Strain identifier

BacDive ID: 14105

Type strain: Yes

Species: Pedobacter hartonius

Strain Designation: WB3.3-3

Strain history: CIP <- 2007, DSMZ <- S. Muurholm, Weyhausen, Germany <- E. Brambilla <- O. Päuker: strain WB3.3-3

NCBI tax ID(s): 425514 (species)

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General

@ref: 7852

BacDive-ID: 14105

DSM-Number: 19033

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

description: Pedobacter hartonius WB3.3-3 is an obligate aerobe, psychrophilic, Gram-negative bacterium that was isolated from stream water.

NCBI tax id

  • NCBI tax id: 425514
  • Matching level: species

strain history

@refhistory
7852<- S. Muurholm <- E. Brambilla <- O. Päuker;
119843CIP <- 2007, DSMZ <- S. Muurholm, Weyhausen, Germany <- E. Brambilla <- O. Päuker: strain WB3.3-3

doi: 10.13145/bacdive14105.20250331.9.3

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 hartonius
  • full scientific name: Pedobacter hartonius Muurholm et al. 2007

@ref: 7852

domain: Bacteria

phylum: Bacteroidetes

class: Sphingobacteriia

order: Sphingobacteriales

family: Sphingobacteriaceae

genus: Pedobacter

species: Pedobacter hartonius

full scientific name: Pedobacter hartonius Muurholm et al. 2007

strain designation: WB3.3-3

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32230negative2 µm0.73 µmrod-shapedyes
119843negativerod-shapedno
125438negative95.75
125439negative99.7

pigmentation

  • @ref: 32230
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7852R2A 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
37562MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
119843CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
119843CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566

culture temp

@refgrowthtypetemperature
7852positivegrowth12
32230positivegrowth06-26
32230positiveoptimum14
37562positivegrowth15

culture pH

@refabilitytypepH
32230positivegrowth5.7-7.8
32230positiveoptimum6.75

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
119843obligate aerobe
125438aerobe90.395

spore formation

@refspore formationconfidence
32230no
125439no98.7

halophily

@refsaltgrowthtested relationconcentration
32230NaClpositivegrowth0-4 %
32230NaClpositiveoptimum2 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3223022599arabinose+carbon source
3223018403L-arabitol+carbon source
3223017057cellobiose+carbon source
3223023652dextrin+carbon source
3223028757fructose+carbon source
3223028260galactose+carbon source
322305291gelatin+carbon source
3223017234glucose+carbon source
3223017716lactose+carbon source
3223017306maltose+carbon source
3223029864mannitol+carbon source
3223037684mannose+carbon source
3223028053melibiose+carbon source
3223037657methyl D-glucoside+carbon source
32230506227N-acetylglucosamine+carbon source
3223026546rhamnose+carbon source
3223017814salicin+carbon source
3223027082trehalose+carbon source
3223053426tween 80+carbon source
3223018222xylose+carbon source
322304853esculin+hydrolysis
11984317632nitrate-reduction
11984316301nitrite-reduction
68371Potassium 5-ketogluconate-builds acid from
6837118305arbutin-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837116988D-ribose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837117992sucrose-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117057cellobiose-builds acid from
6837117814salicin-builds acid from
6837159640N-acetylglucosamine-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837112936D-galactose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from

metabolite production

  • @ref: 119843
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
32230alkaline phosphatase+3.1.3.1
32230catalase+1.11.1.6
32230gelatinase+
32230cytochrome oxidase+1.9.3.1
68382alpha-fucosidase+3.2.1.51
68382alpha-mannosidase+3.2.1.24
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382beta-glucosidase+3.2.1.21
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-galactosidase+3.2.1.23
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382lipase (C 14)-
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382alkaline phosphatase+3.1.3.1
119843oxidase+
119843catalase-1.11.1.6
119843urease-3.5.1.5
68382trypsin-3.4.21.4
68382leucine arylamidase+3.4.11.1

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
119843-+++-+----++-+--++++

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119843---+/--+/-----+/-+/-+/----------+/--+/---+/----+/----+/---+/-+/-+/---+/-+/-----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
7852stream waterLower Saxony, Westhöfer BachGermanyDEUEurope
119843Environment, Fresh waterWesterhöfer Bach, Harz mountainsGermanyDEUEurope2005

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #River (Creek)

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
78521Risk group (German classification)
1198431Risk group (French classification)

Sequence information

16S sequences

  • @ref: 32230
  • description: Pedobacter hartonius partial 16S rRNA gene, type strain WB3.3-3T
  • accession: AM491371
  • length: 1492
  • database: nuccore
  • NCBI tax ID: 425514

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pedobacter hartonius DSM 19033GCA_900107535scaffoldncbi425514
66792Pedobacter hartonius strain DSM 19033425514.7wgspatric425514
66792Pedobacter hartonius DSM 190332693429882draftimg425514

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno95.75yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.911yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes90.395no
125438spore-formingspore-formingAbility to form endo- or exosporesno83.637yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno98.49yes
125438motile2+flagellatedAbility to perform flagellated movementno87no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno98.7
125439BacteriaNetmotilityAbility to perform movementno69.5
125439BacteriaNetgram_stainReaction to gram-stainingnegative99.7
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe89.7

External links

@ref: 7852

culture collection no.: DSM 19033, CIP 109468

straininfo link

  • @ref: 83272
  • straininfo: 310979

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17911287Pedobacter duraquae sp. nov., Pedobacter westerhofensis sp. nov., Pedobacter metabolipauper sp. nov., Pedobacter hartonius sp. nov. and Pedobacter steynii sp. nov., isolated from a hard-water rivulet.Muurholm S, Cousin S, Pauker O, Brambilla E, Stackebrandt EInt J Syst Evol Microbiol10.1099/ijs.0.65166-02007Animals, Bacterial Typing Techniques, Bacteroidetes/chemistry/*classification/*isolation & purification, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Fresh Water/*microbiology, Genes, rRNA, Germany, Molecular Sequence Data, Organic Chemicals/metabolism, Phylogeny, Quinones/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic AcidGenetics
Phylogeny28109203Pedobacter lusitanus sp. nov., isolated from sludge of a deactivated uranium mine.Covas C, Caetano T, Cruz A, Santos T, Dias L, Klein G, Abdulmawjood A, Rodriguez-Alcala LM, Pimentel LL, Gomes A, Freitas AC, Garcia-Serrano A, Fontecha J, Mendo SInt J Syst Evol Microbiol10.1099/ijsem.0.0018142017Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, DNA, Ribosomal Spacer/genetics, Fatty Acids/chemistry, Genes, Bacterial, *Mining, Nucleic Acid Hybridization, Pedobacter/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, Portugal, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Sphingolipids, *Uranium, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
7852Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19033)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19033
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
32230Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2847228776041
37562Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7215
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
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
83272Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID310979.1StrainInfo: A central database for resolving microbial strain identifiers
119843Curators of the CIPCollection of Institut Pasteur (CIP 109468)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109468
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