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Strain identifier

BacDive ID: 7367

Type strain: Yes

Species: Microbacterium testaceum

Strain Designation: Rp-3

Strain history: K. Suzuki CNF 032 <-- AJ 1466 <-- IAM 1561 <-- K. Komagata Rp-3.

NCBI tax ID(s): 2033 (species)

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

@ref: 8589

BacDive-ID: 7367

DSM-Number: 20166

keywords: genome sequence, 16S sequence, Bacteria, mesophilic

description: Microbacterium testaceum Rp-3 is a mesophilic bacterium that was isolated from rice.

NCBI tax id

  • NCBI tax id: 2033
  • Matching level: species

strain history

doi: 10.13145/bacdive7367.20221219.7.1

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 testaceum
  • full scientific name: Microbacterium testaceum (Komagata and Iizuka 1964) Takeuchi and Hatano 1998
  • synonyms

    @refsynonym
    20215Brevibacterium testaceum
    20215Curtobacterium testaceum
    20215Aureobacterium testaceum

@ref: 8589

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Microbacterium

species: Microbacterium testaceum

full scientific name: Microbacterium testaceum (Komagata and Iizuka 1964) Takeuchi and Hatano 1998

strain designation: Rp-3

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: positive
  • confidence: 97.617

colony morphology

@refcolony colorincubation periodmedium used
18634Daffodil yellow (1007)10-14 daysISP 2
18634Daffodil yellow (1007)10-14 daysISP 3
18634Ivory (1014)10-14 daysISP 4
18634Broom yellow (1032)10-14 daysISP 6

multicellular morphology

@refforms multicellular complexmedium name
18634noISP 2
18634noISP 3
18634noISP 4
18634noISP 6

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
18634ISP 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
18634ISP 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:
18634ISP 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
18634ISP 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
38496MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
8589CORYNEBACTERIUM 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

culture temp

@refgrowthtypetemperaturerange
18634positiveoptimum28mesophilic
8589positivegrowth30mesophilic
38496positivegrowth30mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 98.579

halophily

@refsaltgrowthtested relationconcentrationhalophily levelconfidence
18634NaClpositivemaximum5 %
69480non-halophilic89.123

murein

  • @ref: 8589
  • murein short key: B06
  • type: B2ß {Gly} [L-Hsr] D-Glu(Hyg)-Gly-D-Orn

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6837928087glycogen-fermentation
6837917992sucrose+fermentation
6837917716lactose-fermentation
6837917306maltose+fermentation
6837916899D-mannitol+fermentation
6837965327D-xylose-fermentation
6837916988D-ribose+fermentation
6837917634D-glucose-fermentation
683795291gelatin+hydrolysis
6837916199urea+hydrolysis
683794853esculin+hydrolysis
6837917632nitrate+reduction
6836817634D-glucose-fermentation
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin+
6836835581indole-

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
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

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
18634+++++++++++-+-++-+-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
18634+++++++++++-+-++-+-

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLU
18634---------++-

Isolation, sampling and environmental information

isolation

@refsample type
8589rice
47860Paddy
67770Chinese paddy

isolation source categories

  • Cat1: #Host
  • Cat2: #Plants
  • Cat3: #Herbaceous plants (Grass,Crops)

taxonmaps

  • @ref: 69479
  • File name: preview.99_3437.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_137;97_148;98_2638;99_3437&stattab=map
  • Last taxonomy: Microbacterium
  • 16S sequence: X77445
  • Sequence Identity:
  • Total samples: 85
  • soil counts: 1
  • aquatic counts: 6
  • animal counts: 76
  • plant counts: 2

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
186341Risk group (German classification)
85891Risk group (German classification)

Sequence information

16S sequences

  • @ref: 8589
  • description: A.testaceum (DSM 20166) 16S rRNA gene
  • accession: X77445
  • length: 1469
  • database: ena
  • NCBI tax ID: 2033

