Strain identifier

BacDive ID: 14100

Type strain: Yes

Species: Pedobacter terrae

Strain Designation: DS-57

Strain history: <- JH Yoon, KRIBB

NCBI tax ID(s): 405671 (species)

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General

@ref: 7174

BacDive-ID: 14100

DSM-Number: 17933

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

description: Pedobacter terrae DS-57 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 405671
  • Matching level: species

strain history

@refhistory
7174<- J.-H. Yoon, Korea Res. Inst. of Biosci. and Biotechnol. (KRIBB); DS-57
67771<- JH Yoon, KRIBB

doi: 10.13145/bacdive14100.20250331.9.3

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 terrae
  • full scientific name: Pedobacter terrae Yoon et al. 2007

@ref: 7174

domain: Bacteria

phylum: Bacteroidetes

class: Sphingobacteriia

order: Sphingobacteriales

family: Sphingobacteriaceae

genus: Pedobacter

species: Pedobacter terrae

full scientific name: Pedobacter terrae Yoon et al. 2007

strain designation: DS-57

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31965negative2.15 µm0.4 µmrod-shapedno
67771rod-shaped
67771negative
125439negative99.8
125438negative96.444

pigmentation

  • @ref: 31965
  • production: no

Culture and growth conditions

culture medium

  • @ref: 7174
  • name: NUTRIENT AGAR (DSMZ Medium 1)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1
  • composition: Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water

culture temp

@refgrowthtypetemperature
7174positivegrowth25
31965positivegrowth04-35
31965positiveoptimum25
67771positivegrowth25

culture pH

@refabilitytypepHPH range
31965positivegrowth5.5-9.0alkaliphile
31965positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
67771aerobe
125439obligate aerobe98.3

spore formation

@refspore formationconfidence
31965no
67771no
125439no99.1

halophily

@refsaltgrowthtested relationconcentration
31965NaClpositivegrowth<3 %
31965NaClpositiveoptimum0.5 %

observation

  • @ref: 67771
  • observation: quinones: MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3196522599arabinose+carbon source
3196517057cellobiose+carbon source
3196528757fructose+carbon source
3196528260galactose+carbon source
3196517234glucose+carbon source
3196517716lactose+carbon source
3196517306maltose+carbon source
3196537684mannose+carbon source
3196528053melibiose+carbon source
3196537657methyl D-glucoside+carbon source
31965506227N-acetylglucosamine+carbon source
3196517814salicin+carbon source
3196517992sucrose+carbon source
3196527082trehalose+carbon source
3196518222xylose+carbon source
319654853esculin+hydrolysis

enzymes

@refvalueactivityec
31965acid phosphatase+3.1.3.2
31965alkaline phosphatase+3.1.3.1
31965catalase+1.11.1.6
31965gelatinase+
31965cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7174soilDokdoRepublic of KoreaKORAsia
67771From soilDokdoRepublic of KoreaKORAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_8774.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_115;96_1456;97_1737;98_3423;99_8774&stattab=map
  • Last taxonomy: Pedobacter
  • 16S sequence: DQ889723
  • Sequence Identity:
  • Total samples: 565
  • soil counts: 113
  • aquatic counts: 64
  • animal counts: 279
  • plant counts: 109

Safety information

risk assessment

  • @ref: 7174
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 7174
  • description: Pedobacter terrae strain DS-57 16S ribosomal RNA gene, partial sequence
  • accession: DQ889723
  • length: 1477
  • database: nuccore
  • NCBI tax ID: 405671

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pedobacter terrae DSM 17933GCA_900100705scaffoldncbi405671
66792Pedobacter terrae strain DSM 17933405671.6wgspatric405671
66792Pedobacter terrae DSM 179332675903222draftimg405671

GC content

@refGC-contentmethod
717439.7high performance liquid chromatography (HPLC)
3196539.7

