Strain identifier

BacDive ID: 14095

Type strain: Yes

Species: Pseudopedobacter saltans

Strain Designation: 113

Strain history: CIP <- 1998, LMG <- P. Steyn: strain 113

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 4555

BacDive-ID: 14095

DSM-Number: 12145

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

description: Pseudopedobacter saltans 113 is an obligate aerobe, mesophilic, Gram-negative bacterium that was isolated from soil.

NCBI tax id

NCBI tax idMatching level
762903strain
151895species

strain history

@refhistory
4555<- LMG
67770IAM 15374 <-- NBRC 100064 <-- LMG 9526 <-- P. Steyn 113.
122408CIP <- 1998, LMG <- P. Steyn: strain 113

doi: 10.13145/bacdive14095.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Sphingobacteriia
  • order: Sphingobacteriales
  • family: Sphingobacteriaceae
  • genus: Pseudopedobacter
  • species: Pseudopedobacter saltans
  • full scientific name: Pseudopedobacter saltans (Steyn et al. 1998) Cao et al. 2014
  • synonyms

    • @ref: 20215
    • synonym: Pedobacter saltans

@ref: 4555

domain: Bacteria

phylum: Bacteroidetes

class: Sphingobacteriia

order: Sphingobacteriales

family: Sphingobacteriaceae

genus: Pseudopedobacter

species: Pseudopedobacter saltans

full scientific name: Pseudopedobacter saltans (Steyn et al. 1998) Cao et al. 2014 emend. Hahnke et al. 2016

strain designation: 113

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative99.999
122408negativerod-shapedno

pigmentation

  • @ref: 122408
  • production: no
  • name: Pyocyanin

multimedia

  • @ref: 66793
  • multimedia content: EM_DSM_12145_1.jpg
  • caption: electron microscopic image
  • intellectual property rights: © HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4555OXOID NUTRIENT BROTH (DSMZ Medium 948)yeshttps://mediadive.dsmz.de/medium/948Name: OXOID NUTRIENT BROTH (DSMZ Medium 948) Composition: Nutrient broth 13.0 g/l Distilled water
36468MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
122408CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
4555positivegrowth28mesophilic
36468positivegrowth25mesophilic
67770positivegrowth25mesophilic
122408positivegrowth25-41
122408nogrowth5psychrophilic
122408nogrowth10psychrophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 122408
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.994

halophily

@refsaltgrowthtested relationconcentration
122408NaClpositivegrowth0-4 %
122408NaClnogrowth6 %
122408NaClnogrowth8 %
122408NaClnogrowth10 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12240816947citrate-carbon source
1224084853esculin+hydrolysis
12240817632nitrate-reduction
12240816301nitrite-reduction
12240817632nitrate-respiration

antibiotic resistance

  • @ref: 122408
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 122408
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
122408oxidase+
122408beta-galactosidase+3.2.1.23
122408alcohol dehydrogenase-1.1.1.1
122408gelatinase-
122408amylase-
122408DNase-
122408caseinase-3.4.21.50
122408catalase+1.11.1.6
122408tween esterase-
122408lecithinase-
122408lipase-
122408lysine decarboxylase-4.1.1.18
122408ornithine decarboxylase-4.1.1.17
122408tryptophan deaminase-
122408urease-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
122408-+++-+----++-+-+++--

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122408+++-+-++-++++--++-+-++++-------+---+-----+------------++---+--------------------------+------------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
4555soilIcelandISLEurope
54759SoilIcelandISLEurope
67770SoilIcelandISLEurope
122408Environment, SoilIcelandISLEurope

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_2492.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_328;96_1344;97_1595;98_1940;99_2492&stattab=map
  • Last taxonomy: Pseudopedobacter saltans subclade
  • 16S sequence: NR_074586
  • Sequence Identity:
  • Total samples: 1251
  • soil counts: 448
  • aquatic counts: 441
  • animal counts: 283
  • plant counts: 79

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
45551Risk group (German classification)
1224081Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Pedobacter saltans strain LMG 10337 16S ribosomal RNA gene, partial sequenceAF329958680ena762903
20218Pedobacter saltans partial 16S rRNA gene, strain DSM 12145TAJ4381731479ena762903
4555Pseudopedobacter saltans DSM 12145 16S ribosomal RNA, partial sequenceNR_0745861517nuccore762903
67770Pedobacter saltans gene for 16S rRNA, partial sequence, strain: NBRC 100064AB6811431454ena151895

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudopedobacter saltans DSM 12145GCA_000190735completencbi762903
66792Pedobacter saltans DSM 12145762903.4completepatric762903
66792Pseudopedobacter saltans DSM 12145649633082completeimg762903

GC content

@refGC-contentmethod
455537.0
455536.6sequence analysis
6777037

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno91.832no
flagellatedno96.952no
gram-positiveno98.3no
anaerobicno98.395no
aerobicyes87.399no
halophileno93.507no
spore-formingno94.004no
glucose-utilyes89.58no
thermophileno97.35yes
glucose-fermentno85.131no

External links

@ref: 4555

culture collection no.: DSM 12145, CCUG 39354, CIP 105500, JCM 21818, LMG 10337, MCCC 1A06472, NBRC 100064, ATCC 51119, IAM 15374, LMG 9526, NCIMB 13643

straininfo link

  • @ref: 83263
  • straininfo: 11927

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
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
Phylogeny24573160Pseudopedobacter beijingensis gen. nov., sp. nov., isolated from coking wastewater activated sludge, and reclassification of Pedobacter saltans as Pseudopedobacter saltans comb. nov.Cao J, Lai Q, Li G, Shao ZInt J Syst Evol Microbiol10.1099/ijs.0.053991-02014Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, China, *Coke, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Pedobacter/classification, Phosphatidylethanolamines/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/microbiology, Vitamin K 2/analogs & derivatives/chemistry, Waste Water/*microbiologyGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4555Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 12145)https://www.dsmz.de/collection/catalogue/details/culture/DSM-12145
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
36468Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17526
54759Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 39354)https://www.ccug.se/strain?id=39354
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/
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
83263Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID11927.1StrainInfo: A central database for resolving microbial strain identifiers
122408Curators of the CIPCollection of Institut Pasteur (CIP 105500)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105500