Strain identifier

BacDive ID: 7400

Type strain: Yes

Species: Microbacterium terrae

Strain Designation: A-1

Strain history: CIP <- 1993, IFO <- T. sakane: strain A-1

NCBI tax ID(s): 69369 (species)

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General

@ref: 3332

BacDive-ID: 7400

DSM-Number: 8610

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

description: Microbacterium terrae A-1 is an obligate aerobe, mesophilic, Gram-positive bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 69369
  • Matching level: species

strain history

@refhistory
3332<- IFO <- S. Sakane
67770IFO 15300 <-- T. Sakane A-1.
123459CIP <- 1993, IFO <- T. sakane: strain A-1

doi: 10.13145/bacdive7400.20230509.8.1

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

  • synonyms

    • @ref: 20215
    • synonym: Aureobacterium terrae

@ref: 3332

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Microbacterium

species: Microbacterium terrae

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

strain designation: A-1

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480positive100
123459positiverod-shapedno

colony morphology

@refcolony colorincubation periodmedium used
19733Broom yellow10-14 daysISP 2
19733Beige10-14 daysISP 3
19733Beige10-14 daysISP 4
19733Beige10-14 daysISP 5
19733Broom yellow10-14 daysISP 6
19733Beige10-14 daysISP 7
123459

multicellular morphology

@refforms multicellular complexmedium name
19733noISP 2
19733noISP 3
19733noISP 4
19733noISP 5
19733noISP 6
19733noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3332TRYPTICASE 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
19733ISP 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
19733ISP 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:
19733ISP 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
19733ISP 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
19733ISP 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
19733ISP 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
40802MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
123459CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3
123459CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
19733positiveoptimum28mesophilic
3332positivegrowth30mesophilic
40802positivegrowth30mesophilic
67770positivegrowth30mesophilic
123459positivegrowth15-30
123459nogrowth10psychrophilic
123459nogrowth37mesophilic
123459nogrowth41thermophilic
123459nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 123459
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.952

halophily

@refsaltgrowthtested relationconcentration
123459NaClpositivegrowth0-6 %
123459NaClnogrowth8 %
123459NaClnogrowth10 %

murein

  • @ref: 3332
  • murein short key: B06
  • type: B2ß {Gly} [L-Hsr] D-Glu(Hyg)-Gly-D-Orn

observation

  • @ref: 67770
  • observation: quinones: MK-13, MK-14

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
68371D-lyxose-builds acid from62318
68371xylitol-builds acid from17151
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371sucrose+builds acid from17992
68371melibiose+builds acid from28053
68371lactose-builds acid from17716
68371maltose+builds acid from17306
68371esculin+builds acid from4853
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
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
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
123459citrate-carbon source16947
123459esculin+hydrolysis4853
123459hippurate-hydrolysis606565
123459nitrate+reduction17632
123459nitrite-reduction16301
123459tributyrin+hydrolysis35020
123459sodium thiosulfate+builds gas from132112
123459nitrate-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: 123459
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 123459
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12345915688acetoin-
12345917234glucose-

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382alpha-galactosidase+3.2.1.22
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
123459oxidase-
123459beta-galactosidase+3.2.1.23
123459alcohol dehydrogenase-1.1.1.1
123459gelatinase+
123459amylase+
123459DNase+
123459caseinase+3.4.21.50
123459catalase+1.11.1.6
123459gamma-glutamyltransferase-2.3.2.2
123459lecithinase-
123459lipase-
123459lysine decarboxylase-4.1.1.18
123459ornithine decarboxylase-4.1.1.17
123459phenylalanine ammonia-lyase-4.3.1.24
123459protease+
123459tryptophan deaminase-
123459urease-3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
19733-----++--++--------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
19733-++-+-++---++-++---
123459-++++--+--++--+++---

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
123459---+/--+/---+/-++++-+/---+/------+/-++/-+/-+-+++/---+/-+/-+/--+/-+/-------+/--+/-

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123459++-+--+-++++---++-+-++-+-------+-+-+---------------------+--+-----------+--+--+-------+------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
3332soilOsakaJapanJPNAsia
67770Soil
123459Environment, Soil

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
33321Risk group (German classification)
197331Risk group (German classification)
1234591Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Microbacterium terrae 16S rRNA geneY172381462ena69369
20218Microbacterium terrae gene for 16S rRNA, partial sequenceAB0047201427ena69369

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Microbacterium terrae DSM 8610GCA_017831975contigncbi69369
66792Microbacterium terrae strain DSM 861069369.3wgspatric69369
66792Microbacterium terrae DSM 86102893680751draftimg69369

GC content

@refGC-contentmethod
333271high performance liquid chromatography (HPLC)
6777070.7high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveyes92.424no
anaerobicno99.721no
halophileno88.111no
spore-formingno91.326no
glucose-utilyes88.542no
thermophileno99.453no
flagellatedno97.353no
motileno91.015no
aerobicyes96.014no
glucose-fermentno88.198yes

External links

@ref: 3332

culture collection no.: DSM 8610, ATCC 51476, CCM 4374, CIP 103816, IFO 15300, NBRC 15300, NRRL B-24214, JCM 9176, IAM 15209, LMG 16471, VKM Ac-1945

straininfo link

  • @ref: 76849
  • straininfo: 8208

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
3332Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 8610)https://www.dsmz.de/collection/catalogue/details/culture/DSM-8610
19733Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM8610.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
40802Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15655
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/
68371Automatically annotated from API 50CH acid
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
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)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
76849Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID8208.1StrainInfo: A central database for resolving microbial strain identifiers
123459Curators of the CIPCollection of Institut Pasteur (CIP 103816)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103816