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)

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General

@ref: 17367

BacDive-ID: 7467

DSM-Number: 23767

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

@refhistory
17367<- Y. Libo, Key Lab. Marine Biogenetic Resources, Third Institute of Oceanography, Xiamen; YLB-01
67770DSM 23767 <-- L. Yu YLB-01.

doi: 10.13145/bacdive7467.20230509.8.1

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 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

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30121positive5.5 µm1.25 µmrod-shapedyes
69480positive100

pigmentation

  • @ref: 30121
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 17367
  • 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
17367positivegrowth28mesophilic
30121positivegrowth04-50
30121positiveoptimum28mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
30121positivegrowth5.0-10.0alkaliphile
30121positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 30121
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.979

halophily

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

observation

  • @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
301214853esculin+hydrolysis

enzymes

@refvalueactivityec
30121acid phosphatase+3.1.3.2
30121alkaline phosphatase+3.1.3.1
30121catalase+1.11.1.6
30121cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@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

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_67863.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_7448;97_8944;98_10967;99_67863&stattab=map
  • Last taxonomy: Microbacterium sediminis
  • 16S sequence: HQ219727
  • Sequence Identity:
  • Total samples: 45
  • soil counts: 8
  • aquatic counts: 14
  • animal counts: 20
  • plant counts: 3

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 strain YLB-01904291.4wgspatric904291
66792Microbacterium sediminis ylb-012877021139draftimg904291
66792Microbacterium sediminis ylb-012847293147completeimg904291
66792Microbacterium sediminis ylb-012765235862draftimg904291
67770Microbacterium sediminis YLB-01GCA_002741995scaffoldncbi904291
67770Microbacterium sediminis YLB-01GCA_001689915scaffoldncbi904291

GC content

@refGC-contentmethod
1736771
6777071high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes57.238yes
flagellatedno90.627no
gram-positiveyes92.192yes
anaerobicno99.357yes
aerobicyes93.802yes
halophileno84.112no
spore-formingno94.366no
glucose-utilyes85.247yes
thermophileno98.138yes
glucose-fermentno89.383no

External links

@ref: 17367

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

straininfo link

  • @ref: 76912
  • straininfo: 398690

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
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

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
17367Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23767)https://www.dsmz.de/collection/catalogue/details/culture/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
30121Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2647528776041
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)
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 updates33211880Nucleic Acids Res. 49: D498-D508 2020
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
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
76912Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID398690.1StrainInfo: A central database for resolving microbial strain identifiers