Strain identifier

BacDive ID: 11271

Type strain: Yes

Species: Marinomonas ushuaiensis

Strain Designation: U1

Strain history: CIP <- 2005, JCM <- 2003, S. Shivaji, CCMB, Hyderabad, India: strain U1

NCBI tax ID(s): 1122207 (strain), 263818 (species)

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General

@ref: 6131

BacDive-ID: 11271

DSM-Number: 15871

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, motile

description: Marinomonas ushuaiensis U1 is a mesophilic, motile bacterium that was isolated from coastal sea water.

NCBI tax id

NCBI tax idMatching level
1122207strain
263818species

strain history

@refhistory
6131<- S. Shivaji, CCMB; U1
67770S. Shivaji U1.
123762CIP <- 2005, JCM <- 2003, S. Shivaji, CCMB, Hyderabad, India: strain U1

doi: 10.13145/bacdive11271.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Oceanospirillales
  • family: Oceanospirillaceae
  • genus: Marinomonas
  • species: Marinomonas ushuaiensis
  • full scientific name: Marinomonas ushuaiensis Prabagaran et al. 2005

@ref: 6131

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Oceanospirillales

family: Oceanospirillaceae

genus: Marinomonas

species: Marinomonas ushuaiensis

full scientific name: Marinomonas ushuaiensis Prabagaran et al. 2005

strain designation: U1

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes94.718
6948099.993negative
123762yesnegativerod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6131BACTO 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
34009Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
123762CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
6131positivegrowth25mesophilic
34009positivegrowth22psychrophilic
67770positivegrowth22psychrophilic
123762positivegrowth5-30
123762nogrowth37mesophilic
123762nogrowth41thermophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no100

halophily

@refsaltgrowthtested relationconcentration
123762NaClpositivegrowth4-10 %
123762NaClnogrowth0 %
123762NaClnogrowth2 %

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 2-ketogluconate-builds acid from
68371L-arabitol-builds acid from18403
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
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
68371esculin-builds acid from4853
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
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-sorbose-builds acid from17266
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371L-arabinose-builds acid from30849
68371erythritol-builds acid from17113
123762citrate-carbon source16947
123762esculin-hydrolysis4853
123762glucose-fermentation17234
123762lactose-fermentation17716
123762nitrate-reduction17632
123762nitrite-reduction16301
123762sodium thiosulfate-builds gas from132112
123762glucose-degradation17234

metabolite production

  • @ref: 123762
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12376215688acetoin-
12376217234glucose-

enzymes

@refvalueactivityec
123762oxidase-
123762beta-galactosidase-3.2.1.23
123762alcohol dehydrogenase-1.1.1.1
123762gelatinase-
123762amylase-
123762DNase-
123762caseinase-3.4.21.50
123762catalase+1.11.1.6
123762tween esterase-
123762gamma-glutamyltransferase+2.3.2.2
123762lecithinase-
123762lipase-
123762lysine decarboxylase-4.1.1.18
123762ornithine decarboxylase-4.1.1.17
123762phenylalanine ammonia-lyase-4.3.1.24
123762tryptophan deaminase-
123762urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
123762-+++-+----++--------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
123762+/--+/--+/------+/-+/-+/--+/---+/-+/----------------------+/---+/-+/--+/--+/-

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123762-----------------------------------------------------+--------------------------------------------+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6131coastal sea waterUshuaia (sub-Antarctica)ArgentinaARGMiddle and South America
67770Coastal seawater (sub-Antarctica)UshuaiaArgentinaARGMiddle and South America
123762Environment, Coastal sea waterUshuaia (sub-Antarctica)ArgentinaARGMiddle and South America

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Terrestrial#Coast

taxonmaps

  • @ref: 69479
  • File name: preview.99_139710.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_113;96_407;97_26397;98_42875;99_139710&stattab=map
  • Last taxonomy: Marinomonas ushuaiensis subclade
  • 16S sequence: AJ627909
  • Sequence Identity:
  • Total samples: 357
  • aquatic counts: 351
  • animal counts: 6

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
61311Risk group (German classification)
1237621Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6131
  • description: Marinomonas ushuaiensis partial 16S rRNA gene, strain U1
  • accession: AJ627909
  • length: 1496
  • database: ena
  • NCBI tax ID: 263818

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Marinomonas ushuaiensis DSM 158711122207.3wgspatric1122207
66792Marinomonas ushuaiensis DSM 158712563366749draftimg1122207
67770Marinomonas ushuaiensis DSM 15871GCA_000521805contigncbi1122207

GC content

@refGC-contentmethod
613143.6
6777043.6thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes91.488no
flagellatedyes88.104no
gram-positiveno98.634no
anaerobicno97.852no
aerobicyes92.174no
halophileyes91.033no
spore-formingno96.487no
thermophileno99.289yes
glucose-utilyes87.695no
glucose-fermentno81.974no

External links

@ref: 6131

culture collection no.: DSM 15871, JCM 12170, MTCC 6143, CGMCC 1.8483, CGMCC 1.8710, CIP 108668

straininfo link

  • @ref: 80504
  • straininfo: 135118

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15653892Marinomonas ushuaiensis sp. nov., isolated from coastal sea water in Ushuaia, Argentina, sub-Antarctica.Prabagaran SR, Suresh K, Manorama R, Delille D, Shivaji SInt J Syst Evol Microbiol10.1099/ijs.0.63363-02005Antarctic Regions, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Oceanospirillaceae/chemistry/*classification/genetics/*isolation & purification, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNAGenetics
Phylogeny24952743Marinomonas profundimaris sp. nov., isolated from deep-sea sediment sample of the Arctic Ocean.Bai X, Lai Q, Dong C, Li F, Shao ZAntonie Van Leeuwenhoek10.1007/s10482-014-0213-52014Arctic Regions, Bacterial Typing Techniques, Base Composition, Catalase/analysis, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genome, Bacterial, Geologic Sediments/*microbiology, Locomotion, Marinomonas/*classification/genetics/*isolation & purification/physiology, Molecular Sequence Data, Nucleic Acid Hybridization, Oxidoreductases/analysis, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, TemperatureGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6131Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15871)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15871
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
34009Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6322
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 updatesNucleic Acids Res. 49: D498-D508 202033211880
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
80504Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID135118.1StrainInfo: A central database for resolving microbial strain identifiers
123762Curators of the CIPCollection of Institut Pasteur (CIP 108668)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108668