Strain identifier

BacDive ID: 7364

Type strain: Yes

Species: Microbacterium flavescens

Strain Designation: 401

Strain history: CIP <- 1986, DSM <- NCIB <- A.G. Lochhead: strain 401, Arthrobacter flavescens

NCBI tax ID(s): 69366 (species)

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General

@ref: 8863

BacDive-ID: 7364

DSM-Number: 20643

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

description: Microbacterium flavescens 401 is an obligate aerobe, mesophilic bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 69366
  • Matching level: species

strain history

@refhistory
8863<- NCIB <- A.G. Lochhead, 401
67770DSM 20643 <-- NCIB 9221 <-- A. G. Lochhead 401.
119368CIP <- 1986, DSM <- NCIB <- A.G. Lochhead: strain 401, Arthrobacter flavescens

doi: 10.13145/bacdive7364.20230509.8.1

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 flavescens
  • full scientific name: Microbacterium flavescens (Lochhead 1958) Takeuchi and Hatano 1998

  • synonyms

    @refsynonym
    20215Arthrobacter flavescens
    20215Aureobacterium flavescens

@ref: 8863

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Microbacterium

species: Microbacterium flavescens

full scientific name: Microbacterium flavescens (Lochhead 1958) Takeuchi and Hatano 1998

strain designation: 401

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no90.34
69480100positive
119368nopositiverod-shaped

colony morphology

@refincubation periodmedium used
1876710-14 daysISP 2
1876710-14 daysISP 3
119368

multicellular morphology

@refforms multicellular complexmedium name
18767noISP 2
18767noISP 3

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
18767ISP 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
18767ISP 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:
38098MEDIUM 363 - for Microbacterium flavescensyesDistilled water make up to (750.000 ml);Agar (15.000 g);Peptone (5.000 g);Beef extract (3.000 g);Earth extract - M0541 (250.000 ml)
8863TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yesName: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92; with strain-specific modifications) Composition: Soil extract 250.0 g/l Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled waterhttps://mediadive.dsmz.de/medium/92
119368CIP Medium 363yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=363

culture temp

@refgrowthtypetemperaturerange
18767positiveoptimum28mesophilic
8863positivegrowth26mesophilic
38098positivegrowth25mesophilic
67770positivegrowth28mesophilic
119368positivegrowth10-30
119368nogrowth37mesophilic
119368nogrowth41thermophilic
119368nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 119368
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.989

halophily

@refsaltgrowthtested relationconcentration
18767NaClpositivegrowth0 %
119368NaClpositivegrowth0-4 %
119368NaClnogrowth6 %
119368NaClnogrowth8 %
119368NaClnogrowth10 %

murein

  • @ref: 8863
  • 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 5-ketogluconate-builds acid from
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
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371sucrose+builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose+builds acid from62345
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
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose+builds acid from65327
68371D-ribose+builds acid from16988
68371L-arabinose+builds acid from30849
68371D-arabinose+builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
68368tryptophan-energy source27897
68368urea-hydrolysis16199
68368citrate-assimilation16947
68368ornithine-degradation18257
68368lysine-degradation25094
68368arginine-hydrolysis29016
119368citrate-carbon source16947
119368esculin+hydrolysis4853
119368hippurate-hydrolysis606565
119368nitrate+reduction17632
119368nitrite-reduction16301
119368nitrate-respiration17632
68379nitrate-reduction17632
68379esculin+hydrolysis4853
68379D-glucose-fermentation17634
68379sucrose+fermentation17992
68379glycogen-fermentation28087

antibiotic resistance

  • @ref: 119368
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
6836835581indoleno
6836816136hydrogen sulfideno
11936835581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
6836835581indole-
11936815688acetoin+
11936817234glucose+

