Strain identifier

BacDive ID: 7477

Type strain: No

Species: Zimmermannella alba

Strain Designation: A59836

Strain history: CIP <- 2004, IAM <- IFO <- D.A. de Briel, Strasbourg Hosp., Strasbourg, France: strain A59836

NCBI tax ID(s): 1915061 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 6990

BacDive-ID: 7477

DSM-Number: 17449

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

description: Zimmermannella alba A59836 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from human urine.

NCBI tax id

  • NCBI tax id: 1915061
  • Matching level: species

strain history

@refhistory
6990<- IAM <- TISTR (Zimmermannella alba) <- D. A. De Briel; A59836
67770NBRC 15616 (Microbacterium sp.) <-- IFO 15616 <-- D. A. de Briel A59836.
116181CIP <- 2004, IAM <- IFO <- D.A. de Briel, Strasbourg Hosp., Strasbourg, France: strain A59836

doi: 10.13145/bacdive7477.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Microbacteriaceae
  • genus: Zimmermannella
  • species: Zimmermannella alba
  • full scientific name: Zimmermannella alba Lin et al. 2004
  • synonyms

    • @ref: 20215
    • synonym: Pseudoclavibacter albus

@ref: 6990

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Pseudoclavibacter

species: Pseudoclavibacter sp.

full scientific name: Pseudoclavibacter sp.

strain designation: A59836

type strain: no

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
29956positive0.8 µm0.35 µmrod-shapedno
116181positiverod-shapedno

colony morphology

  • @ref: 116181

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6990TRYPTICASE 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
33251MEDIUM 6 - Columbia agar with 10 % horse bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
116181CIP Medium 6yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6

culture temp

@refgrowthtypetemperaturerange
6990positivegrowth28mesophilic
29956positiveoptimum30mesophilic
33251positivegrowth30mesophilic
58790positivegrowth37mesophilic
67770positivegrowth37mesophilic
116181positivegrowth25-41
116181nogrowth10psychrophilic
116181nogrowth15psychrophilic
116181nogrowth45thermophilic

culture pH

  • @ref: 29956
  • ability: positive
  • type: optimum
  • pH: 7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29956aerobe
58790microaerophile
116181obligate aerobe

spore formation

  • @ref: 29956
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
29956NaClpositivegrowth0.2-0.3 %
29956NaClpositiveoptimum0.25 %
116181NaClpositivegrowth0-4 %
116181NaClnogrowth6 %
116181NaClnogrowth8 %
116181NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: MK-10, MK-9, MK-7, MK-8

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11618116947citrate-carbon source
1161814853esculin-hydrolysis
116181606565hippurate+hydrolysis
11618117632nitrate-reduction
11618116301nitrite-reduction
11618117632nitrate-respiration

antibiotic resistance

  • @ref: 116181
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 116181
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11618115688acetoin-
11618117234glucose-

enzymes

@refvalueactivityec
29956alkaline phosphatase+3.1.3.1
29956catalase+1.11.1.6
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
116181oxidase-
116181beta-galactosidase-3.2.1.23
116181alcohol dehydrogenase+1.1.1.1
116181gelatinase-
116181amylase+
116181DNase-
116181caseinase-3.4.21.50
116181catalase+1.11.1.6
116181tween esterase+
116181gamma-glutamyltransferase+2.3.2.2
116181lecithinase+
116181lipase-
116181lysine decarboxylase-4.1.1.18
116181ornithine decarboxylase-4.1.1.17
116181phenylalanine ammonia-lyase-4.3.1.24
116181protease-
116181tryptophan deaminase-
116181urease-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
116181--+--+--+--++-------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116181-+-------+-----------------------------------------------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
6990human urineFranceFRAEurope
58790Human urineFranceFRAEuropeStrasbourg
67770UrineFranceFRAEurope
116181UrineFranceFRAEuropeStrasbourg

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body Product#Fluids#Urine

taxonmaps

  • @ref: 69479
  • File name: preview.99_757.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_459;97_526;98_604;99_757&stattab=map
  • Last taxonomy: Pseudoclavibacter alba subclade
  • 16S sequence: AB012590
  • Sequence Identity:
  • Total samples: 8250
  • soil counts: 1422
  • aquatic counts: 1777
  • animal counts: 4134
  • plant counts: 917

Safety information

risk assessment

  • @ref: 116181
  • biosafety level: 1
  • biosafety level comment: Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6990
  • description: Zimmermannella alba gene for 16S rRNA, partial sequence, strain: IFO 15616
  • accession: AB012590
  • length: 1481
  • database: ena
  • NCBI tax ID: 272241

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Zimmermannella alba NBRC 156161349786.3wgspatric1349786
66792Pseudoclavibacter alba NBRC 156162731957610draftimg1349786
67770[Zimmermannella] alba NBRC 15616GCA_001570905contigncbi1349786

GC content

@refGC-contentmethod
699068
6777064.7genome sequence analysis
6777068high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno93.909no
gram-positiveyes94.457no
anaerobicno98.609no
halophileno88.46yes
spore-formingno93.535no
glucose-utilyes81.467no
flagellatedno97.557no
aerobicyes68.645no
glucose-fermentno80.521no
thermophileno99.323yes

External links

@ref: 6990

culture collection no.: DSM 17449, IAM 14724, NBRC 15616, TISTR 1510, CCUG 50212, IFO 15616, JCM 12865, CIP 108566

straininfo link

  • @ref: 76922
  • straininfo: 62503

literature

  • topic: Phylogeny
  • Pubmed-ID: 15388726
  • title: Zimmermannella helvola gen. nov., sp. nov., Zimmermannella alba sp. nov., Zimmermannella bifida sp. nov., Zimmermannella faecalis sp. nov. and Leucobacter albus sp. nov., novel members of the family Microbacteriaceae.
  • authors: Lin YC, Uemori K, de Briel DA, Arunpairojana V, Yokota A
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.02741-0
  • year: 2004
  • mesh: Actinomycetales/*classification/*isolation & purification/physiology/ultrastructure, Actinomycetales Infections/microbiology, Amino Acids, Diamino/analysis, Animals, Bacterial Typing Techniques, Base Composition, Blood/microbiology, Butter/microbiology, Cattle, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Fatty Acids/analysis, Feces/microbiology, Genes, rRNA, Humans, Microscopy, Electron, Scanning, Molecular Sequence Data, Muramic Acids/chemistry, Peptidoglycan/chemistry, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil Microbiology, Urine/microbiology, Vitamin K 2/analysis, Wounds and Injuries/microbiology
  • topic2: Enzymology

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
6990Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17449)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17449
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
29956Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2632528776041
33251Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6202
58790Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 50212)https://www.ccug.se/strain?id=50212
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
76922Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID62503.1StrainInfo: A central database for resolving microbial strain identifiers
116181Curators of the CIPCollection of Institut Pasteur (CIP 108566)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108566