Strain identifier

BacDive ID: 14094

Type strain: Yes

Species: Pedobacter africanus

Strain Designation: K1/K2

Strain history: CIP <- 1998, LMG <- P. Steyn: strain K1/K2

NCBI tax ID(s): 151894 (species)

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General

@ref: 4608

BacDive-ID: 14094

DSM-Number: 12126

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

description: Pedobacter africanus K1/K2 is an obligate aerobe, mesophilic, Gram-negative bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 151894
  • Matching level: species

strain history

@refhistory
4608<- LMG
116124CIP <- 1998, LMG <- P. Steyn: strain K1/K2

doi: 10.13145/bacdive14094.20230509.8.1

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 africanus
  • full scientific name: Pedobacter africanus Steyn et al. 1998

@ref: 4608

domain: Bacteria

phylum: Bacteroidetes

class: Sphingobacteriia

order: Sphingobacteriales

family: Sphingobacteriaceae

genus: Pedobacter

species: Pedobacter africanus

full scientific name: Pedobacter africanus Steyn et al. 1998

strain designation: K1/K2

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative99.998
116124negativerod-shapedno

pigmentation

  • @ref: 116124
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4608NUTRIENT 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
39305MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
116124CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
4608positivegrowth28mesophilic
39305positivegrowth25mesophilic
116124positivegrowth25-37mesophilic
116124nogrowth5psychrophilic
116124nogrowth10psychrophilic
116124nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 116124
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.952

halophily

@refsaltgrowthtested relationconcentration
116124NaClpositivegrowth0-8 %
116124NaClnogrowth10 %

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
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
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-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-arabinose+builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
116124esculin+hydrolysis4853
116124nitrate+reduction17632
116124nitrite-reduction16301
116124nitrate-respiration17632

antibiotic resistance

  • @ref: 116124
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 116124
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
116124oxidase+
116124beta-galactosidase+3.2.1.23
116124alcohol dehydrogenase-1.1.1.1
116124gelatinase-
116124amylase-
116124DNase-
116124caseinase-3.4.21.50
116124catalase+1.11.1.6
116124tween esterase-
116124lecithinase-
116124lipase-
116124lysine decarboxylase-4.1.1.18
116124ornithine decarboxylase-4.1.1.17
116124tryptophan deaminase-
116124urease-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
116124-+++-++---++-+-+++--

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
116124--++/-+/-----++++-+/-----++/-+++++++++++-+/-+/----++---+/------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116124+-+++-+++++++++++++-++++----------++-+---+------------++---+------------------+-------+---+---+----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
4608soilEastern Transvaal, BelfastSouth AfricaZAFAfrica
54758SoilEastern Transvaal,Belfast,Africa
116124Environment, SoilSouth AfricaZAFAfrica

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_5331.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_115;96_319;97_404;98_3973;99_5331&stattab=map
  • Last taxonomy: Pedobacter africanus
  • 16S sequence: AB681144
  • Sequence Identity:
  • Total samples: 307
  • soil counts: 66
  • aquatic counts: 150
  • animal counts: 39
  • plant counts: 52

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
46081Risk group (German classification)
1161241Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Pedobacter africanus partial 16S rRNA gene, strain DSM 12126TAJ4381711490ena151894
20218Pedobacter africanus strain LMG 10353 16S ribosomal RNA gene, partial sequenceAF329953681ena151894
20218Pedobacter africanus gene for 16S rRNA, partial sequence, strain: NBRC 100065AB6811441447ena151894

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pedobacter africanus DSM 12126GCA_900176535contigncbi151894
66792Pedobacter africanus strain DSM 12126151894.4wgspatric151894
66792Pedobacter africanus DSM 121262622736459draftimg151894

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno86.573no
gram-positiveno98.268no
anaerobicno98.83no
aerobicyes82.52no
halophileno94.549no
spore-formingno94.134no
glucose-utilyes92.03no
flagellatedno95.722no
glucose-fermentno88.327no
thermophileno98.597no

External links

@ref: 4608

culture collection no.: DSM 12126, LMG 10353, CCUG 39353, CIP 105499

straininfo link

  • @ref: 83262
  • straininfo: 11921

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
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
Phylogeny24425748Pedobacter nutrimenti sp. nov., isolated from chilled food.Derichs J, Kampfer P, Lipski AInt J Syst Evol Microbiol10.1099/ijs.0.058677-02014Animals, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Food Microbiology, Meat/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Pedobacter/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Swine, Vitamin K 2/analogs & derivatives/chemistryBiotechnology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4608Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 12126)https://www.dsmz.de/collection/catalogue/details/culture/DSM-12126
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
39305Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17525
54758Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 39353)https://www.ccug.se/strain?id=39353
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
83262Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID11921.1StrainInfo: A central database for resolving microbial strain identifiers
116124Curators of the CIPCollection of Institut Pasteur (CIP 105499)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105499