Strain identifier

BacDive ID: 7411

Type strain: Yes

Species: Microbacterium kitamiense

Strain Designation: C2

Strain history: CIP <- 1999, H. Matsuyama, Hokkaido Tokai Univ., Sapporo, Japan: strain C2

NCBI tax ID(s): 76884 (species)

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General

@ref: 4977

BacDive-ID: 7411

DSM-Number: 13237

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

description: Microbacterium kitamiense C2 is an obligate aerobe, mesophilic, Gram-positive bacterium that was isolated from waste water of sugar-beet factory.

NCBI tax id

  • NCBI tax id: 76884
  • Matching level: species

strain history

@refhistory
4977<- JCM <- H. Matsuyama; Kitami C2
386171999, H. Matsuyama,Dept. Biosci. & Techn., Hokkaido Tokai Univ., Sapporo, Japan: strain C2
67770H. Matsuyama strain Kitami C2.
120449CIP <- 1999, H. Matsuyama, Hokkaido Tokai Univ., Sapporo, Japan: strain C2

doi: 10.13145/bacdive7411.20230509.8.1

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 kitamiense
  • full scientific name: Microbacterium kitamiense Matsuyama et al. 1999

@ref: 4977

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Microbacterium

species: Microbacterium kitamiense

full scientific name: Microbacterium kitamiense Matsuyama et al. 1999

strain designation: C2

type strain: yes

Morphology

cell morphology

  • @ref: 120449
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: no

colony morphology

@refcolony colorincubation periodmedium used
18375Colorless10-14 daysISP 2
18375Saffron yellow (1017)10-14 daysISP 3
18375Saffron yellow (1017)10-14 daysISP 4
18375Saffron yellow (1017)10-14 daysISP 5
18375Saffron yellow (1017)10-14 daysISP 6
18375Saffron yellow (1017)10-14 daysISP 7
120449

multicellular morphology

@refforms multicellular complexmedium name
18375noISP 2
18375noISP 3
18375noISP 4
18375noISP 5
18375noISP 6
18375noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4977TRYPTICASE 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
18375ISP 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
18375ISP 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:
18375ISP 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
18375ISP 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
18375ISP 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
18375ISP 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
38617MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
120449CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
18375positiveoptimum28mesophilic
4977positivegrowth28mesophilic
38617positivegrowth30mesophilic
67770positivegrowth30mesophilic
120449positivegrowth15-37
120449nogrowth10psychrophilic
120449nogrowth41thermophilic
120449nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 120449
  • oxygen tolerance: obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
120449NaClpositivegrowth0-4 %
120449NaClnogrowth6 %
120449NaClnogrowth8 %
120449NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: MK-11, 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
68371sucrose+builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose+builds acid from17306
68371salicin-builds acid from17814
68371esculin-builds acid from4853
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-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
120449citrate-carbon source16947
120449esculin+hydrolysis4853
120449hippurate+hydrolysis606565
120449nitrate+reduction17632
120449nitrite-reduction16301
120449nitrate-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

antibiotic resistance

  • @ref: 120449
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
6777072813exopolysaccharideyes
12044935581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12044915688acetoin-
12044917234glucose+

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
68382alpha-chymotrypsin-3.4.21.1
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
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
120449oxidase-
120449beta-galactosidase+3.2.1.23
120449alcohol dehydrogenase-1.1.1.1
120449gelatinase+/-
120449amylase+
120449DNase-
120449caseinase+3.4.21.50
120449catalase+1.11.1.6
120449tween esterase-
120449gamma-glutamyltransferase-2.3.2.2
120449lecithinase-
120449lipase-
120449lysine decarboxylase-4.1.1.18
120449ornithine decarboxylase-4.1.1.17
120449phenylalanine ammonia-lyase-4.3.1.24
120449protease+
120449tryptophan deaminase-
120449urease-3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
18375+---+++-+--+-------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
18375+++-+--+-+-+++++---
120449+++-+-----++++++----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
120449+/---+-+--+++++-+/---+--------+/-+--++/--++++--+------+-+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120449++-++--++++----+--+-+++--+-----+-+-+---------------------+--+-------------------------+------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
4977waste water of sugar-beet factoryJapan, Hokkaido, KitamiJapanJPNAsia
67770Wastewater of a sugar-beet factoryKitami, HokkaidoJapanJPNAsia
120449Environment, Wastewater of a sugar-beet factoryKitami, HokkaidoJapanJPNAsia1996

isolation source categories

Cat1Cat2Cat3
#Engineered#Industrial#Plant (Factory)
#Engineered#Waste#Wastewater

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
49771Risk group (German classification)
1204491Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Microbacterium kitamiense partial 16S rRNA gene, type strain DSM 13237AM1815051509ena76884
4977Microbacterium kitamiense gene for 16S rRNA, partial sequence, strain kitami C2AB0139071526ena76884
67770Microbacterium kitamiense gene for 16S rRNA, partial sequence, strain kitami C2AB0139191526ena76884

GC content

  • @ref: 4977
  • GC-content: 69.2
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 4977

culture collection no.: DSM 13237, JCM 10270, NRRL B-24226, Kitami C2, CIP 106320, IAM 15189, IFO 16414, LMG 22055, NBRC 16414, NCIMB 13608

straininfo link

  • @ref: 76860
  • straininfo: 49445

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny10555312Microbacterium kitamiense sp. nov., a new polysaccharide-producing bacterium isolated from the wastewater of a sugar-beet factory.Matsuyama H, Kawasaki K, Yumoto I, Shida OInt J Syst Bacteriol10.1099/00207713-49-4-13531999Actinomycetales/*classification/genetics/isolation & purification/*metabolism, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, Food Industry, Genes, rRNA, *Industrial Waste, Molecular Sequence Data, Phylogeny, Polysaccharides, Bacterial/*biosynthesis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sucrose/metabolism, *Water MicrobiologyMetabolism
Phylogeny29458489Microbacterium telephonicum sp. nov., isolated from the screen of a cellular phone.Rahi P, Kurli R, Pansare AN, Khairnar M, Jagtap S, Patel NB, Dastager SG, Lawson PA, Shouche YSInt J Syst Evol Microbiol10.1099/ijsem.0.0026222018Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, *Cell Phone, DNA, Bacterial/genetics, Fatty Acids/chemistry, India, Nucleic Acid Hybridization, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/chemistryTranscriptome
Phylogeny35024967Microbacterium sulfonylureivorans sp. nov., isolated from sulfonylurea herbicides degrading consortium.Ma Q, Kong D, Zhang Q, Li M, Han X, Che J, Zhou Y, Zhang W, Jiang X, Ruan ZArch Microbiol10.1007/s00203-021-02750-42022Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids, *Herbicides, Microbacterium, Phospholipids, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4977Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13237)https://www.dsmz.de/collection/catalogue/details/culture/DSM-13237
18375Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM13237.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
38617Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18438
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
76860Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID49445.1StrainInfo: A central database for resolving microbial strain identifiers
120449Curators of the CIPCollection of Institut Pasteur (CIP 106320)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106320