Strain identifier

BacDive ID: 14099

Type strain: Yes

Species: Pedobacter caeni

Strain history: CIP <- 2005, DSMZ

NCBI tax ID(s): 288992 (species)

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General

@ref: 6593

BacDive-ID: 14099

DSM-Number: 16990

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

description: Pedobacter caeni DSM 16990 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from nitrifying inoculum.

NCBI tax id

  • NCBI tax id: 288992
  • Matching level: species

strain history

@refhistory
6593<- B. Vanparys, LMG
340222005, DSMZ
117094CIP <- 2005, DSMZ

doi: 10.13145/bacdive14099.20230509.8.1

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 caeni
  • full scientific name: Pedobacter caeni Vanparys et al. 2005

@ref: 6593

domain: Bacteria

phylum: Bacteroidetes

class: Sphingobacteriia

order: Sphingobacteriales

family: Sphingobacteriaceae

genus: Pedobacter

species: Pedobacter caeni

full scientific name: Pedobacter caeni Vanparys et al. 2005

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31473negative6.5 µm0.75 µmrod-shapedno
69480negative99.986
117094negativerod-shapedno

colony morphology

  • @ref: 117094
  • hemolysis ability: 1

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6593TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545)yeshttps://mediadive.dsmz.de/medium/545Name: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545) Composition: Casein peptone 17.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l D(+)-Glucose 2.5 g/l K2HPO4 2.5 g/l Distilled water
34022MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
117094CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
6593positivegrowth28mesophilic
31473positivegrowth28-37mesophilic
31473positiveoptimum28mesophilic
34022positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
6593aerobe
31473aerobe
117094obligate aerobe

spore formation

@refspore formationconfidence
31473no
69481no100
69480no99.968

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3147316634raffinose+carbon source
3147317151xylitol+carbon source
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837117992sucrose-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117306maltose-builds acid from
6837117057cellobiose-builds acid from
6837117814salicin-builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-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
6837116024D-mannose-builds acid from
6837115824D-fructose-builds acid from
6837117634D-glucose-builds acid from
6837112936D-galactose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837116988D-ribose-builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
11709417632nitrate-reduction
11709416301nitrite-reduction

metabolite production

  • @ref: 117094
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
31473catalase+1.11.1.6
31473cytochrome oxidase+1.9.3.1
117094oxidase-
117094alcohol dehydrogenase-1.1.1.1
117094catalase+1.11.1.6
117094lysine decarboxylase-4.1.1.18
117094ornithine decarboxylase-4.1.1.17
117094urease-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
117094-+++-+--+-++---+-+--

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
117094------------------------+/------------------------+/-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6593nitrifying inoculumGentBelgiumBELEurope
117094Commercial nitrifying inoculumGhentBelgiumBELEurope

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Laboratory
  • Cat3: #Lab enrichment

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
65931Risk group (German classification)
1170941Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6593
  • description: Pedobacter caeni partial 16S rRNA gene, type strain LMG 22862T
  • accession: AJ786798
  • length: 1337
  • database: ena
  • NCBI tax ID: 288992

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pedobacter caeni DSM 16990GCA_900129215scaffoldncbi288992
66792Pedobacter caeni strain DSM 16990288992.5wgspatric288992
66792Pedobacter caeni DSM 169902622736434draftimg288992

GC content

  • @ref: 31473
  • GC-content: 42.7

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno88.248yes
flagellatedno96.408yes
gram-positiveno97.633no
anaerobicno99.498no
aerobicyes86.84yes
halophileno96.173no
spore-formingno90.657yes
thermophileno99.637yes
glucose-utilyes85.818no
glucose-fermentno90.237no

