Strain identifier

BacDive ID: 7438

Type strain: Yes

Species: Microbacterium flavum

Strain Designation: YM18-098

Strain history: DSM 18909 <-- H. Kasai YM18-098.

NCBI tax ID(s): 415216 (species)

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General

@ref: 7769

BacDive-ID: 7438

DSM-Number: 18909

keywords: genome sequence, 16S sequence, Bacteria, Gram-positive

description: Microbacterium flavum YM18-098 is a Gram-positive bacterium that was isolated from Ascidian .

NCBI tax id

  • NCBI tax id: 415216
  • Matching level: species

strain history

@refhistory
7769<- H. Kasai; YM18-098
67770DSM 18909 <-- H. Kasai YM18-098.

doi: 10.13145/bacdive7438.20240916.9.1

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 flavum
  • full scientific name: Microbacterium flavum Kageyama et al. 2008

@ref: 7769

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Microbacterium

species: Microbacterium flavum

full scientific name: Microbacterium flavum Kageyama et al. 2008

strain designation: YM18-098

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no93.5
6948090.987positive

Culture and growth conditions

culture medium

  • @ref: 7769
  • name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/514
  • composition: Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water

culture temp

@refgrowthtypetemperature
7769positivegrowth28
67770positivegrowth28

Physiology and metabolism

spore formation

  • @ref: 69481
  • spore formation: no
  • confidence: 100

observation

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

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 2-ketogluconate-builds acid from
68371gluconate+builds acid from24265
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
68371turanose+builds acid from32528
68371gentiobiose+builds acid from28066
68371xylitol-builds acid from17151
68371glycogen+builds acid from28087
68371starch+builds acid from28017
68371raffinose+builds acid from16634
68371melezitose+builds acid from6731
68371inulin+builds acid from15443
68371trehalose+builds acid from27082
68371sucrose+builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose+builds acid from17306
68371cellobiose+builds acid from17057
68371esculin+builds acid from4853
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
68371D-sorbitol-builds acid from17924
68371D-mannitol+builds acid from16899
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

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
7769----+-----++++-+--+---+--++/-++--+++++++-++------+-+/-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinenthost species
7769Ascidian (D. moseleyi)NagasakiJapanJPNAsia
67770Ascidian (Didemnum moseleyi), Nomozaki at the tips of Nagasaki PeninsulaNagasaki Pref.JapanJPNAsiaDidemnum moseleyi

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Host#Invertebrates (Other)#Tunicata

Safety information

risk assessment

  • @ref: 7769
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 7769
  • description: Microbacterium flavum gene for 16S rRNA, partial sequence
  • accession: AB286029
  • length: 1467
  • database: nuccore
  • NCBI tax ID: 415216

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Microbacterium flavum DSM 18909GCA_018717645contigncbi415216
66792Microbacterium flavum strain DSM 18909415216.5wgspatric415216

GC content

@refGC-contentmethod
776970
6777070high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno100no
69480gram-positivegram-positivePositive reaction to Gram-stainingyes90.987no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no96.329no
69480spore-formingspore-formingAbility to form endo- or exosporesno83.746no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes84.15no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno95.484no
69480flagellatedmotile2+Ability to perform flagellated movementno93.5no

External links

@ref: 7769

culture collection no.: DSM 18909, JCM 15574, MBIC 08278, NBRC 103923

straininfo link

  • @ref: 76886
  • straininfo: 398142

literature

Pubmed-IDtitleauthorsjournalDOIyearmeshtopictopic2
33682148Protective effect of fermented Diospyros lotus L. extracts against the high glucose-induced apoptosis of MIN6 cells.Yin H, Yan HH, Qin CQ, Li HR, Li X, Ren DFJ Food Biochem10.1111/jfbc.136852021Apoptosis, *Diabetes Mellitus, Type 2, *Diospyros, Glucose, *Insulin-Secreting Cells, Plant Extracts/pharmacology
34807813Microbacterium paulum sp. nov., isolated from microfiltered milk.Bellassi P, Fontana A, Callegari ML, Cappa F, Morelli LInt J Syst Evol Microbiol10.1099/ijsem.0.0051192021Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, *Microbacterium/classification/isolation & purification, Milk/*microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/chemistryPhylogenyTranscriptome

Reference

@idauthorscataloguedoi/urltitle
7769Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18909)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18909
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
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
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
76886Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID398142.1StrainInfo: A central database for resolving microbial strain identifiers