony sizecolony colorcolony shapehemolysis ability
180651-2 days
233461 day2 mmbeige, translucentcircular
1165181

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
18065CASO 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
40075MEDIUM 6 - Columbia agar with 10 % horse bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
116518CIP Medium 6yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6
116518CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
18065positivegrowth30mesophilic
23346positivegrowth25-30mesophilic
40075positivegrowth30mesophilic
57027positivegrowth30-37mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 116518
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
23347no
69481no100
69480no99.998

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2334616865gamma-aminobutyric acid-assimilation
23346178794-hydroxybenzoate-assimilation
2334615963ribitol-assimilation
2334616958beta-alanine-assimilation
2334616947citrate-assimilation
2334617057cellobiose-assimilation
2334615824D-fructose-assimilation
2334612936D-galactose-assimilation
2334617634D-glucose-assimilation
2334617306maltose-assimilation
2334616899D-mannitol-assimilation
2334616024D-mannose-assimilation
2334616988D-ribose-assimilation
2334617924D-sorbitol-assimilation
2334616551D-trehalose-assimilation
2334665327D-xylose-assimilation
23346370543-hydroxybutyrate-assimilation
2334624996lactate-assimilation
2334629806fumarate-assimilation
2334624265gluconate-assimilation
2334617859glutaric acid-assimilation
2334617268myo-inositol-assimilation
2334630849L-arabinose-assimilation
2334629991L-aspartate-assimilation
2334615971L-histidine-assimilation
2334615603L-leucine-assimilation
2334615589L-malate-assimilation
2334662345L-rhamnose-assimilation
2334668428maltitol-assimilation
2334628037N-acetylgalactosamine-assimilation
23346506227N-acetylglucosamine-assimilation
2334618257ornithine-assimilation
2334617272propionate-assimilation
233469300suberic acid-assimilation
2334617992sucrose-assimilation
2334615708trans-aconitate-assimilation
23346gamma-L-glutamate-4-nitroanilide-hydrolysis
2334691050p-nitrophenyl phenyl phosphonate-hydrolysis
2334615361pyruvate-
2334616383cis-aconitate+assimilation
23346L-proline-4-nitroanilide+hydrolysis
6836925115malate+assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine+assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
683695291gelatin-hydrolysis
683694853esculin-hydrolysis
6836916199urea+hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction
11651817632nitrate-reduction
11651816301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
11651835581indoleno

metabolite tests

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

enzymes

@refvalueactivityec
18065catalase+1.11.1.6
18065cytochrome-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
68382naphthol-AS-BI-phosphohydrolase+
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)+
68382alkaline phosphatase+3.1.3.1
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease+3.5.1.5
68369arginine dihydrolase-3.5.3.6
116518oxidase+
116518alcohol dehydrogenase-1.1.1.1
116518catalase+1.11.1.6
116518lysine decarboxylase-4.1.1.18
116518ornithine decarboxylase-4.1.1.17
116518urease-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
116518-+++-+--+-++--------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
18065----+---+---+----++-
18065----+---+---+----+++
18065----+---+/----+----++++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentenrichment culturesampling date
18065knee aspirate of humanUddevallaSwedenSWEEurope
23347knee aspirate of a 66 year old manblood agar
57027Human knee aspirate,66-yr-old manUddevallaSwedenSWEEurope2001-12-21
116518Human, Knee aspirateUddevallaSwedenSWEEurope

isolation source categories

Cat1Cat2Cat3
#Infection#Patient
#Host#Human
#Host Body-Site#Limb#Leg
#Host Body Product#Fluids#Aspirate
#Host#Human#Male

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: AM180485
  • Sequence Identity:
  • Total samples: 1773
  • soil counts: 281
  • aquatic counts: 437
  • animal counts: 988
  • plant counts: 67

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
18065yes, in single cases1Risk group (German classification)
1165181Risk group (French classification)

Sequence information

16S sequences

  • @ref: 18065
  • description: Pseudochrobactrum asaccharolyticum partial 16S rRNA gene, type strain CCUG 46016
  • accession: AM180485
  • length: 1456
  • database: ena
  • NCBI tax ID: 354351

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudochrobactrum asaccharolyticum DSM 25619GCA_003314995scaffoldncbi354351
66792Pseudochrobactrum asaccharolyticum strain DSM 25619354351.3wgspatric354351
66792Pseudochrobactrum asaccharolyticum DSM 256192770939620draftimg354351

GC content

  • @ref: 23347
  • GC-content: 50.9

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno86.899yes
flagellatedno95.919no
gram-positiveno97.429yes
anaerobicno99.341no
aerobicyes89.267no
halophileno72.809no
spore-formingno97.485no
glucose-utilyes78.157yes
thermophileno98.421no
glucose-fermentno87.235no

External links

@ref: 18065

culture collection no.: DSM 25619, CCUG 46016, CIP 108977

straininfo link

  • @ref: 71545
  • straininfo: 110567

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
18065Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25619)https://www.dsmz.de/collection/catalogue/details/culture/DSM-25619
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
23347Peter Kämpfer, Holger Scholz, Birgit Huber, Kathrin Thummes, Hans-Jürgen Busse, Elizabeth W. Maas, Enevold Falsen10.1099/ijs.0.64714-0Description of Pseudochrobactrum kiredjianiae sp. nov.IJSEM 57: 755-760 200717392201
40075Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6666
57027Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 46016)https://www.ccug.se/strain?id=46016
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
68369Automatically annotated from API 20NE
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
71545Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID110567.1StrainInfo: A central database for resolving microbial strain identifiers
116518Curators of the CIPCollection of Institut Pasteur (CIP 108977)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108977