Strain identifier

BacDive ID: 14165

Type strain: Yes

Species: Novosphingobium indicum

Strain Designation: H25

Strain history: <- LMG <- Q. Lai, Key Lab. Marine Biogenetic Resources, Third Institute of Oceanography, Xiamen; H25

NCBI tax ID(s): 462949 (species)

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General

@ref: 17300

BacDive-ID: 14165

DSM-Number: 23608

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

description: Novosphingobium indicum H25 is a mesophilic, Gram-negative, rod-shaped bacterium that was isolated from Deep-sea water.

NCBI tax id

  • NCBI tax id: 462949
  • Matching level: species

strain history

  • @ref: 17300
  • history: <- LMG <- Q. Lai, Key Lab. Marine Biogenetic Resources, Third Institute of Oceanography, Xiamen; H25

doi: 10.13145/bacdive14165.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Sphingomonadales
  • family: Erythrobacteraceae
  • genus: Novosphingobium
  • species: Novosphingobium indicum
  • full scientific name: Novosphingobium indicum Yuan et al. 2009

@ref: 17300

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Erythrobacteraceae

genus: Novosphingobium

species: Novosphingobium indicum

full scientific name: Novosphingobium indicum Yuan et al. 2009

strain designation: H25

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
28970negative1.25 µm0.65 µmrod-shapedno
69480negative99.982

pigmentation

  • @ref: 28970
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 17300
  • name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/514
  • composition: Name: 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

culture temp

@refgrowthtypetemperaturerange
17300positivegrowth28mesophilic
28970positivegrowth10-41
28970positiveoptimum27.5mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.901

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2897021217L-alaninamide+carbon source
2897016449alanine+carbon source
2897040585alpha-cyclodextrin+carbon source
28970286442-oxopentanoate+carbon source
2897023652dextrin+carbon source
2897017234glucose+carbon source
2897029987glutamate+carbon source
2897028087glycogen+carbon source
2897025017leucine+carbon source
2897017306maltose+carbon source
2897037684mannose+carbon source
2897051850methyl pyruvate+carbon source
2897026271proline+carbon source
2897030031succinate+carbon source
2897053423tween 40+carbon source
2897053426tween 80+carbon source
2897017632nitrate+reduction
6836925115malate-assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose+assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose-assimilation
683695291gelatin-hydrolysis
683694853esculin-hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
28970acid phosphatase+3.1.3.2
28970alkaline phosphatase+3.1.3.1
28970catalase+1.11.1.6
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
17300-------------+------+

Isolation, sampling and environmental information

isolation

  • @ref: 17300
  • sample type: Deep-sea water
  • geographic location: Indian Ocean
  • country: China
  • origin.country: CHN
  • continent: Asia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_28315.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_795;97_4189;98_5352;99_28315&stattab=map
  • Last taxonomy: Novosphingobium
  • 16S sequence: EF549586
  • Sequence Identity:
  • Total samples: 1525
  • soil counts: 233
  • aquatic counts: 1021
  • animal counts: 222
  • plant counts: 49

Safety information

risk assessment

  • @ref: 17300
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 17300
  • description: Novosphingobium indicum strain H25 16S ribosomal RNA gene, partial sequence
  • accession: EF549586
  • length: 1456
  • database: ena
  • NCBI tax ID: 462949

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Novosphingobium indicum CGMCC 1.6784GCA_014645195scaffoldncbi462949
66792Novosphingobium indicum strain CGMCC 1.6784462949.3wgspatric462949

GC content

  • @ref: 28970
  • GC-content: 62

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno84.678no
gram-positiveno97.133yes
anaerobicno98.592no
aerobicyes88.037no
halophileno92.362no
spore-formingno93.776no
thermophileno97.484yes
glucose-utilyes88.741no
motileyes59.148no
glucose-fermentno93.925yes

External links

@ref: 17300

culture collection no.: DSM 23608, CGMCC 1.6784, LMG 24713, MCCC 1A01080

straininfo link

  • @ref: 83328
  • straininfo: 351957

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19605709Novosphingobium indicum sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium isolated from a deep-sea environment.Yuan J, Lai Q, Zheng T, Shao ZInt J Syst Evol Microbiol10.1099/ijs.0.002873-02009Bacterial Typing Techniques, Cluster Analysis, DNA Fingerprinting/methods, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Indian Ocean, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Polyamines/analysis, Polycyclic Aromatic Hydrocarbons/*metabolism, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Sphingomonadaceae/*classification/genetics/isolation & purification/*metabolismGenetics
Phylogeny24408529Novosphingobium malaysiense sp. nov. isolated from mangrove sediment.Lee LH, Azman AS, Zainal N, Eng SK, Fang CM, Hong K, Chan KGInt J Syst Evol Microbiol10.1099/ijs.0.059014-02014Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Malaysia, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spermidine/chemistry, Sphingomonadaceae/*classification/genetics/isolation & purification, Ubiquinone/chemistry, *Water MicrobiologyGenetics
Phylogeny25424486Novosphingobium marinum sp. nov., isolated from seawater.Huo YY, You H, Li ZY, Wang CS, Xu XWInt J Syst Evol Microbiol10.1099/ijs.0.070433-02014Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Pacific Ocean, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Sphingomonadaceae/*classification/genetics/isolation & purification, Ubiquinone/chemistryGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
17300Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23608)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23608
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
28970Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2540628776041
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)
68369Automatically annotated from API 20NE
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
83328Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID351957.1StrainInfo: A central database for resolving microbial strain identifiers