Strain identifier

BacDive ID: 7363

Type strain: Yes

Species: Microbacterium barkeri

Strain Designation: 7

Strain history: CIP <- 1986, NCIB <- J.V. Bhat: strain 7, Corynebacterium barkeri

NCBI tax ID(s): 33917 (species)

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General

@ref: 8569

BacDive-ID: 7363

DSM-Number: 20145

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

description: Microbacterium barkeri 7 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from raw domestic sewage.

NCBI tax id

  • NCBI tax id: 33917
  • Matching level: species

strain history

@refhistory
8569<- ATCC <- J.V. Bhat, 7 (Corynebacterium barkeri)
67770K. Suzuki CNF 095 <-- NCIB 9658 <-- J. Bhat 7.
116735CIP <- 1986, NCIB <- J.V. Bhat: strain 7, Corynebacterium barkeri

doi: 10.13145/bacdive7363.20230509.8.1

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 barkeri
  • full scientific name: Microbacterium barkeri (Collins et al. 1983 ex Dias et al. 1962) Takeuchi and Hatano 1998

  • synonyms

    • @ref: 20215
    • synonym: Aureobacterium barkeri

@ref: 8569

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Microbacterium

species: Microbacterium barkeri

full scientific name: Microbacterium barkeri (Collins et al. 1983) Takeuchi and Hatano 1998

strain designation: 7

type strain: yes

Morphology

cell morphology

  • @ref: 116735
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: no

colony morphology

@refcolony colorincubation periodmedium used
18629Ivory (1014)10-14 daysISP 2
18629Ivory (1014)10-14 daysISP 3
18629Ivory (1014)10-14 daysISP 4
18629Golden yellow (1004)10-14 daysISP 6
116735

multicellular morphology

@refforms multicellular complexmedium name
18629noISP 2
18629noISP 3
18629noISP 4
18629noISP 6

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
18629ISP 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
18629ISP 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:
18629ISP 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
18629ISP 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
38104MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
8569CORYNEBACTERIUM AGAR (DSMZ Medium 53)yesName: CORYNEBACTERIUM AGAR (DSMZ Medium 53) Composition: Agar 15.0 g/l Casein peptone 10.0 g/l NaCl 5.0 g/l Glucose 5.0 g/l Yeast extract 5.0 g/l Distilled waterhttps://mediadive.dsmz.de/medium/53
116735CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3
116735CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
18629positiveoptimum28mesophilic
8569positivegrowth30mesophilic
38104positivegrowth30mesophilic
51371positivegrowth37mesophilic
67770positivegrowth28mesophilic
116735positivegrowth15-45
116735nogrowth10psychrophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
51371aerobe
116735obligate aerobe

compound production

@refcompound
8569pectin methylesterase
8569pectin transeliminase
20216Pectin methyl-esterase
20216pectin transeliminase

halophily

@refsaltgrowthtested relationconcentration
18629NaClpositivemaximum5 %
116735NaClpositivegrowth0-8 %
116735NaClnogrowth10 %

murein

  • @ref: 8569
  • murein short key: B06
  • type: B2ß {Gly} [L-Hsr] D-Glu(Hyg)-Gly-D-Orn

observation

  • @ref: 67770
  • observation: quinones: MK-11, MK-12

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1862962968cellulose-
1862916634raffinose-
1862926546rhamnose-
1862928757fructose-
1862929864mannitol-
1862917268myo-inositol+
1862918222xylose-
1862917992sucrose+
1862922599arabinose+
1862917234glucose+
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
683714853esculin+builds acid from
6837127613amygdalin-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837116988D-ribose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis
11673516947citrate+carbon source
1167354853esculin+hydrolysis
116735606565hippurate+hydrolysis
11673517632nitrate-reduction
11673516301nitrite-reduction
11673517632nitrate-respiration
6837917632nitrate+reduction
683794853esculin-hydrolysis
6837916199urea+hydrolysis
683795291gelatin+hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose+fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol+fermentation
6837917306maltose+fermentation
6837917716lactose+fermentation
6837917992sucrose+fermentation
6837928087glycogen-fermentation

antibiotic resistance

  • @ref: 116735
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno
11673535581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin-
6836835581indole-
11673515688acetoin-
11673517234glucose-

enzymes

@refvalueactivityec
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
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin+3.4.21.4
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
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
68368gelatinase+
68368tryptophan deaminase-4.1.99.1
68368urease-3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase-3.5.3.6
68368beta-galactosidase+3.2.1.23
116735oxidase-
116735beta-galactosidase+3.2.1.23
116735alcohol dehydrogenase-1.1.1.1
116735gelatinase+
116735amylase+
116735DNase+
116735caseinase+3.4.21.50
116735catalase+1.11.1.6
116735tween esterase-
116735gamma-glutamyltransferase-2.3.2.2
116735lecithinase-
116735lipase-
116735lysine decarboxylase-4.1.1.18
116735ornithine decarboxylase-4.1.1.17
116735phenylalanine ammonia-lyase-4.3.1.24
116735protease-
116735tryptophan deaminase-
116735urease-3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
18629+++-+++--++-+-++++-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
18629+++-++++-++-+-++++-
116735++++++-+-++++-+++++-

