Strain identifier

BacDive ID: 14155

Type strain: Yes

Species: Novosphingobium taihuense

Strain Designation: T3-B9

Strain history: CIP <- 2005, JCM <- 2004, Y. Zhou: strain T3-B9

NCBI tax ID(s): 260085 (species)

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General

@ref: 7029

BacDive-ID: 14155

DSM-Number: 17507

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

description: Novosphingobium taihuense T3-B9 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from lake sediment.

NCBI tax id

  • NCBI tax id: 260085
  • Matching level: species

strain history

@refhistory
7029<- S.-J. Liu <- B.-J. Wang
67770Y. Zhou T3-B9.
123416CIP <- 2005, JCM <- 2004, Y. Zhou: strain T3-B9

doi: 10.13145/bacdive14155.20230509.8.1

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 taihuense
  • full scientific name: Novosphingobium taihuense Liu et al. 2005

@ref: 7029

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Erythrobacteraceae

genus: Novosphingobium

species: Novosphingobium taihuense

full scientific name: Novosphingobium taihuense Liu et al. 2005

strain designation: T3-B9

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
31399negative2.9 µm0.45 µmrod-shapedno
123416negativerod-shapedno

pigmentation

  • @ref: 31399
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7029MINERAL MEDIUM PH 7.25 (DSMZ Medium 465)yeshttps://mediadive.dsmz.de/medium/465Name: MINERAL MEDIUM PH 7.25 (DSMZ Medium 465; with strain-specific modifications) Composition: Na2HPO4 x 2 H2O 3.5 g/l KH2PO4 1.0 g/l (NH4)2SO4 0.5 g/l None 0.1 g/l MgCl2 x 6 H2O 0.1 g/l Ca(NO3)2 x 4 H2O 0.05 g/l Na2-EDTA 0.0005 g/l H3BO3 0.0003 g/l FeSO4 x 7 H2O 0.0002 g/l CoCl2 x 6 H2O 0.0002 g/l ZnSO4 x 7 H2O 0.0001 g/l MnCl2 x 4 H2O 3e-05 g/l Na2MoO4 x 2 H2O 3e-05 g/l NiCl2 x 6 H2O 2e-05 g/l CuCl2 x 2 H2O 1e-05 g/l Distilled water
7029R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
38312MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
123416CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
123416CIP Medium 368yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=368

culture temp

@refgrowthtypetemperaturerange
7029positivegrowth30mesophilic
31399positivegrowth10-37
31399positiveoptimum25mesophilic
38312positivegrowth30mesophilic
60911positivegrowth30mesophilic
67770positivegrowth30mesophilic
123416positivegrowth10-37
123416nogrowth5psychrophilic
123416nogrowth41thermophilic

culture pH

@refabilitytypepHPH range
31399positivegrowth4.5-8.5alkaliphile
31399positiveoptimum6

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31399aerobe
60911aerobe
123416facultative anaerobe

spore formation

  • @ref: 31399
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
31399NaClpositivegrowth0-2 %
31399NaClpositiveoptimum0.5 %
123416NaClpositivegrowth0-10 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3139916449alanine+carbon source
3139922599arabinose+carbon source
3139917057cellobiose+carbon source
3139928757fructose+carbon source
3139917234glucose+carbon source
3139917306maltose+carbon source
3139937684mannose+carbon source
3139926271proline+carbon source
3139926546rhamnose+carbon source
3139917992sucrose+carbon source
3139918222xylose+carbon source
313994853esculin+hydrolysis
3139917632nitrate+reduction
12341616947citrate-carbon source
1234164853esculin+hydrolysis
12341617632nitrate+reduction
12341616301nitrite-reduction
12341617632nitrate+respiration
6837217754glycerol-assimilation
6837217113erythritol-assimilation
6837217108D-arabinose-assimilation
6837230849L-arabinose+assimilation
6837216988D-ribose-assimilation
6837265327D-xylose+assimilation
6837265328L-xylose-assimilation
6837215963ribitol-assimilation
6837274863methyl beta-D-xylopyranoside-assimilation
6837212936D-galactose-assimilation
6837217634D-glucose+assimilation
6837215824D-fructose+assimilation
6837216024D-mannose+assimilation
6837217266L-sorbose-assimilation
6837262345L-rhamnose+assimilation
6837216813galactitol-assimilation
6837217268myo-inositol-assimilation
6837216899D-mannitol-assimilation
6837230911sorbitol-assimilation
6837243943methyl alpha-D-mannoside-assimilation
68372320061methyl alpha-D-glucopyranoside-assimilation
6837259640N-acetylglucosamine-assimilation
6837227613amygdalin-assimilation
6837218305arbutin+assimilation
683724853esculin+assimilation
6837217814salicin+assimilation
6837217057cellobiose+assimilation
6837217306maltose+assimilation
6837217716lactose-assimilation
6837228053melibiose-assimilation
6837217992sucrose+assimilation
6837227082trehalose-assimilation
6837215443inulin-assimilation
683726731melezitose+assimilation
6837216634raffinose+assimilation
6837228017starch+assimilation
6837228087glycogen-assimilation
6837217151xylitol-assimilation
6837228066gentiobiose+assimilation
6837232528turanose-assimilation
6837262318D-lyxose-assimilation
6837216443D-tagatose-assimilation
6837228847D-fucose-assimilation
6837218287L-fucose-assimilation
6837218333D-arabitol-assimilation
6837218403L-arabitol-assimilation
6837224265gluconate-assimilation
68372Potassium 2-ketogluconate-assimilation
68372Potassium 5-ketogluconate-assimilation

metabolite production

  • @ref: 123416
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
31399catalase+1.11.1.6
123416oxidase+
123416beta-galactosidase+3.2.1.23
123416alcohol dehydrogenase-1.1.1.1
123416gelatinase-
123416amylase+
123416DNase+
123416caseinase+3.4.21.50
123416catalase+1.11.1.6
123416tween esterase+
123416lecithinase-
123416lipase-
123416lysine decarboxylase-4.1.1.18
123416ornithine decarboxylase-4.1.1.17
123416protease-
123416tryptophan deaminase-
123416urease-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
123416-+++-++-+-+++++++---

API 50CHas

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
7029----+-+----+++-+--------+++++--+--+++--+----------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123416+-+----++++----++++-++-+--------------+----------+----+-------++---------+++---++-------++++-+---+-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7029lake sedimentTaihu LakeChinaCHNAsia
60911Lake sedimentChinaCHNAsia
67770Sediment of Taihu LakeJiangsu ProvinceChinaCHNAsia
123416Environment, SedimentTaihu lakeChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Lake (large)
#Environmental#Aquatic#Sediment

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
70291Risk group (German classification)
1234161Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7029
  • description: Novosphingobium taihuense strain T3-B9 16S ribosomal RNA gene, partial sequence
  • accession: AY500142
  • length: 1374
  • database: ena
  • NCBI tax ID: 260085

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Novosphingobium taihuense DSM 17507GCA_014199635scaffoldncbi260085
66792Novosphingobium taihuense CGMCC 1.3432GCA_007830315contigncbi260085
66792Novosphingobium taihuense strain CGMCC 1.3432260085.3wgspatric260085
66792Novosphingobium taihuense strain DSM 17507260085.4wgspatric260085
66792Novosphingobium taihuense DSM 175072828632817draftimg260085
66792Novosphingobium taihuense CGMCC 1.34322596583548draftimg260085

GC content

@refGC-contentmethod
3139963.3
6777063.3thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno91.069yes
gram-positiveno97.048yes
anaerobicno99.309yes
aerobicyes94.566no
halophileno93.094no
spore-formingno94.393yes
glucose-utilyes88.857no
thermophileno95.73yes
motileno51.317no
glucose-fermentno92.07no

External links

@ref: 7029

culture collection no.: DSM 17507, AS 1.3432, JCM 12465, CCUG 56308, BCRC 80740, CGMCC 1.3432, CIP 108789

straininfo link

  • @ref: 83321
  • straininfo: 138993

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15879260Novosphingobium taihuense sp. nov., a novel aromatic-compound-degrading bacterium isolated from Taihu Lake, China.Liu ZP, Wang BJ, Liu YH, Liu SJInt J Syst Evol Microbiol10.1099/ijs.0.63468-02005Bacterial Typing Techniques, Biodegradation, Environmental, China, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Fresh Water/*microbiology, Genes, Bacterial, Genes, rRNA, Geologic Sediments/*microbiology, Hydrocarbons, Aromatic/*metabolism, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sphingomonadaceae/*classification/cytology/*isolation & purification/physiology, Water MicrobiologyEnzymology
Phylogeny22544783Novosphingobium fuchskuhlense sp. nov., isolated from the north-east basin of Lake Grosse Fuchskuhle.Glaeser SP, Bolte K, Martin K, Busse HJ, Grossart HP, Kampfer P, Glaeser JInt J Syst Evol Microbiol10.1099/ijs.0.043083-02012Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Germany, Lakes/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sphingomonadaceae/*classification/genetics/isolation & purification, Ubiquinone/analysis, *Water MicrobiologyGenetics
Phylogeny27599476Novosphingobium bradum sp. nov., isolated from a spring.Sheu SY, Liu LP, Chen WMInt J Syst Evol Microbiol10.1099/ijsem.0.0014752016Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hydroxybutyrates/chemistry, Natural Springs/*microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Polyesters/chemistry, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spermidine/chemistry, Sphingomonadaceae/*classification/genetics/isolation & purification, Taiwan, Ubiquinone/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7029Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17507)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17507
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
31399Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2770828776041
38312Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6456
60911Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 56308)https://www.ccug.se/strain?id=56308
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/
68372Automatically annotated from API 50CH assim
68382Automatically annotated from API zym
83321Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID138993.1StrainInfo: A central database for resolving microbial strain identifiers
123416Curators of the CIPCollection of Institut Pasteur (CIP 108789)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108789