Strain identifier

BacDive ID: 14144

Type strain: Yes

Species: Novosphingobium capsulatum

Strain Designation: 28

Strain history: CIP <- 1982, F. Pichinoty, CNRS, Marseille, France <- ATCC <- E. Leifson: strain 28, Flavobacterium capsulatum

NCBI tax ID(s): 1219042 (strain), 13688 (species)

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General

@ref: 9195

BacDive-ID: 14144

DSM-Number: 30196

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

description: Novosphingobium capsulatum 28 is an obligate aerobe, mesophilic, Gram-negative bacterium that was isolated from distilled water.

NCBI tax id

NCBI tax idMatching level
1219042strain
13688species

strain history

@refhistory
9195<- ATCC <- E. Leifson; 28
67770H. Oyaizu KS 0413 <-- IFO 12533 <-- AJ 2514 <-- ATCC 14666 <-- E. Leifson 28.
117175CIP <- 1982, F. Pichinoty, CNRS, Marseille, France <- ATCC <- E. Leifson: strain 28, Flavobacterium capsulatum

doi: 10.13145/bacdive14144.20250331.9.3

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 capsulatum
  • full scientific name: Novosphingobium capsulatum (Leifson 1962) Takeuchi et al. 2001

  • synonyms

    @refsynonym
    20215Sphingomonas capsulata
    20215Flavobacterium capsulatum

@ref: 9195

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Erythrobacteraceae

genus: Novosphingobium

species: Novosphingobium capsulatum

full scientific name: Novosphingobium capsulatum (Leifson 1962) Takeuchi et al. 2001

strain designation: 28

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
117175negativerod-shapedno
125438negative94.753
125439negative99.5

multimedia

  • @ref: 9195
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_30196.jpg
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9195NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
38753MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
117175CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
117175CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperature
9195positivegrowth26
38753positivegrowth30
67770positivegrowth30

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
117175obligate aerobe
125439aerobe95.5

spore formation

  • @ref: 125439
  • spore formation: no
  • confidence: 98

observation

  • @ref: 67770
  • observation: quinones: Q-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11717517632nitrate+reduction
11717516301nitrite-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

@refChebi-IDmetaboliteproduction
6836935581indoleno
11717535581indoleno

metabolite tests

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

enzymes

@refvalueactivityec
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
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase+3.2.1.23
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 (C 4)+
68382esterase lipase (C 8)+
68382alkaline phosphatase+3.1.3.1
117175oxidase+
117175catalase+1.11.1.6
117175urease-3.5.1.5
68382alpha-fucosidase-3.2.1.51
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 zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
117175-+++-+++--++-++++---

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
9195+----+-++++-+++--+--+

Isolation, sampling and environmental information

isolation

@refsample type
9195distilled water
67770Distilled water
117175Environment, Distilled water

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic
#Engineered#Industrial#Engineered product
#Engineered#Treatment#Sterilized (Desinfected)

taxonmaps

  • @ref: 69479
  • File name: preview.99_6388.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_437;97_499;98_4720;99_6388&stattab=map
  • Last taxonomy: Novosphingobium capsulatum
  • 16S sequence: D16147
  • Sequence Identity:
  • Total samples: 1163
  • soil counts: 144
  • aquatic counts: 532
  • animal counts: 416
  • plant counts: 71

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
91951Risk group (German classification)
1171751Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Novosphingobium capsulatum gene for 16S rRNA, partial sequenceD161471443nuccore13688
20218Sphingomonas capsulata 16S ribosomal RNA, partial sequenceD38431156nuccore13688
20218Novosphingobium capsulatum gene for 16S ribosomal RNAD845321387nuccore13688
2021816S rRNA [Sphingomonas capsulata, LMG 2830T, Genomic, 268 nt]S56775268nuccore13688
20218Novosphingobium capsulatum gene for 16S rRNA, partial sequence, strain: NBRC 12533AB6802901410nuccore13688

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Novosphingobium capsulatum NBRC 125331219042.3wgspatric1219042
66792Novosphingobium capsulatum NBRC 125332681812976draftimg1219042
67770Novosphingobium capsulatum NBRC 12533GCA_001598375contigncbi1219042

GC content

@refGC-contentmethod
919564.3
6777064.3thermal denaturation, midpoint method (Tm)
6777063.1high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthaerobe95.5
125439BacteriaNetgram_stainReaction to gram-stainingnegative99.5
125439BacteriaNetmotilityAbility to perform movementyes69.6
125439BacteriaNetspore_formationAbility to form endo- or exosporesno98
125438gram-positivegram-positivePositive reaction to Gram-stainingno94.753no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no96.801yes
125438spore-formingspore-formingAbility to form endo- or exosporesno89.86no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes88.924yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno97.732yes
125438motile2+flagellatedAbility to perform flagellated movementyes70.298no

External links

@ref: 9195

culture collection no.: DSM 30196, ATCC 14666, GIFU 11526, IAM 14271, IFO 12533, JCM 7508, NBRC 12533, NCIB 9890, JCM 7452, BCRC 10676, CCM 2832, CCUG 17697, CCUG 31202, CECT 4388, CIP 82.103, LMG 2830, NCIMB 9890, VKM B-1564, VTT E-91059, KCTC 22844

straininfo link

  • @ref: 83309
  • straininfo: 9366

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny7544095Aromatic-degrading Sphingomonas isolates from the deep subsurface.Fredrickson JK, Balkwill DL, Drake GR, Romine MF, Ringelberg DB, White DCAppl Environ Microbiol10.1128/aem.61.5.1917-1922.19951995Bacteria, Aerobic/classification/*isolation & purification/metabolism, Base Sequence, Biodegradation, Environmental, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Hydrocarbons/*metabolism, Molecular Sequence Data, Phylogeny, Polycyclic Compounds/metabolism, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Homology, Nucleic Acid, *Soil Microbiology, Species Specificity, Sphingolipids/metabolism, TennesseeMetabolism
Enzymology9750174Prolyl endopeptidase from Sphingomonas capsulata: isolation and characterization of the enzyme and nucleotide sequence of the gene.Kabashima T, Fujii M, Meng Y, Ito K, Yoshimoto TArch Biochem Biophys10.1006/abbi.1998.08361998Amino Acid Sequence, Base Sequence, Cloning, Molecular, Crystallization, *Genes, Bacterial, Kinetics, Molecular Sequence Data, Proline/metabolism, Prolyl Oligopeptidases, Pseudomonadaceae/*enzymology/isolation & purification, Sequence Analysis, DNA, Serine Endopeptidases/biosynthesis/chemistry/*genetics/*isolation & purificationPhylogeny
Metabolism16915702Production and rheological characterization of biopolymer of Sphingomonas capsulata ATCC 14666 using conventional and industrial media.Berwanger AL, Domingues NM, Vanzo LT, Di Luccio M, Treichel H, Padilha FF, Scamparini ARAppl Biochem Biotechnol2006Biopolymers/analysis/*chemistry/*metabolism, Cell Culture Techniques/*methods, Culture Media/classification/metabolism, Industrial Microbiology/methods, Polysaccharides, Bacterial/analysis/*chemistry/*metabolism, Sphingomonas/*metabolism, ViscosityBiotechnology
Phylogeny25320143Proposal of Novosphingobium rhizosphaerae sp. nov., isolated from the rhizosphere.Kampfer P, Martin K, McInroy JA, Glaeser SPInt J Syst Evol Microbiol10.1099/ijs.0.070375-02014Alabama, Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Sphingomonadaceae/*classification/genetics/isolation & purification, Ubiquinone/chemistry, Zea mays/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
Phylogeny27306976Description of Novosphingobiumflavum sp. nov., isolated from soil.Nguyen TM, Myung SW, Jang H, Kim JInt J Syst Evol Microbiol10.1099/ijsem.0.0012422016Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/chemistry, Sphingomonadaceae/*classification/genetics/isolation & purification, Ubiquinone/chemistryTranscriptome
Phylogeny27639667Novosphingobium pokkalii sp nov, a novel rhizosphere-associated bacterium with plant beneficial properties isolated from saline-tolerant pokkali rice.Krishnan R, Menon RR, Likhitha, Busse HJ, Tanaka N, Krishnamurthi S, Rameshkumar NRes Microbiol10.1016/j.resmic.2016.09.0012016Acetoin/metabolism, Axenic Culture, Bacterial Typing Techniques, Biofilms, Crops, Agricultural/*microbiology, DNA Gyrase/genetics, DNA, Bacterial/genetics, Fatty Acids/metabolism, Indoleacetic Acids/metabolism, Nucleic Acid Hybridization, Oryza/*microbiology, Phospholipids/metabolism, Phylogeny, RNA, Ribosomal, 16S, Rec A Recombinases/genetics, *Rhizosphere, Salt-Tolerant Plants/microbiology, Seawater/microbiology, Sequence Analysis, DNA, Siderophores/biosynthesis, Sphingomonadaceae/*genetics/*isolation & purification/metabolismMetabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9195Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 30196)https://www.dsmz.de/collection/catalogue/details/culture/DSM-30196
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
38753Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/11380
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/
68369Automatically annotated from API 20NE
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
83309Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID9366.1StrainInfo: A central database for resolving microbial strain identifiers
117175Curators of the CIPCollection of Institut Pasteur (CIP 82.103)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2082.103
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