Strain identifier

BacDive ID: 5483

Type strain: Yes

Species: Arenibacter troitsensis

Strain Designation: R3674

Strain history: CIP <- 2003, JCM <- 2002, M. Suzuki: strain R3674 <- KMM <- O.I. Nedashkovskaya

NCBI tax ID(s): 188872 (species)

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General

@ref: 8342

BacDive-ID: 5483

DSM-Number: 19835

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

description: Arenibacter troitsensis R3674 is a mesophilic, Gram-negative bacterium that was isolated from bottom sediment sample.

NCBI tax id

  • NCBI tax id: 188872
  • Matching level: species

strain history

@refhistory
8342<- O. I. Nedashkovskaya, Pacific Inst. Bioorg. Chem., RAS, Vladivostok; KMM 3674
67770M. Suzuki R3674 <-- O. I. Nedashkovskaya.
123587CIP <- 2003, JCM <- 2002, M. Suzuki: strain R3674 <- KMM <- O.I. Nedashkovskaya

doi: 10.13145/bacdive5483.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Flavobacteriaceae
  • genus: Arenibacter
  • species: Arenibacter troitsensis
  • full scientific name: Arenibacter troitsensis Nedashkovskaya et al. 2003

@ref: 8342

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Arenibacter

species: Arenibacter troitsensis

full scientific name: Arenibacter troitsensis Nedashkovskaya et al. 2003

strain designation: R3674

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative99.989
123587negativerod-shapedno

colony morphology

  • @ref: 123587

pigmentation

  • @ref: 123587
  • production: no
  • name: Flexirubin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8342BACTO 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
33895Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
123587CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
8342positivegrowth28mesophilic
33895positivegrowth25mesophilic
67770positivegrowth25mesophilic
123587positivegrowth5-37
123587nogrowth41thermophilic
123587nogrowth45thermophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.997

halophily

@refsaltgrowthtested relationconcentration
123587NaClnogrowth0 %
123587NaClnogrowth2 %
123587NaClnogrowth4 %
123587NaClnogrowth6 %
123587NaClnogrowth8 %
123587NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: MK-6

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1235874853esculin+hydrolysis
123587606565hippurate-hydrolysis
12358717632nitrate-reduction
12358716301nitrite-reduction
12358715792malonate-assimilation
12358717632nitrate-respiration

metabolite production

  • @ref: 123587
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12358715688acetoin-
12358717234glucose-

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
123587oxidase-
123587beta-galactosidase+3.2.1.23
123587alcohol dehydrogenase-1.1.1.1
123587gelatinase+/-
123587amylase+
123587caseinase+3.4.21.50
123587catalase+1.11.1.6
123587tween esterase+
123587gamma-glutamyltransferase+2.3.2.2
123587lecithinase-
123587lipase-
123587lysine decarboxylase-4.1.1.18
123587ornithine decarboxylase-4.1.1.17
123587phenylalanine ammonia-lyase-4.3.1.24
123587tryptophan deaminase-
123587urease-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
123587-+++-++---+++---++--

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123587+++++-+++-++-+----+---+------------+-----------------------+-----------------------------++--------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
8342bottom sediment sampleSea of Japan, Gulf of Peter the Great, Troitsa BayRussiaRUSAsia
67770Bottom sediment from Troitsa Bay in the Gulf of Peter the GreatSea of Japan
123587Environment, Marine bottom sedimentJapanJPNAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_2346.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_102;96_1267;97_1502;98_1829;99_2346&stattab=map
  • Last taxonomy: Arenibacter
  • 16S sequence: AB681469
  • Sequence Identity:
  • Total samples: 9391
  • soil counts: 1235
  • aquatic counts: 7063
  • animal counts: 925
  • plant counts: 168

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
83421Risk group (German classification)
1235871Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Arenibacter troitsensis gene for 16S rRNA, partial sequence, strain: NBRC 101532AB6814691449ena188872
8342Arenibacter troitsensis gene for 16S rRNA, partial sequenceAB0807711381ena188872

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Arenibacter troitsensis DSM 19835GCA_900177645scaffoldncbi188872
66792Arenibacter troitsensis strain DSM 19835188872.3wgspatric188872
66792Arenibacter troitsensis DSM 198352595699007draftimg188872

GC content

@refGC-contentmethod
834240.0
6777040thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno88.928no
flagellatedno94.693no
gram-positiveno97.782no
anaerobicno99.673no
aerobicyes92.987no
halophileno84.599no
spore-formingno96.76no
thermophileno99.45yes
glucose-utilyes89.035no
glucose-fermentno89.467no

External links

@ref: 8342

culture collection no.: DSM 19835, JCM 11736, KMM 3674, NBRC 101532, CIP 108149

straininfo link

  • @ref: 74970
  • straininfo: 99609

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny13130008Arenibacter troitsensis sp. nov., isolated from marine bottom sediment.Nedashkovskaya OI, Suzuki M, Vysotskii MV, Mikhailov VVInt J Syst Evol Microbiol10.1099/ijs.0.02384-02003Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Flavobacteriaceae/classification/genetics/*isolation & purification/metabolism, Geologic Sediments/microbiology, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/geneticsGenetics
Phylogeny22544794Arenibacter hampyeongensis sp. nov., a marine bacterium isolated from a tidal flat.Jeong SH, Jin HM, Kim JM, Jeon COInt J Syst Evol Microbiol10.1099/ijs.0.040683-02012Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Flavobacteriaceae/*classification/genetics/isolation & purification, Geologic Sediments/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phosphatidylethanolamines/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/analysisGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8342Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19835)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19835
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
33895Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5739
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/
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
74970Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID99609.1StrainInfo: A central database for resolving microbial strain identifiers
123587Curators of the CIPCollection of Institut Pasteur (CIP 108149)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108149