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno96.444no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no95.928yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes86.673yes
125438spore-formingspore-formingAbility to form endo- or exosporesno84.165yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno96.99yes
125438motile2+flagellatedAbility to perform flagellated movementno83no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno99.1
125439BacteriaNetmotilityAbility to perform movementno77.7
125439BacteriaNetgram_stainReaction to gram-stainingnegative99.8
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe98.3

External links

@ref: 7174

culture collection no.: DSM 17933, KCTC 12762, CCM 9056

straininfo link

  • @ref: 83268
  • straininfo: 402122

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17978200Pedobacter terrae sp. nov., isolated from soil.Yoon JH, Kang SJ, Oh TKInt J Syst Evol Microbiol10.1099/ijs.0.64727-02007Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/*isolation & purification/physiology, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyGenetics
Phylogeny22990491Pedobacter kyungheensis sp. nov., with ginsenoside converting activity.Yang JE, Shin JY, Park SY, T Mavlonov G, Yi EJ, Lee EH, Lee JM, Yi THJ Gen Appl Microbiol10.2323/jgam.58.3092012Aerobiosis, Bacterial Typing Techniques, Base Composition, Biotransformation, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Ginsenosides/*metabolism, Hydrogen-Ion Concentration, Molecular Sequence Data, Nucleic Acid Hybridization, Panax/growth & development, Pedobacter/*classification/*isolation & purification/metabolism/physiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Sodium Chloride/metabolism, Soil Microbiology, Temperature, beta-Glucosidase/metabolismMetabolism
Phylogeny27600161Pedobacter vanadiisoli sp. nov., isolated from soil of a vanadium mine.Wang Z, Tan Y, Xu D, Wang G, Yuan J, Zheng SInt J Syst Evol Microbiol10.1099/ijsem.0.0014802016Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, *Mining, Nucleic Acid Hybridization, Pedobacter/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, *Vanadium, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny27902277Pedobacter zeae sp. nov., an endophytic bacterium isolated from maize root.Gao JL, Sun P, Mao XJ, Du YL, Liu BY, Sun JGInt J Syst Evol Microbiol10.1099/ijsem.0.0016032017Bacterial Typing Techniques, Base Composition, Beijing, DNA, Bacterial/genetics, Endophytes/classification/genetics/isolation & purification, Fatty Acids/chemistry, Pedobacter/*classification/genetics/isolation & purification, Phosphatidylethanolamines/chemistry, *Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/analogs & derivatives/chemistry, Vitamin K 2/analogs & derivatives/chemistry, Zea mays/*microbiologyEnzymology
Phylogeny28875920Pedobacter ardleyensis sp. nov., isolated from soil in Antarctica.Da X, Jiang F, Chang X, Ren L, Qiu X, Kan W, Zhang Y, Deng S, Fang C, Peng FInt J Syst Evol Microbiol10.1099/ijsem.0.0005042015
Phylogeny29047421Pedobacter kyonggii sp. nov., a psychrotolerant bacterium isolated from forest soil.Chaudhary DK, Lee SD, Kim JInt J Syst Evol Microbiol10.1099/ijsem.0.0024282017Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Forests, Glycolipids/chemistry, Nucleic Acid Hybridization, Pedobacter/*classification/genetics/isolation & purification, Phosphatidylethanolamines/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny35442878Pedobacter fastidiosus sp. nov., isolated from glacial habitats of maritime Antarctica.Svec P, Kralova S, Stankova E, Holochova P, Sedlar K, Koudelkova S, Krsek D, Grzesiak J, Sedo O, Vaczi P, Urvashi, Gupta V, Sood U, Lal R, Korpole S, Sedlacek IInt J Syst Evol Microbiol10.1099/ijsem.0.0053092022Antarctic Regions, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Ecosystem, Fatty Acids/chemistry, *Pedobacter, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7174Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17933)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17933
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
31965Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2822028776041
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)
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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
83268Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID402122.1StrainInfo: A central database for resolving microbial strain identifiers
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