Strain identifier

BacDive ID: 13940

Type strain: Yes

Species: Novispirillum itersonii subsp. nipponicum

Strain history: CIP <- 2002, NBRC <- Y. Terasaki: strain KF8, "Spirillum itersonii subsp. nipponicum"

NCBI tax ID(s): 180198 (subspecies)

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General

@ref: 4425

BacDive-ID: 13940

DSM-Number: 11590

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

description: Novispirillum itersonii subsp. nipponicum DSM 11590 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from putrid freshwater from shellfish.

NCBI tax id

  • NCBI tax id: 180198
  • Matching level: subspecies

strain history

@refhistory
4425<- ATCC <- IFO <- Y. Terasaki, KF 8
67770IAM 14945 <-- IFO 13615 <-- Y. Terasaki KF8.
120292CIP <- 2002, NBRC <- Y. Terasaki: strain KF8, "Spirillum itersonii subsp. nipponicum"

doi: 10.13145/bacdive13940.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodospirillales
  • family: Rhodospirillaceae
  • genus: Novispirillum
  • species: Novispirillum itersonii subsp. nipponicum
  • full scientific name: Novispirillum itersonii subsp. nipponicum (Terasaki 1973) Yoon et al. 2007

  • synonyms

    @refsynonym
    20215Levispirillum itersonii subsp. nipponicum
    20215Aquaspirillum itersonii subsp. nipponicum
    20215Spirillum itersonii subsp. nipponicum

@ref: 4425

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodospirillales

family: Rhodospirillaceae

genus: Novispirillum

species: Novispirillum itersonii subsp. nipponicum

full scientific name: Novispirillum itersonii subsp. nipponicum (Terasaki 1973) Yoon et al. 2007

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
120292negativerod-shapedyes
125439negative94.5
125438negative99

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4425PEPTONE-YEAST MEDIUM with MgSO4 (DSMZ Medium 790)yeshttps://mediadive.dsmz.de/medium/790Name: PEPTONE-YEAST MEDIUM with MgSO4 (DSMZ Medium 790) Composition: Peptone 10.0 g/l MgSO4 x 7 H2O 2.0 g/l (NH4)2SO4 2.0 g/l Yeast extract 1.0 g/l Distilled water
4425ANCYLOBACTER - SPIROSOMA MEDIUM (DSMZ Medium 7)yeshttps://mediadive.dsmz.de/medium/7Name: ANCYLOBACTER - SPIROSOMA MEDIUM (DSMZ Medium 7) Composition: Agar 15.0 g/l Yeast extract 1.0 g/l Peptone 1.0 g/l Glucose 1.0 g/l Distilled water
39938MEDIUM 563 - for Novosphingobium roseaeyesDistilled water make up to (1000.000 ml);Magnesium sulphate heptahydrate (1.000 g);Agar (15.000 g);Yeast extract (2.000 g);Polypeptone (10.000 g)
120292CIP Medium 563yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=563

culture temp

@refgrowthtypetemperature
4425positivegrowth30
39938positivegrowth30
58560positivegrowth30-37
67770positivegrowth30
120292positivegrowth22-41
120292nogrowth5
120292nogrowth15

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
58560aerobe
125439obligate aerobe91.4

spore formation

  • @ref: 125439
  • spore formation: no
  • confidence: 91.9

halophily

@refsaltgrowthtested relationconcentration
120292NaClpositivegrowth0 %
120292NaClnogrowth2 %
120292NaClnogrowth4 %
120292NaClnogrowth6 %
120292NaClnogrowth8 %
120292NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12029216947citrate-carbon source
1202924853esculin-hydrolysis
12029217632nitrate+reduction
12029216301nitrite-reduction
12029217632nitrate+respiration
68371Potassium 5-ketogluconate-builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837117754glycerol-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837117992sucrose-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117306maltose-builds acid from
6837117057cellobiose-builds acid from
6837117814salicin-builds acid from
683714853esculin+builds acid from
6837159640N-acetylglucosamine-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose-builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose-builds acid from
6837112936D-galactose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from

antibiotic resistance

  • @ref: 120292
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 120292
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12029215688acetoin-
12029217234glucose-

enzymes

@refvalueactivityec
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
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+
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382trypsin-3.4.21.4
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382alkaline phosphatase+3.1.3.1
120292oxidase+
120292beta-galactosidase-3.2.1.23
120292alcohol dehydrogenase-1.1.1.1
120292gelatinase-
120292amylase-
120292DNase-
120292caseinase-3.4.21.50
120292catalase+1.11.1.6
120292gamma-glutamyltransferase+2.3.2.2
120292lecithinase-
120292lipase-
120292lysine decarboxylase-4.1.1.18
120292ornithine decarboxylase-4.1.1.17
120292phenylalanine ammonia-lyase+4.3.1.24
120292protease-
120292tryptophan deaminase-
120292urease-3.5.1.5
68382alpha-fucosidase-3.2.1.51
68382beta-glucosidase+3.2.1.21

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
120292-+++-+----++----+---

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
120292----+/-------+------------+------------------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120292-+----------------+------------------------+-----+-+--++----------------++-+---++--+----++++-+---+-

Isolation, sampling and environmental information

isolation

@refsample type
4425putrid freshwater from shellfish
58560Putrid freshwater shellfish
67770Putrid freshwater shellfish
120292Putrid freshwater from shellfish

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Freshwater
#Host#Other#Decomposing animal
#Host#Invertebrates (Other)

taxonmaps

  • @ref: 69479
  • File name: preview.99_41551.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_292;96_19274;97_23917;98_30236;99_41551&stattab=map
  • Last taxonomy: Novispirillum itersonii subclade
  • 16S sequence: AB680462
  • Sequence Identity:
  • Total samples: 2678
  • soil counts: 172
  • aquatic counts: 1741
  • animal counts: 678
  • plant counts: 87

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
44251Risk group (German classification)
1202921Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Aquaspirillum itersonii subsp. nipponicum gene for 16S rRNA, partial sequenceAB0745201380nuccore180198
20218Aquaspirillum itersonii gene for 16S rRNA, partial sequence, strain:IFO 13615AB0004781328nuccore189
20218Aquaspirillum itersonii subsp. nipponicum strain LMG 7370 16S ribosomal RNA gene, partial sequenceEF6127661442nuccore180198
20218Novispirillum itersonii subsp. nipponicum gene for 16S rRNA, partial sequence, strain: NBRC 13615AB6804621412nuccore180198

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Novispirillum itersonii DSM 11590GCA_014205675scaffoldncbi189
66792Novispirillum itersonii strain DSM 11590189.8wgspatric189
66792Novispirillum itersonii DSM 115902828310345draftimg189

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno99no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no90.038no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes80.314yes
125438spore-formingspore-formingAbility to form endo- or exosporesno86.515no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno97.002yes
125438motile2+flagellatedAbility to perform flagellated movementyes83.475no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno91.9
125439BacteriaNetmotilityAbility to perform movementyes78.6
125439BacteriaNetgram_stainReaction to gram-stainingnegative94.5
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe91.4

External links

@ref: 4425

culture collection no.: DSM 11590, ATCC 33333, IFO 13615, NBRC 13615, CCUG 49448, IAM 14945, LMG 7370, JCM 21427, CIP 107759

straininfo link

  • @ref: 83113
  • straininfo: 899

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4425Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11590)https://www.dsmz.de/collection/catalogue/details/culture/DSM-11590
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
39938Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5230
58560Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 49448)https://www.ccug.se/strain?id=49448
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
83113Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID899.1StrainInfo: A central database for resolving microbial strain identifiers
120292Curators of the CIPCollection of Institut Pasteur (CIP 107759)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107759
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1