Strain identifier

BacDive ID: 7488

Type strain: Yes

Species: Salinibacterium amurskyense

Strain history: CIP <- 2004, KCTC <- KMM

NCBI tax ID(s): 205941 (species)

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

@ref: 6429

BacDive-ID: 7488

DSM-Number: 16400

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

description: Salinibacterium amurskyense DSM 16400 is an obligate aerobe, mesophilic, Gram-positive bacterium that was isolated from seawater.

NCBI tax id

  • NCBI tax id: 205941
  • Matching level: species

strain history

@refhistory
6429<- S.-B. Kim <- KMM <- O. I. Nedashkovskaya
67770KCTC 9931 <-- S. B. Kim <-- O. I. Nedashkovskaya KMM 3673.
116347CIP <- 2004, KCTC <- KMM

doi: 10.13145/bacdive7488.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Microbacteriaceae
  • genus: Salinibacterium
  • species: Salinibacterium amurskyense
  • full scientific name: Salinibacterium amurskyense Han et al. 2003

@ref: 6429

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Salinibacterium

species: Salinibacterium amurskyense

full scientific name: Salinibacterium amurskyense Han et al. 2003

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480positive100
116347positiverod-shapedno

colony morphology

  • @ref: 116347

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6429BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: 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
33234Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
116347CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
6429positivegrowth25-28mesophilic
33234positivegrowth30mesophilic
67770positivegrowth28mesophilic
116347positivegrowth10-30
116347nogrowth37mesophilic
116347nogrowth41thermophilic
116347nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 116347
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.998

halophily

@refsaltgrowthtested relationconcentration
116347NaClpositivegrowth0-4 %
116347NaClnogrowth6 %
116347NaClnogrowth8 %
116347NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: MK-11

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-sorbose-builds acid from17266
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
116347citrate-carbon source16947
116347esculin-hydrolysis4853
116347hippurate-hydrolysis606565
116347nitrate-reduction17632
116347nitrite-reduction16301
116347nitrate-respiration17632

metabolite production

  • @ref: 116347
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11634715688acetoin-
11634717234glucose-

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase+3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase-3.1.3.1
116347oxidase-
116347beta-galactosidase-3.2.1.23
116347alcohol dehydrogenase-1.1.1.1
116347gelatinase+/-
116347amylase-
116347DNase+
116347caseinase-3.4.21.50
116347catalase+1.11.1.6
116347tween esterase-
116347gamma-glutamyltransferase-2.3.2.2
116347lysine decarboxylase-4.1.1.18
116347ornithine decarboxylase-4.1.1.17
116347phenylalanine ammonia-lyase-4.3.1.24
116347tryptophan deaminase-
116347urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
116347--++-++---+++--+----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
116347+/----+/-+/----+/-+/-+/-+/--+/---+/-------+/-------------------+/------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6429seawaterEast Sea, Amursky BayRussiaRUSEurope
67770SeawaterAmursky Bay of the Gulf of Peter the GreatRussiaRUS
116347Environment, Sea waterAmursky baySea of Japan

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Marine

taxonmaps

  • @ref: 69479
  • File name: preview.99_5731.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_895;97_3383;98_4266;99_5731&stattab=map
  • Last taxonomy: Salinibacterium amurskyense subclade
  • 16S sequence: AF539697
  • Sequence Identity:
  • Total samples: 837
  • soil counts: 348
  • aquatic counts: 328
  • animal counts: 65
  • plant counts: 96

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
64291Risk group (German classification)
1163471Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6429
  • description: Marine bacterium KMM3673 16S ribosomal RNA gene, partial sequence
  • accession: AF539697
  • length: 1431
  • database: ena
  • NCBI tax ID: 205941

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Salinibacterium amurskyense KCTC 9931GCA_014652955contigncbi205941
66792Salinibacterium amurskyense strain DSM 16400205941.3wgspatric205941
66792Salinibacterium amurskyense strain JCM 12362205941.4wgspatric205941
66792Salinibacterium amurskyense strain KCTC 9931205941.11wgspatric205941
66792Salinibacterium amurskyense DSM 164002728369736draftimg205941
66792Salinibacterium amurskyense JCM 123622839424328draftimg205941
67770Salinibacterium amurskyense DSM 16400GCA_002797685contigncbi205941
67770Salinibacterium amurskyense JCM 12362GCA_003668745contigncbi205941

GC content

@refGC-contentmethod
642961
6777061thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno90.889no
gram-positiveyes92.564no
anaerobicno99.402no
aerobicyes94.545no
halophileno86.803no
spore-formingno94.751no
glucose-utilyes84.63no
flagellatedno97.601no
thermophileno99.496yes
glucose-fermentno87.237no

External links

@ref: 6429

culture collection no.: DSM 16400, KCTC 9931, KMM 3673, JCM 12362, CIP 108377, IAM 15155, NBRC 100448

straininfo link

  • @ref: 76934
  • straininfo: 99608

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny14657146Salinibacterium amurskyense gen. nov., sp. nov., a novel genus of the family Microbacteriaceae from the marine environment.Han SK, Nedashkovskaya OI, Mikhailov VV, Kim SB, Bae KSInt J Syst Evol Microbiol10.1099/ijs.0.02627-02003Korea, Micrococcaceae/*classification/genetics/isolation & purification, Molecular Sequence Data, *Phylogeny, Seawater/microbiology, Species SpecificityGenetics
Phylogeny19060050Salinibacterium xinjiangense sp. nov., a psychrophilic bacterium isolated from the China No. 1 glacier.Zhang DC, Liu HC, Xin YH, Yu Y, Zhou PJ, Zhou YGInt J Syst Evol Microbiol10.1099/ijs.0.65802-02008Actinomycetales/*classification/genetics/isolation & purification/*physiology, China, Ice Cover/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Species SpecificityGenetics
Phylogeny22923118Homoserinimonas aerilata gen. nov., sp. nov., a novel member of the family Microbacteriaceae isolated from an air sample in Korea.Kim SJ, Jang YH, Hamada M, Tamura T, Ahn JH, Weon HY, Suzuki K, Kwon SWJ Microbiol10.1007/s12275-012-2096-32012Actinomycetales/*classification/genetics/*isolation & purification/physiology, Aerobiosis, *Air Microbiology, Amino Acids/analysis, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Locomotion, Molecular Sequence Data, Peptidoglycan/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Temperature, Vitamin K 2/analysisGenetics

Reference

@idauthorscataloguedoi/urltitle
6429Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16400)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16400
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
33234Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5992
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
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
76934Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID99608.1StrainInfo: A central database for resolving microbial strain identifiers
116347Curators of the CIPCollection of Institut Pasteur (CIP 108377)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108377