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382alpha-galactosidase-3.2.1.22
68382leucine arylamidase+3.4.11.1
68382esterase lipase (C 8)+
68379catalase-1.11.1.6
68379beta-glucosidase+3.2.1.21
68379N-acetyl-beta-glucosaminidase+3.2.1.52
68379alpha-glucosidase+3.2.1.20
68379pyrazinamidase+3.5.1.B15
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
119368oxidase-
119368beta-galactosidase+3.2.1.23
119368alcohol dehydrogenase-1.1.1.1
119368gelatinase+/-
119368amylase+
119368DNase+
119368caseinase+3.4.21.50
119368catalase+1.11.1.6
119368tween esterase-
119368gamma-glutamyltransferase-2.3.2.2
119368lecithinase-
119368lipase-
119368lysine decarboxylase-4.1.1.18
119368ornithine decarboxylase-4.1.1.17
119368phenylalanine ammonia-lyase+4.3.1.24
119368protease-
119368tryptophan deaminase-
119368urease-3.5.1.5

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    49476C16:01.716
    49476C13:0 ANTEISO112.701
    49476C15:0 ANTEISO62.714.711
    49476C15:0 ISO9.414.621
    49476C16:0 iso6.815.626
    49476C17:0 anteiso11.616.722
    49476C17:0 iso6.816.629
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYGControlCAT
18767-++-++++++--+-++++-
49476-+-+--+++-+--+---+---

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
18767+++-++++++--+-+++--
49476--+-+---+-----+++---
119368+++++++--++---++-+--

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpIND
18767+--------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119368--++++-----+--+--+/-+/------+/-+/-+/-+/---++/-----+/---+/-------+/---

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119368+++++--+-++----+--+--+---------+-+-+-------------+------++--+-----------+--+--+++-+---+--++--+-----

Isolation, sampling and environmental information

isolation

@refsample type
8863soil
49476Soil
67770Soil
119368Environment, Soil

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
187671Risk group (German classification)
88631Risk group (German classification)
1193681Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Microbacterium flavescens 16S rRNA geneY172321471ena69366
20218Microbacterium flavescens gene for 16S rRNA, partial sequenceAB0047161467ena69366

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Microbacterium flavescens JCM 3877GCA_018588945scaffoldncbi69366
66792Microbacterium flavescens strain JCM 387769366.3wgspatric69366

GC content

@refGC-contentmethod
886366.9
6777070.3Buoyant density centrifugation (BD)
6777066.9thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno98.022no
gram-positiveyes92.835no
anaerobicno99.677no
aerobicyes95.325no
halophileno90.138yes
spore-formingno93.837no
thermophileno98.021yes
glucose-utilyes90.391no
motileno90.994no
glucose-fermentno90.954yes

External links

@ref: 8863

culture collection no.: CCUG 29000, DSM 20643, ATCC 13348, NCIB 9221, JCM 3877, BCRC 12361, CCTM 2716, CIP 102401, HAMBI 1871, HAMBI 1909, IAM 15203, IFO 15039, IMET 10367, JCM 11568, KCTC 3389, KCTC 3437, LMG 3028, NBIMCC 2370, NBRC 15039, NCIMB 9221, NRRL B-24238, VKM Ac-1415

straininfo link

  • @ref: 76813
  • straininfo: 1010

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny27506590Microbacterium aureliae sp. nov., a novel actinobacterium isolated from Aurelia aurita, the moon jellyfish.Kaur G, Mual P, Kumar N, Verma A, Kumar A, Krishnamurthi S, Mayilraj SInt J Syst Evol Microbiol10.1099/ijsem.0.0014072016Actinomycetales/*classification/genetics/isolation & purification, Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, India, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Scyphozoa/*microbiology, Sequence Analysis, DNA, Vitamin K 2/chemistryTranscriptome
Phylogeny35024967Microbacterium sulfonylureivorans sp. nov., isolated from sulfonylurea herbicides degrading consortium.Ma Q, Kong D, Zhang Q, Li M, Han X, Che J, Zhou Y, Zhang W, Jiang X, Ruan ZArch Microbiol10.1007/s00203-021-02750-42022Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids, *Herbicides, Microbacterium, Phospholipids, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8863Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20643)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20643
18767Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM20643.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
38098Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/14083
49476Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 29000)https://www.ccug.se/strain?id=29000
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
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
76813Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID1010.1StrainInfo: A central database for resolving microbial strain identifiers
119368Curators of the CIPCollection of Institut Pasteur (CIP 102401)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20102401