External links

@ref: 6593

culture collection no.: DSM 16990, CIP 109035, LMG 22862

straininfo link

  • @ref: 83267
  • straininfo: 129690

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15879274Pedobacter caeni sp. nov., a novel species isolated from a nitrifying inoculum.Vanparys B, Heylen K, Lebbe L, De Vos PInt J Syst Evol Microbiol10.1099/ijs.0.63635-02005Bacterial Proteins/analysis/isolation & purification, Bacterial Typing Techniques, Bacteroidetes/*classification/cytology/*isolation & purification/metabolism, Base Composition, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Electrophoresis, Polyacrylamide Gel, Fatty Acids/analysis/isolation & purification, Genes, Bacterial, Genes, rRNA, Gentian Violet, Molecular Sequence Data, Nitrogen/*metabolism, Nucleic Acid Hybridization, Phenazines, Phylogeny, Proteome, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Water MicrobiologyEnzymology
Phylogeny17082391Pedobacter ginsengisoli sp. nov., a DNase-producing bacterium isolated from soil of a ginseng field in South Korea.Ten LN, Liu QM, Im WT, Lee M, Yang DC, Lee STInt J Syst Evol Microbiol10.1099/ijs.0.64414-02006Bacteroidetes/*classification/cytology/*isolation & purification/physiology, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Deoxyribonucleases/*biosynthesis, Fatty Acids/analysis/chemistry, Genes, rRNA, Korea, Molecular Sequence Data, Movement, Nucleic Acid Hybridization, *Panax, Phylogeny, Quinones/analysis/chemistry, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Soil MicrobiologyGenetics
Phylogeny17267983Pedobacter panaciterrae sp. nov., isolated from soil in South Korea.Yoon MH, Ten LN, Im WT, Lee STInt J Syst Evol Microbiol10.1099/ijs.0.64693-02007Anaerobiosis, Bacterial Typing Techniques, Bacteroidetes/*classification/cytology/*isolation & purification/physiology, Carbohydrate Metabolism, Catalase/analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis/chemistry, Gelatinases/analysis, Genes, rRNA, Hydrogen Sulfide/metabolism, Indoles/metabolism, Korea, Molecular Sequence Data, Movement, Nucleic Acid Hybridization, Oxidoreductases/analysis, Phylogeny, Quinones/analysis/chemistry, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Homology, Nucleic Acid, *Soil MicrobiologyMetabolism
Phylogeny17551054Parapedobacter koreensis gen. nov., sp. nov.Kim MK, Na JR, Cho DH, Soung NK, Yang DCInt J Syst Evol Microbiol10.1099/ijs.0.64677-02007Bacterial Typing Techniques, Bacteroidetes/chemistry/*classification/genetics/physiology, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Korea, Locomotion, Molecular Sequence Data, Oryza/*microbiology, Phylogeny, Quinones/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Spores, BacterialGenetics
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
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
Phylogeny25613852Pedobacter lotistagni sp. nov. isolated from lotus pond water.Singh H, Du J, Ngo HT, Kim KY, Yi THAntonie Van Leeuwenhoek10.1007/s10482-015-0387-52015Aerobiosis, Bacterial Typing Techniques, Base Composition, Cluster Analysis, Culture Media/chemistry, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Korea, Locomotion, Lotus/growth & development, Molecular Sequence Data, Nucleic Acid Hybridization, Pedobacter/*classification/genetics/*isolation & purification/physiology, Phospholipids/analysis, Phylogeny, Ponds/*microbiology, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, TemperatureGenetics
Phylogeny27032079Pedobacter humi sp. nov., isolated from a playground soil.Trinh H, Yi THInt J Syst Evol Microbiol10.1099/ijsem.0.0010322016Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Pedobacter/*classification/genetics/isolation & purification, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/analogs & derivatives/chemistry, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny29231155Pedobacter quisquiliarum sp. nov., isolated from activated sludge.Zhang B, Liu ZQ, Zheng YGInt J Syst Evol Microbiol10.1099/ijsem.0.0025312017Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Pedobacter/*classification/genetics/isolation & purification, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny33502299Pedobacter gandavensis sp. nov., Pedobacter foliorum sp. nov. and Pedobacter planticolens sp. nov., isolated from leaves of Arabidopsis thaliana.Qi SS, Cnockaert M, Carlier A, Vandamme PInt J Syst Evol Microbiol10.1099/ijsem.0.0046672021

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
6593Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16990)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16990
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
31473Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2777328776041
34022Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6732
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
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
83267Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID129690.1StrainInfo: A central database for resolving microbial strain identifiers
117094Curators of the CIPCollection of Institut Pasteur (CIP 109035)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109035