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Microbacterium testaceum strain NBRC 126752033.11wgspatric2033
67770Microbacterium testaceum NBRC 12675GCA_006539145contigncbi2033
66792uncultured Bacteroidetes bacterium Umea2_bin-1995GCA_903915135contigpatric152509

GC content

@refGC-contentmethod
858965.4
6777067.7thermal denaturation, midpoint method (Tm)
6777072.7thermal denaturation, midpoint method (Tm)

External links

@ref: 8589

culture collection no.: DSM 20166, ATCC 15829, CCM 2299, NRRL B-24232, CCUG 23849, LMG 16344, CIP 104324, IAM 1561, JCM 1353, BCRC 12120, CGMCC 1.1907, HAMBI 1889, IFO 12675, IMET 10361, KCTC 9103, KCTC 9228, NBRC 12675, NCFB 2302, NCIMB 11430, VKM Ac-1019, VKM B-1229

straininfo link

@refpassport
20218http://www.straininfo.net/strains/54728
20218http://www.straininfo.net/strains/54724
20218http://www.straininfo.net/strains/54725
20218http://www.straininfo.net/strains/684873

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Genetics8000548In situ probing of gram-positive bacteria with high DNA G + C content using 23S rRNA-targeted oligonucleotides.Roller C, Wagner M, Amann R, Ludwig W, Schleifer KHMicrobiology (Reading)10.1099/00221287-140-10-28491994Base Sequence, Gram-Positive Bacteria/genetics/*isolation & purification, *In Situ Hybridization, Molecular Conformation, Molecular Sequence Data, Oligonucleotides, RNA, Ribosomal, 23S/*genetics, Repetitive Sequences, Nucleic AcidEnzymology
Metabolism18997853Plasmid transformation and expression of the firefly luciferase in Microbacterium testaceum type and endophytic colonizing field strains.Zinniel DK, Feng Z, Blum PH, Barletta RG, Vidaver AKCan J Microbiol10.1139/w08-0862008Actinomycetales/*genetics/metabolism, *Gene Expression, Luciferases, Firefly/*genetics/metabolism, Plasmids/*genetics, *Transformation, Bacterial, Zea mays/*microbiology
Phylogeny25052400Microbacterium hydrothermale sp. nov., an actinobacterium isolated from hydrothermal sediment.Zhang Y, Ren H, Zhang GInt J Syst Evol Microbiol10.1099/ijs.0.061697-02014Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Hydrothermal Vents/*microbiology, Indian Ocean, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/chemistryGenetics
Phylogeny25829331Microbacterium enclense sp. nov., isolated from sediment sample.Mawlankar RR, Mual P, Sonalkar VV, Thorat MN, Verma A, Srinivasan K, Dastager SGInt J Syst Evol Microbiol10.1099/ijs.0.0002212015Actinomycetales/*classification/genetics/isolation & purification, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, India, Islands, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Sequence Analysis, DNA, Vitamin K 2/chemistryGenetics
Metabolism31289903High-density immobilization of a ginsenoside-transforming beta-glucosidase for enhanced food-grade production of minor ginsenosides.Cui CH, Jeon BM, Fu Y, Im WT, Kim SCAppl Microbiol Biotechnol10.1007/s00253-019-09951-42019Actinomycetales/enzymology/genetics, Bacterial Proteins/chemistry/genetics/metabolism, Biotransformation, Cellulose/chemistry, Cloning, Molecular, Corynebacterium glutamicum/enzymology/genetics/metabolism, Enzymes, Immobilized/chemistry/genetics/*metabolism, Gene Expression, Ginsenosides/*metabolism, Recombinant Fusion Proteins/chemistry/genetics/metabolism, Sapogenins/metabolism, beta-Glucosidase/chemistry/genetics/*metabolismEnzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8589Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20166)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20166
18634Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM20166.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
38496Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16220
47860Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 23849)https://www.ccug.se/strain?id=23849
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
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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)