Strain identifier

BacDive ID: 7425

Type strain: Yes

Species: Microbacterium natoriense

Strain Designation: TNJL143-2

Strain history: CIP <- 2005, JCM <- T. Nakayama, Miyagi, Japan: strain TNJL143-2

NCBI tax ID(s): 284570 (species)

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General

@ref: 6869

BacDive-ID: 7425

DSM-Number: 17277

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

description: Microbacterium natoriense TNJL143-2 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 284570
  • Matching level: species

strain history

@refhistory
6869<- JCM <- T.Nakayama, TNJL143-2
67770T. Nakayama TNJL143-2.
121242CIP <- 2005, JCM <- T. Nakayama, Miyagi, Japan: strain TNJL143-2

doi: 10.13145/bacdive7425.20230509.8.1

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 natoriense
  • full scientific name: Microbacterium natoriense Liu et al. 2005

@ref: 6869

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Microbacterium

species: Microbacterium natoriense

full scientific name: Microbacterium natoriense Liu et al. 2005

strain designation: TNJL143-2

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
31304positive1.5 µm0.55 µmrod-shapedno
121242positiverod-shapedno

colony morphology

  • @ref: 121242

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6869R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
6869TRYPTICASE 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
37641MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
121242CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
121242CIP Medium 469yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=469

culture temp

@refgrowthtypetemperaturerange
6869positivegrowth28mesophilic
31304positivegrowth10-50
31304positiveoptimum30mesophilic
37641positivegrowth30mesophilic
67770positivegrowth28mesophilic
121242positivegrowth10-37
121242nogrowth41thermophilic
121242nogrowth45thermophilic

culture pH

@refabilitytypepH
31304positivegrowth05-07
31304positiveoptimum6

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31304aerobe
121242obligate aerobe

spore formation

  • @ref: 31304
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
31304NaClpositivegrowth<7 %
31304NaClpositiveoptimum3.5 %
121242NaClpositivegrowth0-6 %
121242NaClnogrowth8 %
121242NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: MK-9, MK-10, MK-11, MK-12

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3130417754glycerol+carbon source
3130428087glycogen+carbon source
3130428053melibiose+carbon source
31304506227N-acetylglucosamine+carbon source
3130416634raffinose+carbon source
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-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
6837132528turanose-builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837174863methyl beta-D-xylopyranoside-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
12124216947citrate+carbon source
1212424853esculin+hydrolysis
121242606565hippurate-hydrolysis
12124217632nitrate-reduction
12124216301nitrite-reduction
12124217632nitrate-respiration

metabolite production

  • @ref: 121242
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12124215688acetoin-
12124217234glucose-

enzymes

@refvalueactivityec
31304alkaline phosphatase+3.1.3.1
31304catalase+1.11.1.6
31304gelatinase+
31304pyrazinamidase+3.5.1.B15
31304urease+3.5.1.5
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
67770D-aminoacylase3.5.1.14
121242oxidase-
121242beta-galactosidase+3.2.1.23
121242alcohol dehydrogenase-1.1.1.1
121242gelatinase+
121242amylase+
121242DNase+
121242caseinase+3.4.21.50
121242catalase+1.11.1.6
121242tween esterase-
121242gamma-glutamyltransferase-2.3.2.2
121242lecithinase-
121242lipase-
121242lysine decarboxylase-4.1.1.18
121242ornithine decarboxylase-4.1.1.17
121242phenylalanine ammonia-lyase-4.3.1.24
121242tryptophan deaminase-
121242urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
121242-+++-++-++++++-++-+-

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
121242+/---+/--+/----+/-+/-+/-+/-----+/---+/-+/-+/-+/-+/-+/-+/-+/---+/-----+/-+/----+/------+/---

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121242+++++-+++++-+--++++++++--+-----+-+++--++-+---+----+--+-+---++-----------+--+--+-------+-+-------+++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6869soilNatori, MiyagiJapanJPNAsia
67770SoilNatori, Miyagi Pref.JapanJPNAsia
121242Environment, SoilJapanJPNAsia

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
68691Risk group (German classification)
1212421Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6869
  • description: Microbacterium natoriense strain TNJL143-2 16S ribosomal RNA gene, partial sequence
  • accession: AY566291
  • length: 1429
  • database: ena
  • NCBI tax ID: 284570

GC content

@refGC-contentmethod
686969.1
6777069.1high performance liquid chromatography (HPLC)

External links

@ref: 6869

culture collection no.: DSM 17277, ATCC BAA 1032, CIP 108753, JCM 12611

straininfo link

  • @ref: 76874
  • straininfo: 138015

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15774640Microbacterium natoriense sp. nov., a novel D-aminoacylase-producing bacterium isolated from soil in Natori, Japan.Liu J, Nakayama T, Hemmi H, Asano Y, Tsuruoka N, Shimomura K, Nishijima M, Nishino TInt J Syst Evol Microbiol10.1099/ijs.0.63265-02005Actinomycetales/*classification/enzymology/genetics/isolation & purification, Amidohydrolases/*metabolism, Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genotype, Japan, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyGenetics
Phylogeny20081025Microbacterium ginsengiterrae sp. nov., a beta-glucosidase-producing bacterium isolated from soil of a ginseng field.Kim YJ, Kim MK, Bui TPN, Kim HB, Srinivasan S, Yang DCInt J Syst Evol Microbiol10.1099/ijs.0.015784-02010Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Panax/*microbiology, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/chemistry, beta-Glucosidase/metabolismGenetics
Enzymology22721690Purification, characterization, and primary structure of a novel N-acyl-D-amino acid amidohydrolase from Microbacterium natoriense TNJL143-2.Liu J, Asano Y, Ikoma K, Yamashita S, Hirose Y, Shimoyama T, Takahashi S, Nakayama T, Nishino TJ Biosci Bioeng10.1016/j.jbiosc.2012.05.0152012Actinomycetales/*enzymology, Amidohydrolases/*chemistry/genetics/*isolation & purification/metabolism, Amino Acid Sequence, Amino Acids/*biosynthesis/chemistry/genetics/isolation & purification, Cloning, Molecular, *Industrial Microbiology, Molecular Sequence Data, Molecular Weight, Phylogeny, Sequence Alignment, TemperaturePhylogeny

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
6869Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17277)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17277
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
31304Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2762128776041
37641Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6416
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
76874Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID138015.1StrainInfo: A central database for resolving microbial strain identifiers
121242Curators of the CIPCollection of Institut Pasteur (CIP 108753)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108753