Strain identifier
BacDive ID: 13940
Type strain:
Species: Novispirillum itersonii subsp. nipponicum
Strain history: CIP <- 2002, NBRC <- Y. Terasaki: strain KF8, "Spirillum itersonii subsp. nipponicum"
NCBI tax ID(s): 180198 (subspecies)
General
@ref: 4425
BacDive-ID: 13940
DSM-Number: 11590
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, motile
description: Novispirillum itersonii subsp. nipponicum DSM 11590 is an aerobe, mesophilic, motile bacterium that was isolated from putrid freshwater from shellfish.
NCBI tax id
- NCBI tax id: 180198
- Matching level: subspecies
strain history
@ref | history |
---|---|
4425 | <- ATCC <- IFO <- Y. Terasaki, KF 8 |
67770 | IAM 14945 <-- IFO 13615 <-- Y. Terasaki KF8. |
120292 | CIP <- 2002, NBRC <- Y. Terasaki: strain KF8, "Spirillum itersonii subsp. nipponicum" |
doi: 10.13145/bacdive13940.20230509.8.1
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
@ref synonym 20215 Aquaspirillum itersonii subsp. nipponicum 20215 Spirillum itersonii subsp. nipponicum 20215 Levispirillum 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
@ref | motility | confidence | gram stain | cell shape |
---|---|---|---|---|
69480 | yes | 94.172 | ||
69480 | 99.996 | negative | ||
120292 | yes | negative | rod-shaped |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
4425 | PEPTONE-YEAST MEDIUM with MgSO4 (DSMZ Medium 790) | yes | https://mediadive.dsmz.de/medium/790 | Name: 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 |
4425 | ANCYLOBACTER - SPIROSOMA MEDIUM (DSMZ Medium 7) | yes | https://mediadive.dsmz.de/medium/7 | Name: 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 |
39938 | MEDIUM 563 - for Novosphingobium roseae | yes | Distilled 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) | |
120292 | CIP Medium 563 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=563 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
4425 | positive | growth | 30 | mesophilic |
39938 | positive | growth | 30 | mesophilic |
58560 | positive | growth | 30-37 | mesophilic |
67770 | positive | growth | 30 | mesophilic |
120292 | positive | growth | 22-41 | |
120292 | no | growth | 5 | psychrophilic |
120292 | no | growth | 15 | psychrophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 58560
- oxygen tolerance: aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.993 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
120292 | NaCl | positive | growth | 0 % |
120292 | NaCl | no | growth | 2 % |
120292 | NaCl | no | growth | 4 % |
120292 | NaCl | no | growth | 6 % |
120292 | NaCl | no | growth | 8 % |
120292 | NaCl | no | growth | 10 % |
metabolite utilization
@ref | metabolite | utilization activity | kind of utilization tested | Chebi-ID |
---|---|---|---|---|
68371 | Potassium 5-ketogluconate | - | builds acid from | |
68371 | Potassium 2-ketogluconate | - | builds acid from | |
68371 | gluconate | - | builds acid from | 24265 |
68371 | L-arabitol | - | builds acid from | 18403 |
68371 | D-arabitol | - | builds acid from | 18333 |
68371 | L-fucose | - | builds acid from | 18287 |
68371 | D-fucose | - | builds acid from | 28847 |
68371 | D-tagatose | - | builds acid from | 16443 |
68371 | D-lyxose | - | builds acid from | 62318 |
68371 | turanose | - | builds acid from | 32528 |
68371 | gentiobiose | - | builds acid from | 28066 |
68371 | xylitol | - | builds acid from | 17151 |
68371 | glycogen | - | builds acid from | 28087 |
68371 | starch | - | builds acid from | 28017 |
68371 | raffinose | - | builds acid from | 16634 |
68371 | melezitose | - | builds acid from | 6731 |
68371 | inulin | - | builds acid from | 15443 |
68371 | trehalose | - | builds acid from | 27082 |
68371 | sucrose | - | builds acid from | 17992 |
68371 | melibiose | - | builds acid from | 28053 |
68371 | lactose | - | builds acid from | 17716 |
68371 | maltose | - | builds acid from | 17306 |
68371 | cellobiose | - | builds acid from | 17057 |
68371 | salicin | - | builds acid from | 17814 |
68371 | esculin | + | builds acid from | 4853 |
68371 | arbutin | - | builds acid from | 18305 |
68371 | amygdalin | - | builds acid from | 27613 |
68371 | N-acetylglucosamine | - | builds acid from | 59640 |
68371 | methyl alpha-D-glucopyranoside | - | builds acid from | 320061 |
68371 | methyl alpha-D-mannoside | - | builds acid from | 43943 |
68371 | D-sorbitol | - | builds acid from | 17924 |
68371 | D-mannitol | - | builds acid from | 16899 |
68371 | myo-inositol | - | builds acid from | 17268 |
68371 | galactitol | - | builds acid from | 16813 |
68371 | L-rhamnose | - | builds acid from | 62345 |
68371 | L-sorbose | - | builds acid from | 17266 |
68371 | D-mannose | - | builds acid from | 16024 |
68371 | D-fructose | + | builds acid from | 15824 |
68371 | D-glucose | - | builds acid from | 17634 |
68371 | D-galactose | - | builds acid from | 12936 |
68371 | methyl beta-D-xylopyranoside | - | builds acid from | 74863 |
68371 | ribitol | - | builds acid from | 15963 |
68371 | L-xylose | - | builds acid from | 65328 |
68371 | D-xylose | - | builds acid from | 65327 |
68371 | L-arabinose | - | builds acid from | 30849 |
68371 | D-arabinose | - | builds acid from | 17108 |
68371 | erythritol | - | builds acid from | 17113 |
68371 | glycerol | - | builds acid from | 17754 |
120292 | citrate | - | carbon source | 16947 |
120292 | esculin | - | hydrolysis | 4853 |
120292 | nitrate | + | reduction | 17632 |
120292 | nitrite | - | reduction | 16301 |
120292 | nitrate | + | respiration | 17632 |
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
@ref | Chebi-ID | metabolite | voges-proskauer-test | methylred-test |
---|---|---|---|---|
120292 | 15688 | acetoin | - | |
120292 | 17234 | glucose | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
120292 | oxidase | + | |
120292 | beta-galactosidase | - | 3.2.1.23 |
120292 | alcohol dehydrogenase | - | 1.1.1.1 |
120292 | gelatinase | - | |
120292 | amylase | - | |
120292 | DNase | - | |
120292 | caseinase | - | 3.4.21.50 |
120292 | catalase | + | 1.11.1.6 |
120292 | gamma-glutamyltransferase | + | 2.3.2.2 |
120292 | lecithinase | - | |
120292 | lipase | - | |
120292 | lysine decarboxylase | - | 4.1.1.18 |
120292 | ornithine decarboxylase | - | 4.1.1.17 |
120292 | phenylalanine ammonia-lyase | + | 4.3.1.24 |
120292 | protease | - | |
120292 | tryptophan deaminase | - | |
120292 | urease | - | 3.5.1.5 |
68382 | alkaline phosphatase | + | 3.1.3.1 |
68382 | esterase (C 4) | + | |
68382 | esterase lipase (C 8) | + | |
68382 | lipase (C 14) | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | valine arylamidase | - | |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | trypsin | - | 3.4.21.4 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | alpha-glucosidase | - | 3.2.1.20 |
68382 | beta-glucosidase | + | 3.2.1.21 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
120292 | - | + | + | + | - | + | - | - | - | - | + | + | - | - | - | - | + | - | - | - |
API 50CHac
@ref | GLY | ERY | DARA | LARA | RIB | DXYL | LXYL | ADO | MDX | GAL | GLU | FRU | MNE | SBE | RHA | DUL | INO | MAN | SOR | MDM | MDG | NAG | AMY | ARB | ESC | SAL | CEL | MAL | LAC | MEL | SAC | TRE | INU | MLZ | RAF | AMD | GLYG | XLT | GEN | TUR | LYX | TAG | DFUC | LFUC | DARL | LARL | GNT | 2KG | 5KG |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
