Strain identifier

BacDive ID: 7367

Type strain: Yes

Species: Microbacterium testaceum

Strain Designation: Rp-3

Strain history: CIP <- 1995, ATCC <- K. Komagata: strain Rp-3, Brevibacterium testaceum

NCBI tax ID(s): 2033 (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: 8589

BacDive-ID: 7367

DSM-Number: 20166

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

description: Microbacterium testaceum Rp-3 is an obligate aerobe, mesophilic, Gram-positive bacterium that was isolated from rice.

NCBI tax id

  • NCBI tax id: 2033
  • Matching level: species

strain history

@refhistory
8589<- ATCC <- K. Komagata, Rp-3
67770K. Suzuki CNF 032 <-- AJ 1466 <-- IAM 1561 <-- K. Komagata Rp-3.
123484CIP <- 1995, ATCC <- K. Komagata: strain Rp-3, Brevibacterium testaceum

doi: 10.13145/bacdive7367.20230509.8.1

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 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: 123484
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: yes

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
123484

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
123484CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
123484CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
18634positiveoptimum28mesophilic
8589positivegrowth30mesophilic
38496positivegrowth30mesophilic
67770positivegrowth28mesophilic
123484positivegrowth15-37
123484nogrowth10psychrophilic
123484nogrowth41thermophilic
123484nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 123484
  • oxygen tolerance: obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
18634NaClpositivemaximum5 %
123484NaClpositivegrowth0-4 %
123484NaClnogrowth6 %
123484NaClnogrowth8 %
123484NaClnogrowth10 %

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

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 2-ketogluconate-builds acid from
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
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371inulin-builds acid from15443
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371esculin+builds acid from4853
68371amygdalin-builds acid from27613
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-ribose-builds acid from16988
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
68368D-glucose-fermentation17634
68368gelatin+hydrolysis5291
68368tryptophan-energy source27897
68368urea-hydrolysis16199
68368citrate-assimilation16947
68368ornithine-degradation18257
68368lysine-degradation25094
68368arginine-hydrolysis29016
123484citrate+carbon source16947
123484esculin+hydrolysis4853
123484hippurate+hydrolysis606565
123484nitrate+reduction17632
123484nitrite-reduction16301
123484sodium thiosulfate+builds gas from132112
123484nitrate-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: 123484
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno
12348435581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin+
6836835581indole-
12348415688acetoin-
12348417234glucose-

enzymes

@refvalueactivityec
68382alpha-mannosidase+3.2.1.24
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase+3.2.1.20
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
68382cystine arylamidase+3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382esterase lipase (C 8)+
68382esterase (C 4)+
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
123484oxidase-
123484beta-galactosidase+3.2.1.23
123484alcohol dehydrogenase-1.1.1.1
123484gelatinase+
123484amylase-
123484DNase+
123484caseinase+3.4.21.50
123484catalase+1.11.1.6
123484tween esterase-
123484gamma-glutamyltransferase-2.3.2.2
123484lecithinase-
123484lipase+
123484lysine decarboxylase-4.1.1.18
123484ornithine decarboxylase-4.1.1.17
123484phenylalanine ammonia-lyase-4.3.1.24
123484protease+
123484tryptophan deaminase-
123484urease+3.5.1.5

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- FucosidaseControl
18634+++++++++++-+-++-+-
123484-++-+++++++++++++++-

API 20E

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

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
123484---+/--+/----+/-+/-+/-+/-----+/----+/--+/-++/-+/-+/---+/-+/--+/------+/-+/------+/--+/-

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123484+++++--+-+++---++++-+++--+-----+-+++---+---------+---+--++-++-+-+-------+-----+++--------++-------+

Isolation, sampling and environmental information

isolation

@refsample type
8589rice
47860Paddy
67770Chinese paddy
123484Paddy

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
85891Risk group (German classification)
186341Risk group (German classification)
1234841Risk group (French 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

GC content

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

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno53.671no
gram-positiveyes92.079no
anaerobicno99.552no
aerobicyes95.403no
halophileno89.379no
spore-formingno94.733no
glucose-utilyes83.303no
flagellatedno94.243no
thermophileno99.059yes
glucose-fermentno91.538yes

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

  • @ref: 76816
  • straininfo: 311061

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/urltitle
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
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
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
76816Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID311061.1StrainInfo: A central database for resolving microbial strain identifiers
123484Curators of the CIPCollection of Institut Pasteur (CIP 104324)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104324