Strain identifier

BacDive ID: 14093

Type strain: No

Species: Pedobacter antarcticus

Strain Designation: KS0420, P-48

Strain history: CIP <- 1994, IFO <- JCM <- H. Oyaizu: strain AJ 2502 <- K. Komagata and H. Ogawa: strain P-48

NCBI tax ID(s): 34086 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 9.1 (current version):
version 9:
version 8.1:
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 9.1 (current version)

General

@ref: 4457

BacDive-ID: 14093

DSM-Number: 11725

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

description: Pedobacter antarcticus KS0420 is an obligate aerobe, Gram-negative, rod-shaped bacterium that was isolated from frozen rainbow trout.

NCBI tax id

  • NCBI tax id: 34086
  • Matching level: species

strain history

@refhistory
4457<- JCM <- H. Oyaizu; KS0420 <- AJ2502 <- K. Komagata and H. Ogawa; P-48
67770H. Oyaizu KS 0420 <-- AJ 2502 <-- K. Komagata and H. Ogawa P-48.
121845CIP <- 1994, IFO <- JCM <- H. Oyaizu: strain AJ 2502 <- K. Komagata and H. Ogawa: strain P-48

doi: 10.13145/bacdive14093.20240916.9.1

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 antarcticus
  • full scientific name: Pedobacter antarcticus (Shivaji et al. 1992) Farfán et al. 2014

  • synonyms

    @refsynonym
    20215Sphingobacterium antarcticum
    20215Pedobacter piscium
    20215Sphingobacterium antarcticus
    20215Sphingobacterium piscium

@ref: 4457

domain: Bacteria

phylum: Bacteroidetes

class: Sphingobacteriia

order: Sphingobacteriales

family: Sphingobacteriaceae

genus: Pedobacter

species: Pedobacter antarcticus

full scientific name: Pedobacter antarcticus (Shivaji et al. 1992) Farfán et al. 2014

strain designation: KS0420, P-48

type strain: no

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
121845negativerod-shapedno
69480negative96

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4457NUTRIENT 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
41043MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
121845CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperature
4457positivegrowth28
41043positivegrowth30
67770positivegrowth30
121845positivegrowth10-30
121845nogrowth37
121845nogrowth41

Physiology and metabolism

oxygen tolerance

  • @ref: 121845
  • oxygen tolerance: obligate aerobe

spore formation

  • @ref: 69481
  • spore formation: no
  • confidence: 100

observation

  • @ref: 67770
  • observation: quinones: MK-7

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose+builds acid from32528
68371gentiobiose+builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch+builds acid from28017
68371raffinose+builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose+builds acid from27082
68371sucrose+builds acid from17992
68371melibiose+builds acid from28053
68371lactose+builds acid from17716
68371maltose+builds acid from17306
68371cellobiose+builds acid from17057
68371salicin+builds acid from17814
68371esculin+builds acid from4853
68371arbutin+builds acid from18305
68371amygdalin+builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose+builds acid from16024
68371D-fructose+builds acid from15824
68371D-glucose+builds acid from17634
68371D-galactose+builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose-builds acid from16988
68371L-arabinose+builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
121845citrate-carbon source16947
121845esculin+hydrolysis4853
121845nitrate-reduction17632
121845nitrite-reduction16301
121845nitrate-respiration17632

metabolite production

  • @ref: 121845
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
121845oxidase+
121845beta-galactosidase+3.2.1.23
121845alcohol dehydrogenase-1.1.1.1
121845DNase+
121845catalase+1.11.1.6
121845gamma-glutamyltransferase+2.3.2.2
121845lysine decarboxylase-4.1.1.18
121845ornithine decarboxylase-4.1.1.17
121845phenylalanine ammonia-lyase+4.3.1.24
121845tryptophan deaminase-
121845urease-3.5.1.5

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
121845---+-----++++-------+/--++++++++++--++--++---------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121845+++++-+++++++++++++-++++----------++-----+-------+----+----+--------------------------+--+++-----+-

Isolation, sampling and environmental information

isolation

@refsample type
4457frozen rainbow trout
67770Frozen rainbow trout
121845Frozen rainbow traut

isolation source categories

  • Cat1: #Host
  • Cat2: #Fishes
  • Cat3: #Salmonidae

taxonmaps

  • @ref: 69479
  • File name: preview.99_488.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_115;96_319;97_355;98_401;99_488&stattab=map
  • Last taxonomy: Pedobacter antarcticus
  • 16S sequence: AJ438174
  • Sequence Identity:
  • Total samples: 314
  • soil counts: 82
  • aquatic counts: 29
  • animal counts: 136
  • plant counts: 67

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
44571Risk group (German classification)
1218451Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
4457Pedobacter piscium partial 16S rRNA gene, strain DSM 11725TAJ4381741494nuccore34086
124043Pedobacter piscium gene for 16S rRNA, partial sequence, strain: NBRC 14985.AB6807331447nuccore34086

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pedobacter antarcticus DSM 11725GCA_900103515scaffoldncbi34086
66792Pedobacter antarcticus strain DSM 1172534086.10wgspatric34086
66792Pedobacter piscium DSM 117252622736436draftimg34086

GC content

@refGC-contentmethod
6777040.4
6777038.7thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno100no
69480gram-positivegram-positivePositive reaction to Gram-stainingno96no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.629yes
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes88.697no
69480spore-formingspore-formingAbility to form endo- or exosporesno89.194no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno96.99yes
69480flagellatedmotile2+Ability to perform flagellated movementno88.095no

External links

@ref: 4457

culture collection no.: DSM 11725, CIP 104195, JCM 14985, JCM 7454, AJ 2502, CCM 4602, IFO 14985, KCTC 12489, LMG 14024, NBRC 14985, NCIMB 13704

straininfo link

  • @ref: 83261
  • straininfo: 264392

Reference

@idauthorscataloguedoi/urltitle
4457Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11725)https://www.dsmz.de/collection/catalogue/details/culture/DSM-11725
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
41043Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16076
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/
68371Automatically annotated from API 50CH acid
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
83261Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID264392.1StrainInfo: A central database for resolving microbial strain identifiers
121845Curators of the CIPCollection of Institut Pasteur (CIP 104195)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104195
124043Dr. Isabel Schober, Dr. Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy