Strain identifier

BacDive ID: 5735

Type strain: Yes

Species: Salinimicrobium terrae

Strain Designation: YIM-C338

Strain history: <- X.-L. Cui, YIM <- Y.-G. Chen and X.-L. Cui

NCBI tax ID(s): 1123234 (strain), 470866 (species)

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General

@ref: 7147

BacDive-ID: 5735

DSM-Number: 17865

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

description: Salinimicrobium terrae YIM-C338 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from saline soil from the bank of Chaka salt lake.

NCBI tax id

NCBI tax idMatching level
1123234strain
470866species

strain history

  • @ref: 7147
  • history: <- X.-L. Cui, YIM <- Y.-G. Chen and X.-L. Cui

doi: 10.13145/bacdive5735.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Flavobacteriaceae
  • genus: Salinimicrobium
  • species: Salinimicrobium terrae
  • full scientific name: Salinimicrobium terrae Chen et al. 2008

@ref: 7147

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Salinimicrobium

species: Salinimicrobium terrae

full scientific name: Salinimicrobium terrae Chen et al. 2008 emend. Hahnke et al. 2016

strain designation: YIM-C338

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32658negative02-04 µm0.6-1 µmrod-shapedno
69480negative99.985

pigmentation

  • @ref: 32658
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 7147
  • name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/514
  • composition: Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
7147positivegrowth28mesophilic
32658positivegrowth04-37
32658positiveoptimum28mesophilic

culture pH

@refabilitytypepHPH range
32658positivegrowth06-09alkaliphile
32658positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 32658
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
32658no
69481no100
69480no99.999

halophily

@refsaltgrowthtested relationconcentration
32658NaClpositivegrowth0.5-8 %
32658NaClpositiveoptimum01-03 %

observation

  • @ref: 32658
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3265830089acetate+carbon source
3265840585alpha-cyclodextrin+carbon source
3265822599arabinose+carbon source
3265818403L-arabitol+carbon source
3265817057cellobiose+carbon source
3265816947citrate+carbon source
3265823652dextrin+carbon source
3265815740formate+carbon source
3265828757fructose+carbon source
3265828260galactose+carbon source
3265824265gluconate+carbon source
3265817234glucose+carbon source
3265829987glutamate+carbon source
3265817754glycerol+carbon source
3265828087glycogen+carbon source
3265824996lactate+carbon source
3265825017leucine+carbon source
3265815792malonate+carbon source
3265817306maltose+carbon source
3265829864mannitol+carbon source
3265837684mannose+carbon source
3265826271proline+carbon source
3265851850methyl pyruvate+carbon source
3265830031succinate+carbon source
3265817992sucrose+carbon source
3265826986threonine+carbon source
3265827082trehalose+carbon source
326584853esculin+hydrolysis
3265817632nitrate+reduction

enzymes

  • @ref: 32658
  • value: catalase
  • activity: +
  • ec: 1.11.1.6

Isolation, sampling and environmental information

isolation

  • @ref: 7147
  • sample type: saline soil from the bank of Chaka salt lake
  • geographic location: north-west China, Qinghai Province, Qaidam Basin
  • country: China
  • origin.country: CHN
  • continent: Asia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Lake (large)
#Environmental#Terrestrial#Soil
#Condition#Saline

Safety information

risk assessment

  • @ref: 7147
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 7147
  • description: Salinimicrobium terrae strain YIM-C338 16S ribosomal RNA gene, partial sequence
  • accession: EU135614
  • length: 1467
  • database: ena
  • NCBI tax ID: 470866

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Salinimicrobium terrae DSM 17865GCA_000424665scaffoldncbi1123234
66792Salinimicrobium terrae DSM 178651123234.4wgspatric1123234
66792Salinimicrobium terrae DSM 178652522125157draftimg1123234

GC content

@refGC-contentmethod
714742.8thermal denaturation, midpoint method (Tm)
3265842.8
714740.4sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno88.458yes
flagellatedno94.152yes
gram-positiveno97.83no
anaerobicno98.783yes
aerobicyes86.483yes
halophileyes66.469no
spore-formingno93.903yes
thermophileno99.429no
glucose-utilyes86.216yes
glucose-fermentno85.487no

External links

@ref: 7147

culture collection no.: DSM 17865, CGMCC 1.6308

straininfo link

  • @ref: 75215
  • straininfo: 404047

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18984683Salinimicrobium terrae sp. nov., isolated from saline soil, and emended description of the genus Salinimicrobium.Chen YG, Cui XL, Zhang YQ, Li WJ, Wang YX, Kim CJ, Lim JM, Xu LH, Jiang CLInt J Syst Evol Microbiol10.1099/ijs.0.65860-02008Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Flavobacteriaceae/*classification/genetics/isolation & purification/physiology, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Sodium Chloride, *Soil Microbiology, Species SpecificityGenetics
Phylogeny24425818Salinimicrobium sediminis sp. nov., isolated from a deep-sea sediment.Subhash Y, Sasikala C, Ramana CVInt J Syst Evol Microbiol10.1099/ijs.0.058149-02013Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacteriaceae/*classification/genetics/isolation & purification, Geologic Sediments/*microbiology, India, Molecular Sequence Data, Nucleic Acid Hybridization, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Sequence Analysis, DNA, Triterpenes/chemistry, Vitamin K 2/analogs & derivatives/chemistry, *Water MicrobiologyGenetics
Phylogeny36209246Salinimicrobium sediminilitoris sp. nov., Isolated from a Tidal Flat.Xia CQ, Niu HJ, Dong KS, Guan L, Sun LP, Wang Q, Zhang YJ, Li Y, Pei CXCurr Microbiol10.1007/s00284-022-03037-72022Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids, Geologic Sediments/microbiology, Nucleotides, *Phosphatidylethanolamines, Phylogeny, RNA, Ribosomal, 16S/genetics, *Seawater/microbiology, Sequence Analysis, DNA, Vitamin K 2Transcriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7147Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17865)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17865
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
32658Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2886928776041
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)
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
75215Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID404047.1StrainInfo: A central database for resolving microbial strain identifiers