Strain identifier

BacDive ID: 7405

Type strain: Yes

Species: Microbacterium chocolatum

Strain Designation: 207

Strain history: CIP <- 1998, IFO <- BUCSAV: strain 207 <- NCIB

NCBI tax ID(s): 84292 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 4753

BacDive-ID: 7405

DSM-Number: 12507

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

description: Microbacterium chocolatum 207 is an obligate aerobe, mesophilic, Gram-positive bacterium that was isolated from culture contamination.

NCBI tax id

  • NCBI tax id: 84292
  • Matching level: species

strain history

@refhistory
4753<- IFO <- BUCSAV <- NCIB <- ATCC <- M.H. Knutsen (Chromobacterium chocolatum)
67770NBRC 3758 <-- IFO 3758 <-- BUCSAV 207 <-- NCIB 8181 <-- ATCC 7319 <-- M. H. Knutsen ("Chromobacterium chocolatum").
118248CIP <- 1998, IFO <- BUCSAV: strain 207 <- NCIB

doi: 10.13145/bacdive7405.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Microbacteriaceae
  • genus: Microbacterium
  • species: Microbacterium chocolatum
  • full scientific name: Microbacterium chocolatum Takeuchi and Hatano 1998

@ref: 4753

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Microbacterium

species: Microbacterium chocolatum

full scientific name: Microbacterium chocolatum Takeuchi and Hatano 1998

strain designation: 207

type strain: yes

Morphology

cell morphology

  • @ref: 118248
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: no

colony morphology

@refcolony colorincubation periodmedium used
18365Yellow orange (2000)10-14 daysISP 2
18365Yellow orange (2000)10-14 daysISP 3
18365Yellow orange (2000)10-14 daysISP 4
18365Yellow orange (2000)10-14 daysISP 5
18365Yellow orange (2000)10-14 daysISP 6
18365Yellow orange (2000)10-14 daysISP 7
118248

multicellular morphology

@refforms multicellular complexmedium name
18365noISP 2
18365noISP 3
18365noISP 4
18365noISP 5
18365noISP 6
18365noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4753TRYPTICASE 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
18365ISP 2yesName: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
18365ISP 3yesName: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
18365ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
18365ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
18365ISP 6yesName: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
18365ISP 7yesName: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
40195MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
118248CIP Medium 1yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=1
118248CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
18365positiveoptimum28mesophilic
4753positivegrowth28mesophilic
40195positivegrowth30mesophilic
67770positivegrowth28mesophilic
118248positivegrowth15-41
118248nogrowth10psychrophilic
118248nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 118248
  • oxygen tolerance: obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
118248NaClpositivegrowth0-8 %
118248NaClnogrowth10 %

murein

  • @ref: 4753
  • murein short key: B06
  • type: B2ß {Gly} [L-Hsr] D-Glu(Hyg)-Gly-D-Orn

observation

  • @ref: 67770
  • observation: quinones: MK-12

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate+builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose+builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen+builds acid from28087
68371starch+builds acid from28017
68371raffinose+builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose+builds acid from27082
68371sucrose+builds acid from17992
68371melibiose-builds acid from28053
68371lactose+builds acid from17716
68371maltose+builds acid from17306
68371cellobiose+builds acid from17057
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol+builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose+builds acid from16024
68371D-fructose+builds acid from15824
68371D-glucose+builds acid from17634
68371D-galactose+builds acid from12936
68371methyl beta-D-xylopyranoside+builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose+builds acid from65327
68371D-ribose-builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol+builds acid from17754
118248esculin-hydrolysis4853
118248hippurate-hydrolysis606565
118248nitrate-reduction17632
118248nitrite-reduction16301
118248nitrate-respiration17632
68379nitrate-reduction17632
68379esculin-hydrolysis4853
68379urea-hydrolysis16199
68379gelatin-hydrolysis5291
68379D-glucose-fermentation17634
68379D-ribose-fermentation16988
68379D-xylose-fermentation65327
68379D-mannitol-fermentation16899
68379maltose-fermentation17306
68379lactose-fermentation17716
68379sucrose-fermentation17992
68379glycogen-fermentation28087

metabolite production

  • @ref: 118248
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11824815688acetoin-
11824817234glucose-

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-glucosidase+3.2.1.20
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382esterase lipase (C 8)+
68382alkaline phosphatase+3.1.3.1
68379gelatinase-
68379urease-3.5.1.5
68379beta-glucosidase-3.2.1.21
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alpha-glucosidase+3.2.1.20
68379beta-galactosidase+3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase+3.1.3.1
68379pyrrolidonyl arylamidase+3.4.19.3
68379pyrazinamidase-3.5.1.B15
118248oxidase-
118248beta-galactosidase+3.2.1.23
118248alcohol dehydrogenase-1.1.1.1
118248gelatinase+/-
118248amylase+
118248DNase-
118248caseinase-3.4.21.50
118248catalase+1.11.1.6
118248tween esterase-
118248gamma-glutamyltransferase-2.3.2.2
118248lecithinase-
118248lipase-
118248lysine decarboxylase-4.1.1.18
118248ornithine decarboxylase-4.1.1.17
118248phenylalanine ammonia-lyase-4.3.1.24
118248protease-
118248tryptophan deaminase-
118248urease-3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
18365--++-++------------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
18365+-+-++++++++++++---
118248++++++---++---+-----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
118248+----+--+++++----+------+/-+/-+++-++--+++--+------+--

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
118248+--+---++++++--+--+--+---------+-+-----------------------------+--------+--------------------------

Isolation, sampling and environmental information

isolation

@refsample type
4753culture contamination
67770Culture contamination
118248Culture contamination

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Laboratory
  • Cat3: #Contaminant

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
47531Risk group (German classification)
1182481Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Microbacterium chocolatum partial 16S rRNA gene, type strain DSM 12507AM1815031509ena84292
4753Microbacterium chocolatum gene for 16S rRNA, partial sequenceAB0047251472ena84292

GC content

@refGC-contentmethod
475369.5
6777069.5high performance liquid chromatography (HPLC)

External links

@ref: 4753

culture collection no.: DSM 12507, ATCC 7319, BUCSAV 207, IFO 3758, NBRC 3758, NCIMB 8181, NRRL B-24218, JCM 12412, CIP 105729, IAM 15199, VKM Ac-2078

straininfo link

  • @ref: 76854
  • straininfo: 34854

literature

  • topic: Phylogeny
  • Pubmed-ID: 9734054
  • title: Proposal of six new species in the genus Microbacterium and transfer of Flavobacterium marinotypicum ZoBell and Upham to the genus Microbacterium as Microbacterium maritypicum comb. nov.
  • authors: Takeuchi M, Hatano K
  • journal: Int J Syst Bacteriol
  • DOI: 10.1099/00207713-48-3-973
  • year: 1998
  • mesh: Actinomycetales/chemistry/*classification/genetics, DNA, Bacterial/analysis, Flavobacterium/*classification, Nucleic Acid Hybridization

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4753Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 12507)https://www.dsmz.de/collection/catalogue/details/culture/DSM-12507
18365Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM12507.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
40195Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17781
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
76854Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID34854.1StrainInfo: A central database for resolving microbial strain identifiers
118248Curators of the CIPCollection of Institut Pasteur (CIP 105729)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105729