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Strain identifier

BacDive ID: 24188

Type strain: Yes

Species: Microbacterium saccharophilum

Strain Designation: K-1

Strain history: <- NBRC; NBRC 108778 <- K. Mikuni, Ensuiko Sugar Refining Co., LTD; K-1

NCBI tax ID(s): 1213358 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 20654

BacDive-ID: 24188

DSM-Number: 28107

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

description: Microbacterium saccharophilum K-1 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from soil, sucrose refining factory.

NCBI tax id

  • NCBI tax id: 1213358
  • Matching level: species

strain history: <- NBRC; NBRC 108778 <- K. Mikuni, Ensuiko Sugar Refining Co., LTD; K-1

doi: 10.13145/bacdive24188.20221219.7.1

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 saccharophilum
  • full scientific name: Microbacterium saccharophilum Ohta et al. 2013

@ref: 20654

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Microbacterium

species: Microbacterium saccharophilum

full scientific name: Microbacterium saccharophilum Ohta et al. 2013

strain designation: K-1

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30909positive0.8 µm0.4 µmrod-shapedno
69480positive97.06

pigmentation

  • @ref: 30909
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 20654
  • 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

@refgrowthtypetemperaturerange
20654positivegrowth28mesophilic
30909positivegrowth09-37
30909positiveoptimum30mesophilic

culture pH

@refabilitytypepHPH range
30909positivegrowth6.0-11.0alkaliphile
30909positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 30909
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
30909no
69480no98.84

halophily

@refsaltgrowthtested relationconcentrationhalophily levelconfidence
30909NaClpositivegrowth0-1 %
69480non-halophilic93.962

observation

  • @ref: 30909
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3090928757fructose+carbon source
3090929864mannitol+carbon source
3090918222xylose+carbon source

enzymes

@refvalueactivityec
30909catalase+1.11.1.6
30909gelatinase+

Isolation, sampling and environmental information

isolation

  • @ref: 20654
  • sample type: soil, sucrose refining factory
  • country: Japan
  • origin.country: JPN
  • continent: Asia

isolation source categories

Cat1Cat2Cat3
#Engineered#Industrial#Plant (Factory)
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_1973.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_137;97_148;98_1544;99_1973&stattab=map
  • Last taxonomy: Microbacterium
  • 16S sequence: AB736273
  • Sequence Identity:
  • Total samples: 13220
  • soil counts: 4083
  • aquatic counts: 3329
  • animal counts: 5014
  • plant counts: 794

Safety information

risk assessment

  • @ref: 20654
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 20654
  • description: Microbacterium saccharophilum gene for 16S ribosomal RNA, partial sequence
  • accession: AB736273
  • length: 1482
  • database: ena
  • NCBI tax ID: 1213358

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Microbacterium saccharophilum NBRC 108778GCA_007992455contigncbi1213358
66792Microbacterium saccharophilum K-1GCA_008017435contigncbi1213358
66792Microbacterium saccharophilum strain NBRC 1087781213358.6wgspatric1213358
66792Microbacterium saccharophilum NBRC 1087782903864575draftimg1213358
66792Microbacterium saccharophilum K-12903861677draftimg1213358
66792Microbacterium saccharophilum DSM 28107GCA_023155775contigncbi1213358
66792Prochlorococcus sp. AG-321-K11 AG-321-K11GCA_003283305contigpatric2162447
66792uncultured Ruminococcus sp. RUG10174GCA_902756675scaffoldpatric165186

GC content

  • @ref: 20654
  • GC-content: 73

External links

@ref: 20654

culture collection no.: DSM 28107, NBRC 108778, NCIMB 14782

straininfo link

@refpassport
20218http://www.straininfo.net/strains/890469
20218http://www.straininfo.net/strains/890470

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny23315408Microbacterium saccharophilum sp. nov., isolated from a sucrose-refining factory.Ohta Y, Ito T, Mori K, Nishi S, Shimane Y, Mikuni K, Hatada YInt J Syst Evol Microbiol10.1099/ijs.0.047258-02013Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Japan, Lysine/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Sucrose/*metabolism, Vitamin K 2/analysisGenetics
Phylogeny25239238Microbacterium endophyticum sp. nov. and Microbacterium halimionae sp. nov., endophytes isolated from the salt-marsh plant Halimione portulacoides and emended description of the genus Microbacterium.Alves A, Correia A, Igual JM, Trujillo MESyst Appl Microbiol10.1016/j.syapm.2014.08.0042014Actinobacteria/*classification/genetics/*isolation & purification, Amaranthaceae/*microbiology, Bacterial Typing Techniques, Cell Wall/chemistry, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Endophytes/*classification/genetics/*isolation & purification, Fatty Acids/analysis, Molecular Sequence Data, Molecular Typing, Nucleic Acid Hybridization, Ornithine/analysis, Peptidoglycan/analysis, Phylogeny, Polymerase Chain Reaction, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Vitamin K 2/analysisEnzymology
Phylogeny36167780Microbacterium kunmingensis sp. nov., an attached bacterium of Microcystis aeruginosa.Xiao Y, Chen M, Chen J, Mao LN, Peng YR, Gui SS, Zhang BHJ Antibiot (Tokyo)10.1038/s41429-022-00568-w2022RNA, Ribosomal, 16S/genetics, *Microcystis, Microbacterium, DNA, Bacterial/genetics, Bacterial Typing Techniques, Phylogeny, Sequence Analysis, DNA, *Actinomycetales, Fatty Acids/chemistry, Vitamin K 2/chemistryTranscriptome

Reference

@idauthorstitledoi/urljournalpubmedcatalogueID_cross_reference
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.StrainInfo introduces electronic passports for microorganisms.10.1016/j.syapm.2013.11.002Syst Appl Microbiol. 37: 42-50 201424321274
20654Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-28107Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 28107)
2723910.1099/ijs.0.047258-023315408
30909Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172877604127239
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes