Strain identifier

BacDive ID: 14092

Type strain: Yes

Species: Pedobacter heparinus

Strain history: CIP <- 1994, IFO <- Nagoya Univ., Japan <- ATCC, Cytophaga heparina <- E.K. Korn, NIH, USA, Flavobacterium heparinum

NCBI tax ID(s): 485917 (strain), 984 (species)

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General

@ref: 1051

BacDive-ID: 14092

DSM-Number: 2366

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

description: Pedobacter heparinus DSM 2366 is an obligate aerobe, mesophilic, Gram-negative bacterium that was isolated from soil.

NCBI tax id

NCBI tax idMatching level
485917strain
984species

strain history

@refhistory
1051<- W. Mannheim, HIM 762-3 <- ATCC <- E.K. Korn (NIH)
67770H. Oyaizu KS 0426 <-- IFO 12017 <-- Nagoya Univ. <-- ATCC 13125 <-- E. D. Korn.
119875CIP <- 1994, IFO <- Nagoya Univ., Japan <- ATCC, Cytophaga heparina <- E.K. Korn, NIH, USA, Flavobacterium heparinum

doi: 10.13145/bacdive14092.20230509.8.1

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 heparinus
  • full scientific name: Pedobacter heparinus (Payza and Korn 1956) Steyn et al. 1998

  • synonyms

    @refsynonym
    20215Flavobacterium heparinum
    20215Sphingobacterium heparinum
    20215Cytophaga heparina

@ref: 1051

domain: Bacteria

phylum: Bacteroidetes

class: Sphingobacteriia

order: Sphingobacteriales

family: Sphingobacteriaceae

genus: Pedobacter

species: Pedobacter heparinus

full scientific name: Pedobacter heparinus (Payza and Korn 1956) Steyn et al. 1998 emend. Zhou et al. 2012

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative99.996
119875negativerod-shapedno

multimedia

  • @ref: 66793
  • multimedia content: EM_DSM_2366_1.jpg
  • caption: electron microscopic image
  • intellectual property rights: © HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
1051NUTRIENT 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
40684MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
119875CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
1051positivegrowth25-30mesophilic
40684positivegrowth30mesophilic
67770positivegrowth30mesophilic
119875positivegrowth25-30mesophilic
119875nogrowth10psychrophilic
119875nogrowth37mesophilic
119875nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 119875
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.931

compound production

@refcompound
1051chondroitinase (ABC and AC)
1051alpha glucuronidase
1051heparinase
1051heparinitase
1051sulfoamidases
1051sulfoesterases

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
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371salicin-builds acid from17814
68371esculin+builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
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
119875citrate-carbon source16947
119875esculin+hydrolysis4853
119875glucose-fermentation17234
119875lactose-fermentation17716
119875nitrate-reduction17632
119875nitrite-reduction16301
119875sodium thiosulfate-builds gas from132112

metabolite production

  • @ref: 119875
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
119875oxidase+
119875beta-galactosidase+3.2.1.23
119875alcohol dehydrogenase-1.1.1.1
119875gelatinase-
119875DNase+
119875catalase+1.11.1.6
119875gamma-glutamyltransferase+2.3.2.2
119875lysine decarboxylase-4.1.1.18
119875ornithine decarboxylase-4.1.1.17
119875phenylalanine ammonia-lyase+4.3.1.24
119875tryptophan deaminase-
119875urease-3.5.1.5

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119875+/--++-+---++++-----+/------+-+/-+/-+/-+/-+/-+/-------+/-+/----+-----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119875+++++-++--+++--+--+-+++++------+-+++++---+------------++----------------------------------+---+----

Isolation, sampling and environmental information

isolation

@refsample type
1051soil
45833Soil
119875Environment, Dry soil

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_5580.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_115;96_319;97_404;98_3973;99_5580&stattab=map
  • Last taxonomy: Pedobacter heparinus
  • 16S sequence: AJ438172
  • Sequence Identity:
  • Total samples: 1154
  • soil counts: 529
  • aquatic counts: 264
  • animal counts: 283
  • plant counts: 78

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
10511Risk group (German classification)
1198751Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Pedobacter heparinus gene for 16S rRNA, partial sequence, strain: NBRC 12017AB6802151447ena984
20218Pedobacter heparinus partial 16S rRNA gene, strain DSM 2366TAJ4381721482ena485917

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pedobacter heparinus DSM 2366GCA_000023825completencbi485917
66792Pedobacter heparinus DSM 2366485917.13wgspatric485917
66792Pedobacter heparinus DSM 2366485917.6completepatric485917
66792Pedobacter heparinus HIM 762-3, DSM 2366644736398draftimg485917
67770Pedobacter heparinus DSM 2366GCA_000410815contigncbi485917

GC content

@refGC-contentmethod
105140.4-45.0
6777042.3-43.0
6777040.4thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno88.987no
flagellatedno96.657no
gram-positiveno98.126no
anaerobicno99.166no
aerobicyes85.457no
halophileno93.912no
spore-formingno95.181no
thermophileno98.009yes
glucose-utilyes91.522no
glucose-fermentno89.37no

External links

@ref: 1051

culture collection no.: DSM 2366, ATCC 13125, IFO 12017, NBRC 12017, NCIB 9290, CCUG 12810, LMG 10339, HIM 762-3, JCM 7457, BCRC 11563, CIP 104194, IAM 12655, KCTC 12437, LMG 10344, LMG 4024, LMG 8360, NCIMB 9290, NRRL B-14731

straininfo link

  • @ref: 83260
  • straininfo: 44080

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Enzymology803822Chondroitinase-producing bacteria in natural habitats.Kitamikado M, Lee YZAppl Microbiol10.1128/am.29.3.414-421.19751975Aerobiosis, Aeromonas/enzymology/ultrastructure, Anaerobiosis, Arthrobacter/enzymology, Bacteria/*enzymology, Biodegradation, Environmental, Chondroitin/metabolism, Electrophoresis, Disc, Flavobacterium/enzymology, Glucuronidase/metabolism, Gram-Negative Aerobic Bacteria/enzymology, Lyases/*biosynthesis, Micrococcus/enzymology, Microscopy, Electron, Proteus vulgaris/enzymology, Seawater, *Soil Microbiology, Vibrio/enzymology, *Water MicrobiologyMetabolism
Phylogeny16902016Pedobacter roseus sp. nov., isolated from a hypertrophic pond, and emended description of the genus Pedobacter.Hwang CY, Choi DH, Cho BCInt J Syst Evol Microbiol10.1099/ijs.0.64045-02006Bacteroides/*classification/isolation & purification/physiology, DNA, Bacterial/genetics, Fresh Water/*microbiology, Hydrogen-Ion Concentration, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Homology, Nucleic Acid, Species Specificity, Temperature, *Water MicrobiologyGenetics
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
Genetics21304637Complete genome sequence of Pedobacter heparinus type strain (HIM 762-3).Han C, Spring S, Lapidus A, Del Rio TG, Tice H, Copeland A, Cheng JF, Lucas S, Chen F, Nolan M, Bruce D, Goodwin L, Pitluck S, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CC, Saunders E, Chertkov O, Brettin T, Goker M, Rohde M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Detter JCStand Genomic Sci10.4056/sigs.221382009
Phylogeny23291764Identification and characterization of cellobiose 2-epimerases from various aerobes.Ojima T, Saburi W, Yamamoto T, Mori H, Matsui HBiosci Biotechnol Biochem10.1271/bbb.1207422013Aerobiosis, Bacteria, Aerobic/chemistry/*enzymology, Bacterial Proteins/classification/*isolation & purification/*metabolism, Carbohydrate Epimerases/classification/*isolation & purification/*metabolism, Cellobiose/*metabolism, Enzyme Assays, Enzyme Stability, Escherichia coli/genetics, Glucose/metabolism, Hydrogen-Ion Concentration, Isoenzymes/classification/isolation & purification/metabolism, Kinetics, Lactose/metabolism, Mannose/metabolism, Phylogeny, Recombinant Proteins/classification/isolation & purification/metabolism, Species Specificity, Stereoisomerism, Substrate Specificity, TemperatureEnzymology
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
Phylogeny27798744Pedobacter panacis sp. nov., isolated from Panax ginseng soil.Singh P, Singh H, Kim YJ, Yang DCAntonie Van Leeuwenhoek10.1007/s10482-016-0794-22016DNA, Bacterial/genetics, *Panax, Pedobacter/*classification/genetics/metabolism, Phospholipids/metabolism, Phylogeny, *Soil MicrobiologyMetabolism
Metabolism28067452Expanding the Catalytic Promiscuity of Heparinase III from Pedobacter heparinus.Gu Y, Lu M, Wang Z, Wu X, Chen YChemistry10.1002/chem.2016059292017Biocatalysis, Dimerization, Disulfides/chemistry, Glycosaminoglycans/metabolism, Heparitin Sulfate/metabolism, Kinetics, Mutagenesis, Site-Directed, Pedobacter/*enzymology, Polysaccharide-Lyases/chemistry/genetics/*metabolism, Protein Structure, Tertiary, Substrate SpecificityEnzymology
Phylogeny35819898Pedobacter mucosus sp. nov., isolated from a soil sample of glacier foreland in Austre Lovenbreen, Arctic.Huang J, Peng X, Qin K, Liu Y, Niu J, Liu J, Dong J, Zhang Y, Peng FInt J Syst Evol Microbiol10.1099/ijsem.0.0054482022Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Ice Cover, *Pedobacter, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil, Soil MicrobiologyTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1051Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 2366)https://www.dsmz.de/collection/catalogue/details/culture/DSM-2366
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
40684Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16075
45833Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 12810)https://www.ccug.se/strain?id=12810
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)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life 35: 676-683 201728604660
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 updatesNucleic Acids Res. 49: D498-D508 202033211880
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
83260Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID44080.1StrainInfo: A central database for resolving microbial strain identifiers
119875Curators of the CIPCollection of Institut Pasteur (CIP 104194)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104194