Strain identifier

BacDive ID: 7492

Type strain: Yes

Species: Microcella putealis

Strain Designation: CV-2

Strain history: CIP <- 2004, I. Tiago, Coimbra Univ., Coimbra, Portugal: strain CV-2

NCBI tax ID(s): 337005 (species)

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

@ref: 8219

BacDive-ID: 7492

DSM-Number: 19627

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

description: Microcella putealis CV-2 is an obligate aerobe, mesophilic, rod-shaped bacterium that was isolated from alkaline groundwater.

NCBI tax id

  • NCBI tax id: 337005
  • Matching level: species

strain history

@refhistory
8219<- CIP <- I. Tiago, strain CV-2
122067CIP <- 2004, I. Tiago, Coimbra Univ., Coimbra, Portugal: strain CV-2

doi: 10.13145/bacdive7492.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Microbacteriaceae
  • genus: Microcella
  • species: Microcella putealis
  • full scientific name: Microcella putealis Tiago et al. 2005

@ref: 8219

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Microcella

species: Microcella putealis

full scientific name: Microcella putealis Tiago et al. 2005

strain designation: CV-2

type strain: yes

Morphology

cell morphology

  • @ref: 122067
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 122067
  • hemolysis ability: 1

pigmentation

  • @ref: 122067
  • production: no
  • name: Flexirubin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8219CASTENHOLZ MEDIUM (DSMZ Medium 86)yeshttps://mediadive.dsmz.de/medium/86Name: CASTENHOLZ MEDIUM (DSMZ Medium 86; with strain-specific modifications) Composition: Yeast extract 5.0 g/l Tryptone 1.0 g/l NaNO3 0.689 g/l Na2HPO4 x 2 H2O 0.14 g/l KNO3 0.103 g/l MgSO4 x 7 H2O 0.1 g/l Nitrilotriacetic acid 0.1 g/l CaSO4 x 2 H2O 0.06 g/l NaCl 0.008 g/l MnSO4 x H2O 0.0022 g/l H3BO3 0.0005 g/l ZnSO4 x 7 H2O 0.0005 g/l FeCl3 x 6 H2O 0.00047 g/l CoCl2 x 6 H2O 4.6e-05 g/l CuSO4 x 5 H2O 2.5e-05 g/l Na2MoO4 x 2 H2O 2.5e-05 g/l Distilled water
34321MEDIUM 591 - for No nameyesDistilled water make up to (690.000 ml);Agar (15.000 g);Yeast extract (5.000 g);Tryptone (5.000 g);Ketoglutaric acid (1.000 g);Thermus macronutrients 10X solution - M00976 (100.000 ml);Thermus micronutrients 100X solution - M00975 (10.000 ml);Carbonatebic
122067CIP Medium 591yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=591

culture temp

@refgrowthtypetemperaturerange
8219positivegrowth35mesophilic
34321positivegrowth37mesophilic
122067positivegrowth25-37mesophilic
122067nogrowth5psychrophilic
122067nogrowth15psychrophilic
122067nogrowth41thermophilic
122067nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 122067
  • oxygen tolerance: obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
122067NaClnogrowth0 %
122067NaClnogrowth2 %
122067NaClnogrowth4 %
122067NaClnogrowth6 %
122067NaClnogrowth8 %
122067NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12206716947citrate-carbon source
1220674853esculin+hydrolysis
122067606565hippurate-hydrolysis
12206717632nitrate-builds gas from
12206717632nitrate-reduction
12206716301nitrite-builds gas from
12206716301nitrite-reduction
12206715792malonate-assimilation

antibiotic resistance

  • @ref: 122067
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 122067
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12206715688acetoin-
12206717234glucose-

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
122067oxidase-
122067beta-galactosidase+3.2.1.23
122067alcohol dehydrogenase-1.1.1.1
122067gelatinase-
122067catalase+1.11.1.6
122067gamma-glutamyltransferase-2.3.2.2
122067lysine decarboxylase-4.1.1.18
122067ornithine decarboxylase-4.1.1.17
122067phenylalanine ammonia-lyase-4.3.1.24
122067tryptophan deaminase-
122067urease-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
122067--++-++----+---+----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122067------------------+--------------------------------------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
8219alkaline groundwaterCabeco de VidePortugalPRTEurope
122067Environment, Alkaline ground waterCabeco de VidePortugalPRTEurope2000

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Groundwater
#Condition#Alkaline

taxonmaps

  • @ref: 69479
  • File name: preview.99_50742.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_2880;97_3539;98_7730;99_50742&stattab=map
  • Last taxonomy: Microcella
  • 16S sequence: AJ717388
  • Sequence Identity:
  • Total samples: 1981
  • soil counts: 530
  • aquatic counts: 882
  • animal counts: 298
  • plant counts: 271

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
82191Risk group (German classification)
1220671Risk group (French classification)

Sequence information

16S sequences

  • @ref: 8219
  • description: Microcella putealis 16S rRNA gene, type strain CV2T
  • accession: AJ717388
  • length: 1497
  • database: ena
  • NCBI tax ID: 337005

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Microcella putealis DSM 19627GCA_006716545contigncbi337005
66792Microcella putealis strain DSM 19627337005.6wgspatric337005
66792Microcella putealis DSM 196272818991222draftimg337005

GC content

  • @ref: 8219
  • GC-content: 68.8

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
gram-positiveyes93.674no
anaerobicno98.678no
halophileno73.325no
spore-formingno93.144no
glucose-utilyes86.7no
motileno91.231no
flagellatedno97.335no
thermophileno96.937yes
aerobicyes90.211no
glucose-fermentno87.431no

External links

@ref: 8219

culture collection no.: DSM 19627, CIP 108471, LMG 22692, KCTC 19625

straininfo link

  • @ref: 76938
  • straininfo: 132329

literature

  • topic: Phylogeny
  • Pubmed-ID: 34628559
  • title: Microcella flavibacter sp. nov., isolated from marine sediment, and reclassification of Chryseoglobus frigidaquae, Chryseoglobus indicus, and Yonghaparkia alkaliphila as Microcella frigidaquae comb. nov., Microcella indica nom. nov., and Microcella alkalica nom. nov.
  • authors: Xie F, Pei S, Huang X, Wang L, Kou J, Zhang G
  • journal: Antonie Van Leeuwenhoek
  • DOI: 10.1007/s10482-021-01668-7
  • year: 2021
  • mesh: Actinobacteria, Bacterial Typing Techniques, DNA, Bacterial/genetics, *Fatty Acids/analysis, *Geologic Sediments, Phospholipids, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2
  • topic2: Transcriptome

Reference

@idauthorscataloguedoi/urltitle
8219Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19627)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19627
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
34321Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6097
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)
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
76938Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID132329.1StrainInfo: A central database for resolving microbial strain identifiers
122067Curators of the CIPCollection of Institut Pasteur (CIP 108471)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108471