Strain identifier

BacDive ID: 7447

Type strain: Yes

Species: Microbacterium insulae

Strain Designation: DS-66

Strain history: <- JH Yoon, KRIBB

NCBI tax ID(s): 483014 (species)

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General

@ref: 16654

BacDive-ID: 7447

DSM-Number: 23024

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

description: Microbacterium insulae DS-66 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 483014
  • Matching level: species

strain history

@refhistory
16654<- CCUG <- J.-H. Yoon, KRIBB
67770CCUG 54523 <-- J.-H. Yoon DS-66.
67771<- JH Yoon, KRIBB

doi: 10.13145/bacdive7447.20250331.9.3

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 insulae
  • full scientific name: Microbacterium insulae Yoon et al. 2009

@ref: 16654

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Microbacterium

species: Microbacterium insulae

full scientific name: Microbacterium insulae Yoon et al. 2009

strain designation: DS-66

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29157positive1.15 µm0.35 µmcoccus-shapedno
67771positive
125438no93
125438positive91.335
125439positive99.3

colony morphology

  • @ref: 60213
  • incubation period: 1-2 days

pigmentation

  • @ref: 29157
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 16654
  • name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/92
  • composition: Name: 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

culture temp

@refgrowthtypetemperature
16654positivegrowth28
29157positivegrowth20-38
29157positiveoptimum30
60213positivegrowth30-37
67770positivegrowth28
67771positivegrowth30

culture pH

@refabilitytypepH
29157positivegrowth5.5-8.0
29157positiveoptimum6.75

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
60213aerobe
67771aerobe
125439obligate aerobe98.5

spore formation

  • @ref: 29157
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
29157NaClpositivegrowth0-5 %
29157NaClpositiveoptimum0.75 %

murein

  • @ref: 16654
  • murein short key: B06
  • type: B2ß {Gly} [L-Hsr] D-Glu(Hyg)-Gly-D-Orn

observation

  • @ref: 67770
  • observation: quinones: MK-13, MK-12, MK-14

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2915722599arabinose+carbon source
2915717057cellobiose+carbon source
2915728757fructose+carbon source
2915728260galactose+carbon source
291575291gelatin+carbon source
2915717234glucose+carbon source
2915717754glycerol+carbon source
2915717716lactose+carbon source
2915717306maltose+carbon source
2915729864mannitol+carbon source
2915737684mannose+carbon source
2915737657methyl D-glucoside+carbon source
2915726546rhamnose+carbon source
2915717814salicin+carbon source
2915717992sucrose+carbon source
2915727082trehalose+carbon source
2915753424tween 20+carbon source
2915753423tween 40+carbon source
2915753425tween 60+carbon source
2915753426tween 80+carbon source
2915718222xylose+carbon source
291574853esculin+hydrolysis

enzymes

  • @ref: 29157
  • value: cytochrome oxidase
  • activity: +
  • ec: 1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
16654soilDokdoRepublic of KoreaKORAsia
60213SoilDokdoRepublic of KoreaKORAsia2004-05-01
67770Soil
67771From soilDokdoRepublic of KoreaKORAsia

isolation source categories

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

Safety information

risk assessment

  • @ref: 16654
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 16654
  • description: Microbacterium insulae strain DS-66 16S ribosomal RNA gene, partial sequence
  • accession: EU239498
  • length: 1447
  • database: nuccore
  • NCBI tax ID: 483014

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Microbacterium insulae strain DSM 23024483014.3wgspatric483014
66792Microbacterium insulae DSM 230242893599951draftimg483014

GC content

@refGC-contentmethod
1665469.9high performance liquid chromatography (HPLC)
2915769.9

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes91.335no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.671yes
125438spore-formingspore-formingAbility to form endo- or exosporesno72.373yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes89.258yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno96.429yes
125438motile2+flagellatedAbility to perform flagellated movementno93yes
125439BacteriaNetspore_formationAbility to form endo- or exosporesno76.5
125439BacteriaNetmotilityAbility to perform movementno71.4
125439BacteriaNetgram_stainReaction to gram-stainingpositive99.3
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe98.5

External links

@ref: 16654

culture collection no.: DSM 23024, CCUG 54523, KCTC 19247, JCM 19115

straininfo link

  • @ref: 76895
  • straininfo: 407518

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19542140Microbacterium insulae sp. nov., isolated from soil.Yoon JH, Schumann P, Kang SJ, Lee CS, Lee SY, Oh TKInt J Syst Evol Microbiol10.1099/ijs.0.007591-02009Actinomycetales/*classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, Genes, rRNA, Genotype, Korea, Lipids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species SpecificityGenetics
Phylogeny20656817Microbacterium arthrosphaerae sp. nov., isolated from the faeces of the pill millipede Arthrosphaera magna Attems.Kampfer P, Rekha PD, Schumann P, Arun AB, Young CC, Chen WM, Sridhar KRInt J Syst Evol Microbiol10.1099/ijs.0.026401-02010Actinomycetales/*classification/genetics/*isolation & purification, Amino Acids/analysis, Animals, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Feces/*microbiology, India, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analysisGenetics
Phylogeny22280899Microbacterium marinum sp. nov., isolated from deep-sea water.Zhang L, Xi L, Ruan J, Huang YSyst Appl Microbiol10.1016/j.syapm.2011.11.0042012Actinomycetales/*classification/*genetics/isolation & purification, Aquatic Organisms/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition/genetics, Base Sequence, DNA, Bacterial/analysis/genetics, DNA, Ribosomal/analysis/genetics, Indian Ocean, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/analysis/genetics, Seawater/*microbiology, Sequence Alignment, Sequence Analysis, DNAEnzymology
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

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
16654Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23024)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23024
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
29157Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2558128776041
60213Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 54523)https://www.ccug.se/strain?id=54523
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/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
76895Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID407518.1StrainInfo: A central database for resolving microbial strain identifiers
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1