Strain identifier

BacDive ID: 17758

Type strain: Yes

Species: Niabella aurantiaca

Strain Designation: R2A15-11

Strain history: CIP <- 2007, DSMZ <- KACC <- Korea: strain R2A15-11

NCBI tax ID(s): 1122605 (strain), 379900 (species)

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General

@ref: 7090

BacDive-ID: 17758

DSM-Number: 17617

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

description: Niabella aurantiaca R2A15-11 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from greenhouse soil.

NCBI tax id

NCBI tax idMatching level
379900species
1122605strain

strain history

@refhistory
7090<- S.-W. Kwon, KACC; R2A15-11
116554CIP <- 2007, DSMZ <- KACC <- Korea: strain R2A15-11

doi: 10.13145/bacdive17758.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Chitinophagia
  • order: Chitinophagales
  • family: Chitinophagaceae
  • genus: Niabella
  • species: Niabella aurantiaca
  • full scientific name: Niabella aurantiaca Kim et al. 2007

@ref: 7090

domain: Bacteria

phylum: Bacteroidetes

class: Chitinophagia

order: Sphingobacteriales

family: Chitinophagaceae

genus: Niabella

species: Niabella aurantiaca

full scientific name: Niabella aurantiaca Kim et al. 2007 emend. Hahnke et al. 2016

strain designation: R2A15-11

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31897negative1.25 µm0.8 µmrod-shapedno
69480negative99.995
116554negativeoval-shapedno

pigmentation

  • @ref: 31897
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7090R2A 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
33310MEDIUM 372 - for AquabacteriumyesDistilled water make up to (1000.000 ml);Magnesium sulphate heptahydrate (0.050 g);Agar (15.000 g);Glucose (0.500 g);Yeast extract (0.500 g);Pyruvic acid (0.300g);Tween 80 (1.000 ml);Casamino acids (0.500 g);Proteose Peptone N°3 (0.500 g);Di Potassium mon
116554CIP Medium 372yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=372

culture temp

@refgrowthtypetemperaturerange
7090positivegrowth28mesophilic
31897positivegrowth10-35
31897positiveoptimum27.5mesophilic
33310positivegrowth25mesophilic

culture pH

@refabilitytypepH
31897positivegrowth5.0-8.0
31897positiveoptimum6.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31897aerobe
116554obligate aerobe

spore formation

@refspore formationconfidence
31897no
69481no100
69480no99.994

halophily

@refsaltgrowthtested relationconcentration
31897NaClpositivegrowth0-3 %
31897NaClpositiveoptimum1.5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3189717306maltose+carbon source
3189728053melibiose+carbon source
3189726546rhamnose+carbon source
3189717814salicin+carbon source
3189717992sucrose+carbon source
318974853esculin+hydrolysis
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
683714853esculin+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
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837116988D-ribose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
11655417632nitrate-reduction
11655416301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
3189735581indoleyes
11655435581indoleyes

metabolite tests

  • @ref: 31897
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: +

enzymes

@refvalueactivityec
31897acid phosphatase+3.1.3.2
31897alkaline phosphatase+3.1.3.1
31897alpha-galactosidase+3.2.1.22
31897catalase+1.11.1.6
31897gelatinase+
116554oxidase-
116554catalase+1.11.1.6
116554urease-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
116554-+++-+----++++-+++++

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
116554--+/-+/--+/----+/-+/-+/-+/-------+/-+/-+/-+/-+/-++/-+/-+/-+/-+/-+/-+/---+/-+/---+/-+/-+/---+/-----+/-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7090greenhouse soilYeoju regionRepublic of KoreaKORAsia
116554Environment, Soil, greenhouseYeoju regionRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture#Greenhouse
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_1647.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_185;96_939;97_1092;98_1303;99_1647&stattab=map
  • Last taxonomy: Niabella aurantiaca subclade
  • 16S sequence: DQ457019
  • Sequence Identity:
  • Total samples: 1009
  • soil counts: 340
  • aquatic counts: 291
  • animal counts: 214
  • plant counts: 164

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
70901Risk group (German classification)
1165541Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7090
  • description: Niabella aurantiaca strain R2A15-11 16S ribosomal RNA gene, partial sequence
  • accession: DQ457019
  • length: 1465
  • database: ena
  • NCBI tax ID: 379900

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Niabella aurantiaca DSM 17617GCA_000374125scaffoldncbi1122605
66792Niabella aurantiaca DSM 176171122605.3wgspatric1122605
66792Niabella aurantiaca DSM 176172515154175draftimg1122605

GC content

@refGC-contentmethod
709045.0
3189745
709048.6sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno93.957yes
flagellatedno98.318yes
gram-positiveno96.439yes
anaerobicno99.381no
aerobicyes83.272yes
halophileno96.105no
spore-formingno93.563yes
glucose-utilyes86.365no
thermophileno97.551yes
glucose-fermentno87.426no

External links

@ref: 7090

culture collection no.: DSM 17617, CIP 109580, KACC 11698

straininfo link

  • @ref: 86749
  • straininfo: 297283

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17329780Niabella aurantiaca gen. nov., sp. nov., isolated from a greenhouse soil in Korea.Kim BY, Weon HY, Yoo SH, Hong SB, Kwon SW, Stackebrandt E, Go SJInt J Syst Evol Microbiol10.1099/ijs.0.64614-02007DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Flavobacterium/*classification/cytology/genetics/isolation & purification, Korea, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil MicrobiologyGenetics
Phylogeny18218950Niabella soli sp. nov., isolated from soil from Jeju Island, Korea.Weon HY, Kim BY, Joa JH, Kwon SW, Kim WG, Koo BSInt J Syst Evol Microbiol10.1099/ijs.0.65304-02008Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/*isolation & purification/physiology, Base Composition, DNA, Bacterial, Fatty Acids/analysis, Genes, rRNA, Korea, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S, Sequence Analysis, DNA, *Soil Microbiology, Species SpecificityGenetics
Phylogeny18768628Sediminibacterium salmoneum gen. nov., sp. nov., a member of the phylum Bacteroidetes isolated from sediment of a eutrophic reservoir.Qu JH, Yuan HLInt J Syst Evol Microbiol10.1099/ijs.0.65514-02008Aerobiosis, Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/*isolation & purification/physiology, Base Composition, China, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Geologic Sediments/*microbiology, Locomotion, Molecular Sequence Data, Phylogeny, Pigments, Biological/biosynthesis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic AcidGenetics
Phylogeny19502302Niabella ginsengisoli sp. nov., isolated from soil cultivated with Korean ginseng.Weon HY, Yoo SH, Kim BY, Son JA, Kim YJ, Kwon SWInt J Syst Evol Microbiol10.1099/ijs.0.004333-02009Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification/physiology, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Molecular Sequence Data, *Panax, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species SpecificityGenetics
Phylogeny27031646Niabella aquatica sp. nov., isolated from lake water.Siddiqi MZ, Im WTInt J Syst Evol Microbiol10.1099/ijsem.0.0010532016Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Lakes/*microbiology, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7090Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17617)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17617
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
31897Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2815528776041
33310Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7339
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)
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
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
86749Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297283.1StrainInfo: A central database for resolving microbial strain identifiers
116554Curators of the CIPCollection of Institut Pasteur (CIP 109580)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109580