120292 | - | - | - | - | +/- | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
API biotype100
@ref | GLU | FRU | GAL | TRE | MNE | SBE | MEL | SAC | RAF | MTE | MAL | LAC | LTE | MbGa | MaGa | CEL | GEN | MbGu | ESC | RIB | ARA | XYL | PLE | RHA | FUC | MLZ | DARL | LARL | XLT | DUL | TAG | GLY | INO | MAN | MTL | TUR | SOR | ADO | HBG | LYX | ERY | MDG | 3MDG | SAT | MUC | LTAT | DTAT | MTAT | DMLT | LMLT | CATE | TATE | TTE | CIT | GRT | GAT | 2KG | 5KG | TRY | NAG | GNT | PAC | PAT | pOBE | QAT | GTE | mOBE | BAT | PPAT | CMT | TGE | BET | PCE | ABT | HIN | LAT | CAP | CYT | HIS | SUC | FUM | GRE | GYT | AVT | ETN | TTN | GLN | ITA | 3OBU | APT | GTT | PRO | DALA | LALA | SER | MNT | PROP | TYR | 2KT |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
120292 | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | + | - | + | - | - | + | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | + | - | + | - | - | - | + | + | - | - | + | - | - | - | - | + | + | + | + | - | + | - | - | - | + | - |
Isolation, sampling and environmental information
isolation
@ref | sample type |
---|---|
4425 | putrid freshwater from shellfish |
58560 | Putrid freshwater shellfish |
67770 | Putrid freshwater shellfish |
120292 | Putrid freshwater from shellfish |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | biosafety level | biosafety level comment |
---|---|---|
4425 | 1 | Risk group (German classification) |
120292 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Aquaspirillum itersonii subsp. nipponicum gene for 16S rRNA, partial sequence | AB074520 | 1380 | ena | 180198 |
20218 | Aquaspirillum itersonii gene for 16S rRNA, partial sequence, strain:IFO 13615 | AB000478 | 1328 | ena | 189 |
20218 | Aquaspirillum itersonii subsp. nipponicum strain LMG 7370 16S ribosomal RNA gene, partial sequence | EF612766 | 1442 | ena | 180198 |
20218 | Novispirillum itersonii subsp. nipponicum gene for 16S rRNA, partial sequence, strain: NBRC 13615 | AB680462 | 1412 | ena | 180198 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Novispirillum itersonii DSM 11590 | GCA_014205675 | scaffold | ncbi | 189 |
66792 | Novispirillum itersonii strain DSM 11590 | 189.8 | wgs | patric | 189 |
66792 | Novispirillum itersonii DSM 11590 | 2828310345 | draft | img | 189 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
flagellated | yes | 89.281 | no |
gram-positive | no | 99.012 | no |
anaerobic | no | 95.718 | yes |
aerobic | yes | 83.668 | yes |
halophile | no | 88.392 | no |
spore-forming | no | 95.035 | no |
glucose-util | yes | 78.582 | no |
thermophile | no | 98.355 | yes |
motile | yes | 95.974 | no |
glucose-ferment | no | 88.316 | no |
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
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
4425 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11590) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-11590 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
39938 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/5230 | ||||
58560 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 49448) | https://www.ccug.se/strain?id=49448 | |||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
68371 | Automatically annotated from API 50CH acid | |||||
68382 | Automatically annotated from API zym | |||||
69479 | João 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 | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
83113 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID899.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
120292 | Curators of the CIP | Collection of Institut Pasteur (CIP 107759) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107759 |