Strain identifier

BacDive ID: 7467

Type strain: Yes

Species: Microbacterium sediminis

Strain Designation: YLB-01

Strain history: DSM 23767 <-- L. Yu YLB-01.

NCBI tax ID(s): 904291 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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@ref: 17367

BacDive-ID: 7467

DSM-Number: 23767

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

description: Microbacterium sediminis YLB-01 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from deep-sea sediment.

NCBI tax id

  • NCBI tax id: 904291
  • Matching level: species

strain history

doi: 10.13145/bacdive7467.20220920.7

Name and taxonomic classification


  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Microbacteriaceae
  • genus: Microbacterium
  • species: Microbacterium sediminis
  • full scientific name: Microbacterium sediminis Yu et al. 2013

@ref: 17367

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Microbacterium

species: Microbacterium sediminis

full scientific name: Microbacterium sediminis Yu et al. 2013

strain designation: YLB-01

type strain: yes


cell morphology

  • @ref: 30121
  • gram stain: positive
  • cell length: 5.5 µm
  • cell width: 1.25 µm
  • cell shape: rod-shaped
  • motility: yes


  • @ref: 30121
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 17367
  • growth: yes
  • link:
  • 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


culture pH


Physiology and metabolism

oxygen tolerance

  • @ref: 30121
  • oxygen tolerance: aerobe


  • @ref: 30121
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-8 %


  • @ref: 67770
  • observation: quinones: MK-10, MK-11, MK-8, MK-9

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3012121217L-alaninamide+carbon source
3012116449alanine+carbon source
3012128757fructose+carbon source
3012124148galactonate+carbon source
3012128260galactose+carbon source
3012124265gluconate+carbon source
3012117234glucose+carbon source
3012115428glycine+carbon source
3012125017leucine+carbon source
3012129864mannitol+carbon source
3012137684mannose+carbon source
3012130911sorbitol+carbon source
3012153258sodium citrate+carbon source


30121acid phosphatase+
30121alkaline phosphatase+
30121cytochrome oxidase+

Isolation, sampling and environmental information


@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
17367deep-sea sedimentIndian Ocean (49.8405° E 37.8111° S) at 2327 m water depthChinaCHNAsia-37.811149.8405
67770Sediment of the Indian Ocean

isolation source categories


Safety information

risk assessment

  • @ref: 17367
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 17367
  • description: Microbacterium sediminis strain YLB-01 16S ribosomal RNA gene, partial sequence
  • accession: HQ219727
  • length: 1487
  • database: ena
  • NCBI tax ID: 904291

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Microbacterium sediminis YLB-01GCA_004564075completencbi904291
66792Microbacterium sediminis YLB-01GCA_001689915scaffoldncbi904291
66792Microbacterium sediminis YLB-01GCA_002741995scaffoldncbi904291
66792Microbacterium sediminis strain YLB-01904291.4wgspatric904291
66792Microbacterium sediminis ylb-012877021139draftimg904291
66792Microbacterium sediminis ylb-012847293147completeimg904291
66792Microbacterium sediminis ylb-012765235862draftimg904291
67770Microbacterium sediminis strain YLB-01, whole genome shotgun sequencing projectJRNY00000000ncbi904291
67770Microbacterium sediminis strain YLB-01, whole genome shotgun sequencing projectLXMD00000000ncbi904291

GC content

6777071high performance liquid chromatography (HPLC)

