Strain identifier

BacDive ID: 134301

Type strain: Yes

Species: Sinomonas albida

Strain Designation: LC13

Strain history: CCTCC AB 206018 <-- L. Ding and A. Yokota; IAM, Japan; LC13.

NCBI tax ID(s): 369942 (species)

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General

@ref: 32315

BacDive-ID: 134301

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

description: Sinomonas albida LC13 is an aerobe, Gram-positive, rod-shaped bacterium that was isolated from volcanic rock.

NCBI tax id

  • NCBI tax id: 369942
  • Matching level: species

strain history

  • @ref: 67770
  • history: CCTCC AB 206018 <-- L. Ding and A. Yokota; IAM, Japan; LC13.

doi: 10.13145/bacdive134301.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Micrococcaceae
  • genus: Sinomonas
  • species: Sinomonas albida
  • full scientific name: Sinomonas albida (Ding et al. 2009) Zhou et al. 2012

  • synonyms

    • @ref: 20215
    • synonym: Arthrobacter albidus

@ref: 32315

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Micrococcales

family: Micrococcaceae

genus: Sinomonas

species: Sinomonas albida

strain designation: LC13

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
32315positiverod-shapedno
69480positive100

pigmentation

  • @ref: 32315
  • production: yes

Culture and growth conditions

culture temp

@refgrowthtypetemperaturerange
32315positivegrowth10-40
32315positiveoptimum30mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
32315positivegrowth06-10alkaliphile
32315positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 32315
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
32315no
69480no99.989

halophily

  • @ref: 32315
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 03-07 %

observation

  • @ref: 67770
  • observation: quinones: MK-9(H2), MK-10(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3231517234glucose+carbon source
3231529864mannitol+carbon source
3231533942ribose+carbon source
3231517992sucrose+carbon source
3231518222xylose+carbon source

enzymes

@refvalueactivityec
32315alkaline phosphatase+3.1.3.1
32315catalase+1.11.1.6
32315pyrazinamidase+3.5.1.B15
32315urease+3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
32315volcanic rock
67770Filtration substrate made from volcanic rock from NiigataJapanJPNAsia

isolation source categories

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

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
32315Arthrobacter albidus gene for 16S rRNA, partial sequenceAB2485331484nuccore369942
67770Sinomonas albida JCM 30149 gene for 16S ribosomal RNA, partial sequenceLC4387591458ena369942

Genome sequences

  • @ref: 66792
  • description: Sinomonas albida LC13
  • accession: GCA_004919045
  • assembly level: scaffold
  • database: ncbi
  • NCBI tax ID: 369942

GC content

@refGC-contentmethod
3231570.8
6777070.8high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno58no
motileno67.244yes
flagellatedno93.826yes
gram-positiveyes92.441yes
anaerobicno99.521yes
aerobicyes94.753no
halophileno91.32no
spore-formingno91.384yes
glucose-utilyes86.772yes
thermophileno97.48yes
glucose-fermentno79.432no

External links

@ref: 32315

culture collection no.: IAM 15386, CCTCC AB 206018, JCM 30149, DSM 107966, JCM 21830

straininfo link

  • @ref: 91883
  • straininfo: 404879

literature

  • topic: Phylogeny
  • Pubmed-ID: 19329620
  • title: Four novel Arthrobacter species isolated from filtration substrate.
  • authors: Ding L, Hirose T, Yokota A
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.65301-0
  • year: 2009
  • mesh: Amino Acids/analysis, Arthrobacter/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Sodium Chloride/metabolism, *Soil Microbiology, Temperature, Vitamin K 2/analysis
  • topic2: Genetics

Reference

@idauthorstitledoi/urlID_cross_referencepubmed
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
32315Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172855228776041
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
91883Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID404879.1