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
18629+---------+

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
116735---+/--+/---+/-+/-+/-+/-+/----+/-+/----+/--+/-++/-+/-+/-+/-+/-+/---+/-+/-+/-+/---+/----------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116735+++++-+++++++--+--+-+++--+--+--+++++-----+-------++--+--++-++-+---------+-----+++-----+--+---------

Isolation, sampling and environmental information

isolation

@refsample type
8569raw domestic sewage
67770Raw domestic sewage
116735Environment, Sewage

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Waste
  • Cat3: #Wastewater

taxonmaps

  • @ref: 69479
  • File name: preview.99_31221.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_14599;97_17811;98_22142;99_31221&stattab=map
  • Last taxonomy: Actinomycetia
  • 16S sequence: X77446
  • Sequence Identity:
  • Total samples: 598
  • soil counts: 98
  • aquatic counts: 173
  • animal counts: 294
  • plant counts: 33

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
85691Risk group (German classification)
186291German classification
1167351Risk group (French classification)

Sequence information

16S sequences

  • @ref: 8569
  • description: A.barkeri (DSM 20145) 16S rRNA gene
  • accession: X77446
  • length: 1468
  • database: ena
  • NCBI tax ID: 33917

Genome sequences

  • @ref: 66792
  • description: Microbacterium barkeri DSM 20145
  • accession: 2919382452
  • assembly level: draft
  • database: img
  • NCBI tax ID: 33917

GC content

@refGC-contentmethod
856974.4
6777068.7thermal denaturation, midpoint method (Tm)
6777074.4thermal denaturation, midpoint method (Tm)

External links

@ref: 8569

culture collection no.: DSM 20145, ATCC 15954, CCM 1928, NCIB 9658, NRRL B-24231, CCUG 33090, LMG 16341, CIP 102692, IAM 12585, IFO 15036, JCM 1343, BCRC 11642, CGMCC 1.1902, HAMBI 1894, IMET 10688, IMSNU 10306, KCTC 3197, NBRC 15036, NCFB 2287, NCIMB 9658, VKM Ac-1020, VTT E-072706, NCDO 2287

straininfo link

  • @ref: 76812
  • straininfo: 13956

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17684264Microbacterium indicum sp. nov., isolated from a deep-sea sediment sample from the Chagos Trench, Indian Ocean.Shivaji S, Bhadra B, Rao RS, Chaturvedi P, Pindi PK, Raghukumar CInt J Syst Evol Microbiol10.1099/ijs.0.64782-02007Actinomycetales/classification/genetics/*isolation & purification, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Geologic Sediments/*microbiology, Indian Ocean, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiologyGenetics
Phylogeny23203624Microbacterium oryzae sp. nov., an actinobacterium isolated from rice field soil.Kumari P, Bandyopadhyay S, Das SKInt J Syst Evol Microbiol10.1099/ijs.0.046870-02012Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, India, Molecular Sequence Data, Nucleic Acid Hybridization, Oryza/*microbiology, Phospholipids/analysis, *Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyGenetics
Phylogeny27260265Microbacterium gilvum sp. nov., isolated from civet faeces.Chen X, Li QY, Li GD, Xu FJ, Jiang Y, Han L, Jiang CL, Huang XSAntonie Van Leeuwenhoek10.1007/s10482-016-0718-12016Actinomycetales/*classification/genetics/*isolation & purification/metabolism, Animals, Cell Wall/chemistry, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Feces/*microbiology, Malaysia, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity, Vitamin K 2/metabolism, Viverridae/*microbiologyMetabolism

Reference

@idauthorscataloguedoi/urltitle
8569Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20145)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20145
18629Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM20145.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
20216Curators of the HKIhttp://www.leibniz-hki.de/de/Collection Description Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V. Hans-Knöll-Institut (HKI)
38104Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/14406
51371Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 33090)https://www.ccug.se/strain?id=33090
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/
68368Automatically annotated from API 20E
68371Automatically annotated from API 50CH acid
68379Automatically annotated from API Coryne
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
76812Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID13956.1StrainInfo: A central database for resolving microbial strain identifiers
116735Curators of the CIPCollection of Institut Pasteur (CIP 102692)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20102692