External links

@ref: 17367

culture collection no.: DSM 23767, CCTCC AB 2010363, JCM 19554, MCCC 1A06153

straininfo link



Phylogeny22328608Microbacterium sediminis sp. nov., a psychrotolerant, thermotolerant, halotolerant and alkalitolerant actinomycete isolated from deep-sea sediment.Yu L, Lai Q, Yi Z, Zhang L, Huang Y, Gu L, Tang XInt J Syst Evol Microbiol10.1099/ijs.0.029652-02012Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Indian Ocean, Molecular Sequence Data, *Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Phylogeny25253073Microbacterium petrolearium sp. nov., isolated from an oil-contaminated water sample.Wang H, Xiang T, Wang Y, Song J, Zhai Y, Chen X, Li Y, Zhao B, Zhao B, Ruan ZInt J Syst Evol Microbiol10.1099/ijs.0.061119-02014Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Oil and Gas Fields/*microbiology, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/chemistry, *Water Microbiology, Water Pollution, ChemicalGenetics
Phylogeny25675340Microbacterins A and B, new peptaibols from the deep sea actinomycete Microbacterium sediminis sp. nov. YLB-01(T).Liu D, Lin H, Proksch P, Tang X, Shao Z, Lin WOrg Lett10.1021/acs.orglett.5b001722015Actinobacteria/*chemistry, Actinomycetales/*chemistry, Amino Acids/*chemistry/pharmacology, Anti-Bacterial Agents/*chemistry/pharmacology, Cell Line, Tumor, Humans, Magnetic Resonance Spectroscopy, Molecular Structure, Peptaibols/chemical synthesis/*chemistry/isolation & purification/pharmacology, Tandem Mass SpectrometryPathogenicity
Phylogeny27260265Microbacterium gilvum sp. nov., isolated from civet faeces.Chen X, Li QY, Li GD, Xu FJ, Jiang Y, Han L, Jiang CL, Huang XSAntonie Van Leeuwenhoek10.1007/s10482-016-0718-12016Actinomycetales/*classification/genetics/*isolation & purification/metabolism, Animals, Cell Wall/chemistry, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Feces/*microbiology, Malaysia, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity, Vitamin K 2/metabolism, Viverridae/*microbiologyMetabolism
Metabolism31728583Metabolic profiling of cold adaptation of a deep-sea psychrotolerant Microbacterium sediminis to prolonged low temperature under high hydrostatic pressure.Xia JM, Hu XM, Huang CH, Yu LB, Xu RF, Tang XX, Lin DHAppl Microbiol Biotechnol10.1007/s00253-019-10134-42019Actinobacteria/genetics/growth & development/*metabolism, *Adaptation, Physiological, Amino Acids/metabolism, Aquatic Organisms/genetics/metabolism, Carbohydrate Metabolism, Citric Acid Cycle, *Cold Temperature, Cold-Shock Response, Gene Expression Profiling, Geologic Sediments/microbiology, *Hydrostatic Pressure, *Metabolomics
Enzymology31933418Characterization of cold-tolerant trehalose-6-phosphate synthase from the deep-sea bacterium Microbacterium sediminis YLB-01.Tang X, Yi Z, Xu X, Xu R, Huang P, Yu LBiosci Biotechnol Biochem10.1080/09168451.2020.17130442020Amino Acid Sequence, Barium/chemistry, Cobalt/chemistry, *Cold Temperature, Enzyme Stability, Escherichia coli/genetics/metabolism, Geologic Sediments/microbiology, Glucosyltransferases/*chemistry/*genetics, Hydrogen Bonding, Hydrogen-Ion Concentration, Indian Ocean, Ions/chemistry, Kinetics, Magnesium/chemistry, Microbacterium/enzymology/genetics, Molecular Dynamics Simulation, Phylogeny, Protein Structure, Secondary, Protein Structure, Tertiary, Recombinant ProteinsPhylogeny
Genetics33632425Genomic analysis of Microbacterium sediminis YLB-01(T) reveals backgrounds related to its deep-sea environment adaptation.Yi Z, Cao X, Li H, Jian H, Xu X, Yu L, Tang XMar Genomics10.1016/j.margen.2020.1008182020Adaptation, Biological/*genetics, Environment, *Genome, Bacterial, Geologic Sediments/*microbiology, Indian Ocean, Microbacterium/genetics, Whole Genome Sequencing
Transcriptome35150317Transcriptomic Analysis Reveals that Changes in Gene Expression Contribute to Microbacterium sediminis YLB-01 Adaptation at Low Temperature Under High Hydrostatic Pressure.Qiu X, Cao X, Jian H, Wu H, Xu G, Tang XCurr Microbiol10.1007/s00284-022-02786-92022*Actinomycetales/genetics, Hydrostatic Pressure, Microbacterium, Temperature, *Transcriptome


17367Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23767)
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
30121Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604126475
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCM