Strain identifier

BacDive ID: 14111

Type strain: Yes

Species: Pedobacter nyackensis

Strain Designation: NWG-II14

Strain history: CIP <- 2009, DSMZ <- N.S. Gordon, Montana Univ., Missoula, USA: strain NWG-II14

NCBI tax ID(s): 475255 (species)

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For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 8217

BacDive-ID: 14111

DSM-Number: 19625

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

description: Pedobacter nyackensis NWG-II14 is an aerobe, psychrophilic, Gram-negative bacterium that was isolated from hyporheic sediments.

NCBI tax id

  • NCBI tax id: 475255
  • Matching level: species

strain history

@refhistory
8217<- N. S. Gordon, Univ. Montana, Missoula, USA; NWG-II14 <- N. S. Gordon {2004}
121374CIP <- 2009, DSMZ <- N.S. Gordon, Montana Univ., Missoula, USA: strain NWG-II14

doi: 10.13145/bacdive14111.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Sphingobacteriia
  • order: Sphingobacteriales
  • family: Sphingobacteriaceae
  • genus: Pedobacter
  • species: Pedobacter nyackensis
  • full scientific name: Pedobacter nyackensis Gordon et al. 2009

@ref: 8217

domain: Bacteria

phylum: Bacteroidetes

class: Sphingobacteriia

order: Sphingobacteriales

family: Sphingobacteriaceae

genus: Pedobacter

species: Pedobacter nyackensis

full scientific name: Pedobacter nyackensis Gordon et al. 2009

strain designation: NWG-II14

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
28877negative2.5 µm0.45 µmrod-shapedno
69480negative99.986
121374negativerod-shapedno

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8217R2A 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
42246MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromatiyesDistilled water make up to (1000.000 ml);R2A agar (18.200 g)
121374CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566

culture temp

@refgrowthtypetemperaturerange
8217positivegrowth20psychrophilic
28877positivegrowth02-32
28877positiveoptimum17psychrophilic
42246positivegrowth20psychrophilic

culture pH

@refabilitytypepHPH range
28877positivegrowth05-10alkaliphile
28877positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
28877aerobe
121374obligate aerobe

spore formation

@refspore formationconfidence
28877no
69481no100
69480no99.962

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2887722599arabinose+carbon source
2887717057cellobiose+carbon source
2887728757fructose+carbon source
2887728260galactose+carbon source
2887717234glucose+carbon source
2887728087glycogen+carbon source
2887717716lactose+carbon source
2887717306maltose+carbon source
2887737684mannose+carbon source
28877506227N-acetylglucosamine+carbon source
2887716634raffinose+carbon source
2887726546rhamnose+carbon source
2887733942ribose+carbon source
2887718222xylose+carbon source
288774853esculin+hydrolysis
12137417632nitrate-reduction
12137416301nitrite-reduction

metabolite production

  • @ref: 121374
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
28877acid phosphatase+3.1.3.2
28877alkaline phosphatase+3.1.3.1
28877alpha-galactosidase+3.2.1.22
28877catalase+1.11.1.6
28877cytochrome oxidase+1.9.3.1
121374oxidase+
121374catalase+1.11.1.6
121374urease-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
121374-+-+-++---++---+++--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
8217hyporheic sedimentsnorth-western Montana, Middle Fork Flathead River, Nyack FloodplainUSAUSANorth America
121374Environment, Sediments, hyporheicMontanaUnited States of AmericaUSANorth America

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_4306.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_115;96_319;97_404;98_3241;99_4306&stattab=map
  • Last taxonomy: Pedobacter nyackensis
  • 16S sequence: EU030686
  • Sequence Identity:
  • Total samples: 536
  • soil counts: 296
  • aquatic counts: 42
  • animal counts: 136
  • plant counts: 62

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
82171Risk group (German classification)
1213741Risk group (French classification)

Sequence information

16S sequences

  • @ref: 8217
  • description: Pedobacter nyackensis strain NWG-II14 16S ribosomal RNA gene, partial sequence
  • accession: EU030686
  • length: 1466
  • database: ena
  • NCBI tax ID: 475255

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pedobacter nyackensis DSM 19625GCA_900176505scaffoldncbi475255
66792Pedobacter nyackensis strain DSM 19625475255.4wgspatric475255
66792Pedobacter nyackensis DSM 196252622736511draftimg475255

GC content

@refGC-contentmethod
821736.1
821741.1±0.4high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno89.635yes
flagellatedno96.878no
gram-positiveno97.742yes
anaerobicno99.183yes
aerobicyes85.684no
halophileno96.63no
spore-formingno94.616no
thermophileno97.982no
glucose-utilyes90.635yes
glucose-fermentno87.354no

External links

@ref: 8217

culture collection no.: DSM 19625, CIP 110034, LMG 24260

straininfo link

  • @ref: 83278
  • straininfo: 309278

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19542109Pedobacter nyackensis sp. nov., Pedobacter alluvionis sp. nov. and Pedobacter borealis sp. nov., isolated from Montana flood-plain sediment and forest soil.Gordon NS, Valenzuela A, Adams SM, Ramsey PW, Pollock JL, Holben WE, Gannon JEInt J Syst Evol Microbiol10.1099/ijs.0.000158-02009Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification/physiology, DNA, Bacterial/analysis, *Floods, Genes, rRNA, Genotype, Geologic Sediments/*microbiology, Molecular Sequence Data, Montana, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species Specificity, Tracheophyta, *TreesGenetics
Phylogeny24659428Pedobacter seoulensis sp. nov., isolated from soil of a bamboo field.Ngo HT, Son HM, Park SY, Kim KY, Yi THAntonie Van Leeuwenhoek10.1007/s10482-014-0154-z2014Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Pedobacter/*classification/genetics/*isolation & purification/physiology, Phospholipids/analysis, Phylogeny, Polyamines/analysis, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyGenetics
Phylogeny25634950Pedobacter daejeonensis sp. nov. and Pedobacter trunci sp. nov., isolated from an ancient tree trunk, and emended description of the genus Pedobacter.Du J, Singh H, Ngo HTT, Won KH, Kim KY, Yi THInt J Syst Evol Microbiol10.1099/ijs.0.0000872015Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Pedobacter/*classification/genetics/isolation & purification, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Trees/*microbiology, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny27902181Pedobacterlycopersici sp. nov., isolated from the rhizosphere of tomato plant (Solanum lycopersicum L.).Cho H, Ahn JH, Weon HY, Joa JH, Kwon SW, Kim SJInt J Syst Evol Microbiol10.1099/ijsem.0.0015322016Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Lycopersicon esculentum/*microbiology, Nucleic Acid Hybridization, Pedobacter/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Sphingolipids/chemistry, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Metabolism32273530Pedobacter schmidteae sp. nov., a new bacterium isolated from the microbiota of the planarian Schmidtea mediterranea.Kangale LJ, Raoult D, Ghigo E, Fournier PESci Rep10.1038/s41598-020-62985-x2020Animals, Bacterial Proteins/genetics/metabolism, Catalase/genetics/metabolism, *Genome, Bacterial, Microbiota, Oxidoreductases/genetics/metabolism, Pedobacter/genetics/metabolism/*pathogenicity, Planarians/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence HomologyPhylogeny

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
8217Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19625)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19625
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
28877Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2531728776041
42246Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7846
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updates33211880Nucleic Acids Res. 49: D498-D508 2020
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
83278Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID309278.1StrainInfo: A central database for resolving microbial strain identifiers
121374Curators of the CIPCollection of Institut Pasteur (CIP 110034)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110034