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, rod-shaped

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
984species
485917strain

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/bacdive14092.20250331.9.3

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

  • synonyms

    @refsynonym
    20215Sphingobacterium heparinum
    20215Flavobacterium 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 staincell shapemotilityconfidence
119875negativerod-shapedno
125439negative97
125438negative97.478

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

@refgrowthtypetemperature
1051positivegrowth25-30
40684positivegrowth30
67770positivegrowth30
119875positivegrowth25-30
119875nogrowth10
119875nogrowth37
119875nogrowth41

Physiology and metabolism

oxygen tolerance

  • @ref: 119875
  • oxygen tolerance: obligate aerobe

compound production

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

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11987516947citrate-carbon source
1198754853esculin+hydrolysis
11987517234glucose-fermentation
11987517716lactose-fermentation
11987517632nitrate-reduction
11987516301nitrite-reduction
119875132112sodium thiosulfate-builds gas from
68371Potassium 5-ketogluconate-builds acid from
6837127613amygdalin-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837116899D-mannitol-builds acid from
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
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837117814salicin-builds acid from
683714853esculin+builds acid from
6837118305arbutin-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
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

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 12017AB6802151447nuccore984
20218Pedobacter heparinus partial 16S rRNA gene, strain DSM 2366TAJ4381721482nuccore485917
124043Pedobacter heparinus strain LMG 10339 16S ribosomal RNA gene, partial sequence.AF329951681nuccore485917
124043Pedobacter heparinus strain LMG 10344 16S ribosomal RNA gene, partial sequence.AF329952681nuccore984

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

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno97.478no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no95.521no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes86.524yes
125438spore-formingspore-formingAbility to form endo- or exosporesno85.912no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno97.1yes
125438motile2+flagellatedAbility to perform flagellated movementno83.5no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno85
125439BacteriaNetmotilityAbility to perform movementno55.7
125439BacteriaNetgram_stainReaction to gram-stainingnegative97
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe84.9

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
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
124043Isabel Schober, Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy
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