Strain identifier

BacDive ID: 7578

Type strain: Yes

Species: Pseudoglutamicibacter cumminsii

Strain history: CIP <- 1996, G. Funke, Inst. Med. Mikrobiol., Zürich, Switzerland: strain DMMZ 445

NCBI tax ID(s): 156979 (species)

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General

@ref: 3940

BacDive-ID: 7578

DSM-Number: 10493

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic

description: Pseudoglutamicibacter cumminsii DSM 10493 is an obligate aerobe, mesophilic bacterium that was isolated from urine.

NCBI tax id

  • NCBI tax id: 156979
  • Matching level: species

strain history

@refhistory
3940<- G. Funke, DMMZ 445
373081996, G. Funke, Inst. Med. Mikrobiol., Zürich, Switzerland: strain DMMZ 445
67770CCUG 36788 <-- G. Funke DMMZ 445.
118813CIP <- 1996, G. Funke, Inst. Med. Mikrobiol., Zürich, Switzerland: strain DMMZ 445

doi: 10.13145/bacdive7578.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Micrococcaceae
  • genus: Pseudoglutamicibacter
  • species: Pseudoglutamicibacter cumminsii
  • full scientific name: Pseudoglutamicibacter cumminsii (Funke et al. 1997) Busse 2016

  • synonyms

    • @ref: 20215
    • synonym: Arthrobacter cumminsii

@ref: 3940

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micrococcaceae

genus: Pseudoglutamicibacter

species: Pseudoglutamicibacter cumminsii

full scientific name: Pseudoglutamicibacter cumminsii (Funke et al. 1997) Busse 2016

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no95.256
69480100positive
118813nopositiverod-shaped

colony morphology

  • @ref: 118813
  • hemolysis ability: 1

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3940TRYPTICASE 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
37308MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
118813CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
3940positivegrowth30mesophilic
37308positivegrowth37mesophilic
67770positivegrowth37mesophilic
118813positivegrowth25-41
118813nogrowth10psychrophilic
118813nogrowth15psychrophilic
118813nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 118813
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.999

halophily

  • @ref: 118813
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-10 %

murein

  • @ref: 3940
  • murein short key: A11.58
  • type: A4alpha L-Lys-L-Ser-L-Glu

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11881316947citrate-carbon source
1188134853esculin-hydrolysis
118813606565hippurate+hydrolysis
11881317632nitrate-reduction
11881316301nitrite-reduction
11881317632nitrate-respiration

antibiotic resistance

  • @ref: 118813
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 118813
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11881315688acetoin+
11881317234glucose-

enzymes

@refvalueactivityec
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
118813oxidase+
118813beta-galactosidase+3.2.1.23
118813alcohol dehydrogenase-1.1.1.1
118813gelatinase+/-
118813amylase-
118813DNase-
118813caseinase+3.4.21.50
118813catalase+1.11.1.6
118813tween esterase-
118813gamma-glutamyltransferase-2.3.2.2
118813lecithinase+
118813lipase-
118813lysine decarboxylase-4.1.1.18
118813ornithine decarboxylase-4.1.1.17
118813phenylalanine ammonia-lyase-4.3.1.24
118813tryptophan deaminase-
118813urease-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
118813--++-+-++-++--------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
118813-------------------------------------------------------------+-++----+--+--------------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
3940urine
53392Human urineZürichSwitzerlandCHEEurope
67770Human urineZurichSwitzerlandCHEEurope
118813Human, UrineZurichSwitzerlandCHEEurope

isolation source categories

  • Cat1: #Host Body Product
  • Cat2: #Fluids
  • Cat3: #Urine

taxonmaps

  • @ref: 69479
  • File name: preview.99_26621.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_2056;97_2481;98_3072;99_26621&stattab=map
  • Last taxonomy: Pseudoglutamicibacter cumminsii
  • 16S sequence: X93354
  • Sequence Identity:
  • Total samples: 13267
  • soil counts: 471
  • aquatic counts: 793
  • animal counts: 11840
  • plant counts: 163

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
39402Risk group (German classification)
1188131Risk group (French classification)

Sequence information

16S sequences

  • @ref: 3940
  • description: Arthrobacter cumminsii 16S rRNA gene (strain 445)
  • accession: X93354
  • length: 1483
  • database: ena
  • NCBI tax ID: 156979

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudoglutamicibacter cumminsii DSM 10493GCA_016907775contigncbi156979
66792Pseudoglutamicibacter cumminsii strain DSM 10493156979.27wgspatric156979
66792Pseudoglutamicibacter cumminsii DSM 104932893672949draftimg156979

GC content

@refGC-contentmethod
394061high performance liquid chromatography (HPLC)
6777060high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno95.455no
gram-positiveyes93.869no
anaerobicno98.49no
aerobicyes86.633no
halophileyes58.785no
spore-formingno93.92no
thermophileno97.819yes
glucose-utilyes76.05no
flagellatedno98.05no
glucose-fermentno90.26no

External links

@ref: 3940

culture collection no.: DSM 10493, ATCC 700218, CCM 4574, CCUG 36788, CIP 104907, JCM 11675, KCTC 9904, DMMZ 445

straininfo link

  • @ref: 77022
  • straininfo: 43830

Reference

@idauthorscataloguedoi/urltitle
3940Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 10493)https://www.dsmz.de/collection/catalogue/details/culture/DSM-10493
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
37308Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16868
53392Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 36788)https://www.ccug.se/strain?id=36788
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
77022Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID43830.1StrainInfo: A central database for resolving microbial strain identifiers
118813Curators of the CIPCollection of Institut Pasteur (CIP 104907)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104907