Strain identifier

BacDive ID: 7401

Type strain: Yes

Species: Microbacterium arabinogalactanolyticum

Strain Designation: M-2

Strain history: CIP <- 1993, IFO <- A. Misaki, Osaka Univ., Japan <- S. Kotani, Osaka Univ., Japan: strain M-2

NCBI tax ID(s): 69365 (species)

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General

@ref: 3333

BacDive-ID: 7401

DSM-Number: 8611

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

description: Microbacterium arabinogalactanolyticum M-2 is an obligate aerobe, mesophilic, Gram-positive bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 69365
  • Matching level: species

strain history

@refhistory
3333<- IFO <- A. Misaki <- S. Kotani, M-2
67770IFO 14344 <-- A. Misaki <-- S. Kotani M-2.
116465CIP <- 1993, IFO <- A. Misaki, Osaka Univ., Japan <- S. Kotani, Osaka Univ., Japan: strain M-2

doi: 10.13145/bacdive7401.20230509.8.1

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 arabinogalactanolyticum
  • full scientific name: Microbacterium arabinogalactanolyticum (Yokota et al. 1993) Takeuchi and Hatano 1998

  • synonyms

    • @ref: 20215
    • synonym: Aureobacterium arabinogalactanolyticum

@ref: 3333

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Microbacterium

species: Microbacterium arabinogalactanolyticum

full scientific name: Microbacterium arabinogalactanolyticum (Yokota et al. 1993) Takeuchi and Hatano 1998

strain designation: M-2

type strain: yes

Morphology

cell morphology

  • @ref: 116465
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: no

colony morphology

@refcolony colorincubation periodmedium usedhemolysis ability
19734Beige10-14 daysISP 2
19734Beige10-14 daysISP 3
19734Beige10-14 daysISP 4
1973410-14 daysISP 5
1973410-14 daysISP 6
19734beige10-14 daysISP 7
1164651

multicellular morphology

@refforms multicellular complexmedium name
19734noISP 2
19734noISP 3
19734noISP 4
19734noISP 5
19734noISP 6
19734noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3333TRYPTICASE 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
19734ISP 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
19734ISP 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:
19734ISP 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
19734ISP 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
19734ISP 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
19734ISP 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
38149MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
116465CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
19734positiveoptimum28mesophilic
3333positivegrowth30mesophilic
38149positivegrowth30mesophilic
67770positivegrowth28mesophilic
116465positivegrowth15-37
116465nogrowth10psychrophilic
116465nogrowth41thermophilic
116465nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 116465
  • oxygen tolerance: obligate aerobe

compound production

  • @ref: 3333
  • compound: alpha-D arabinofuranidase

halophily

@refsaltgrowthtested relationconcentration
116465NaClpositivegrowth2-6 %
116465NaClnogrowth0 %
116465NaClnogrowth8 %
116465NaClnogrowth10 %

murein

  • @ref: 3333
  • murein short key: B06
  • type: B2ß {Gly} [L-Hsr] D-Glu(Hyg)-Gly-D-Orn

observation

  • @ref: 67770
  • observation: quinones: MK-12, MK-13

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
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-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
116465citrate-carbon source16947
116465esculin+hydrolysis4853
116465hippurate-hydrolysis606565
116465nitrate-reduction17632
116465nitrite-reduction16301
116465tributyrin-hydrolysis35020
116465sodium thiosulfate+builds gas from132112
116465nitrate-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: 116465
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 116465
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11646515688acetoin-
11646517234glucose-

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)+
67770alpha-L-arabinofuranosidase3.2.1.55
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
116465oxidase-
116465beta-galactosidase+3.2.1.23
116465alcohol dehydrogenase-1.1.1.1
116465gelatinase+
116465amylase+
116465DNase+
116465caseinase+3.4.21.50
116465catalase+1.11.1.6
116465gamma-glutamyltransferase-2.3.2.2
116465lecithinase-
116465lipase-
116465lysine decarboxylase-4.1.1.18
116465ornithine decarboxylase-4.1.1.17
116465phenylalanine ammonia-lyase-4.3.1.24
116465protease+
116465tryptophan deaminase-
116465urease-3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
19734+-++-+++++-+---+++-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
19734+-+-++++-++-+-+++++
116465-++-++++-++-+-+++++-

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
116465-------------------------------------------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116465-++++--+-++----+--+-+------------+-----+-++-----+--+----++-++-------+---------+------+-----------+-

Isolation, sampling and environmental information

isolation

@refsample type
3333soil
67770Soil
116465Environment, Soil

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
33331Risk group (German classification)
197341Risk group (German classification)
1164651Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Microbacterium arabinogalactanolyticum 16S rRNA geneY172281462ena69365
20218Microbacterium arabinogalactanolyticum gene for 16S rRNA, partial sequenceAB0047151447ena69365

GC content

@refGC-contentmethod
333369high performance liquid chromatography (HPLC)
6777069.3high performance liquid chromatography (HPLC)

External links

@ref: 3333

culture collection no.: DSM 8611, CCM 4370, CIP 103814, IFO 14344, NBRC 14344, NRRL B-24215, JCM 9171, ATCC 51926, IAM 15200, LMG 16469, VKM Ac-1943

straininfo link

  • @ref: 76850
  • straininfo: 8198

literature

  • topic: Phylogeny
  • Pubmed-ID: 8347513
  • title: Proposal of six new species in the genus Aureobacterium and transfer of Flavobacterium esteraromaticum Omelianski to the genus Aureobacterium as Aureobacterium esteraromaticum comb. nov.
  • authors: Yokota A, Takeuchi M, Sakane T, Weiss N
  • journal: Int J Syst Bacteriol
  • DOI: 10.1099/00207713-43-3-555
  • year: 1993
  • mesh: Bacterial Typing Techniques, Base Composition, Carbohydrate Sequence, DNA, Bacterial/chemistry, Fatty Acids/analysis, Flavobacterium/chemistry/*classification/cytology, Gram-Positive Asporogenous Rods/chemistry/*classification/cytology, Molecular Sequence Data, Mycolic Acids/analysis, Peptidoglycan/chemistry, Vitamin K/analysis
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3333Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 8611)https://www.dsmz.de/collection/catalogue/details/culture/DSM-8611
19734Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM8611.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
38149Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15653
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
76850Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID8198.1StrainInfo: A central database for resolving microbial strain identifiers
116465Curators of the CIPCollection of Institut Pasteur (CIP 103814)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103814