Strain identifier

BacDive ID: 2981

Type strain: Yes

Species: Roseateles saccharophilus

Strain history: CIP <- 2008, DSMZ <- ATCC <- M. Doudoroff, California Univ., USA: strain IAM

NCBI tax ID(s): 304 (species)

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General

@ref: 246

BacDive-ID: 2981

DSM-Number: 654

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, motile

description: Roseateles saccharophilus DSM 654 is an obligate aerobe, mesophilic, motile bacterium that was isolated from water.

NCBI tax id

  • NCBI tax id: 304
  • Matching level: species

strain history

@refhistory
246<- ATCC <- M. Doudoroff
67770DSM 654 <-- ATCC 15946 <-- M. Doudoroff.
122338CIP <- 2008, DSMZ <- ATCC <- M. Doudoroff, California Univ., USA: strain IAM

doi: 10.13145/bacdive2981.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Comamonadaceae
  • genus: Roseateles
  • species: Roseateles saccharophilus
  • full scientific name: Roseateles saccharophilus (Doudoroff 1940) Liu et al. 2023

  • synonyms

    @refsynonym
    20215Pelomonas saccharophila
    20215Pseudomonas saccharophila

@ref: 246

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Comamonadaceae

genus: Pelomonas

species: Pelomonas saccharophila

full scientific name: Pelomonas saccharophila (Doudoroff 1940) Xie and Yokota 2005

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes93.178
6948099.985negative
122338yesnegativerod-shaped

pigmentation

  • @ref: 122338
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
246MINERAL MEDIUM FOR CHEMOLITHOTROPHIC GROWTH (H-3) (DSMZ Medium 81)yeshttps://mediadive.dsmz.de/medium/81Name: MINERAL MEDIUM FOR CHEMOLITHOTROPHIC GROWTH (H-3) (DSMZ Medium 81) Composition: Agar 20.1005 g/l Na2HPO4 x 2 H2O 2.91457 g/l KH2PO4 2.31156 g/l NH4Cl 1.00503 g/l MgSO4 x 7 H2O 0.502512 g/l Ferric ammonium citrate 0.0502513 g/l CaCl2 x 2 H2O 0.0100503 g/l NaVO3 x H2O 0.00502512 g/l Calcium pantothenate 0.00251256 g/l Pyridoxine hydrochloride 0.00251256 g/l Nicotinic acid 0.00251256 g/l Thiamine-HCl x 2 H2O 0.00251256 g/l H3BO3 0.00150754 g/l CoCl2 x 6 H2O 0.00100503 g/l Riboflavin 0.000502513 g/l ZnSO4 x 7 H2O 0.000502513 g/l MnCl2 x 4 H2O 0.000150754 g/l Na2MoO4 x 2 H2O 0.000150754 g/l NiCl2 x 6 H2O 0.000100503 g/l CuCl2 x 2 H2O 5.02513e-05 g/l Vitamin B12 5.02513e-05 g/l Folic acid 1.00503e-05 g/l Biotin 5.02513e-06 g/l Distilled water
246NUTRIENT 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
37699MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
122338CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3
122338CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
122338CIP Medium 328yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=328

culture temp

@refgrowthtypetemperaturerange
246positivegrowth30mesophilic
37699positivegrowth30mesophilic
67770positivegrowth30mesophilic
122338positivegrowth25-37mesophilic
122338nogrowth5psychrophilic
122338nogrowth10psychrophilic
122338nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 122338
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no99
69480no99.918

halophily

@refsaltgrowthtested relationconcentration
122338NaClpositivegrowth0-4 %
122338NaClnogrowth6 %
122338NaClnogrowth8 %
122338NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12233816947citrate-carbon source
1223384853esculin+hydrolysis
12233817632nitrate-reduction
12233816301nitrite-reduction
12233817632nitrate-respiration

antibiotic resistance

  • @ref: 122338
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 122338
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase+3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin+3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
122338oxidase+
122338beta-galactosidase+3.2.1.23
122338alcohol dehydrogenase-1.1.1.1
122338gelatinase+/-
122338amylase-
122338DNase-
122338caseinase-3.4.21.50
122338catalase+1.11.1.6
122338tween esterase-
122338lecithinase-
122338lipase-
122338lysine decarboxylase-4.1.1.18
122338ornithine decarboxylase-4.1.1.17
122338tryptophan deaminase-
122338urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
122338-+++-++--+++-+-++---

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122338+++++-+++++++++++++-++++----------++-----+-------+---++-----+-+++----------++-+++-------++++----++-

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentisolation date
246water
67770Mud from a stagnant pool
122338Environment, WaterUnited States of AmericaUSANorth America1940

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic

taxonmaps

  • @ref: 69479
  • File name: preview.99_12880.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_1;96_1238;97_1469;98_4049;99_12880&stattab=map
  • Last taxonomy: Pelomonas
  • 16S sequence: AM501432
  • Sequence Identity:
  • Total samples: 3097
  • soil counts: 199
  • aquatic counts: 1061
  • animal counts: 1602
  • plant counts: 235

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
2461Risk group (German classification)
1223381Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Pelomonas saccharophila partial 16S rRNA gene, type strain ATCC 15946TAM5014281471ena304
20218Pelomonas saccharophila partial 16S rRNA gene, type strain CCUG 32988TAM5014291391ena304
20218Pelomonas saccharophila gene for 16S rRNA, strain: DSM 654AB0214071502ena304
20218Pelomonas saccharophila partial 16S rRNA gene, type strain DSM 654TAM5014311345ena304
20218Pelomonas saccharophila partial 16S rRNA gene, type strain IAM 14368TAM5014321391ena304
20218Pelomonas saccharophila partial 16S rRNA gene, type strain LMG 2256TAM5014301386ena304
20218Pelomonas saccharophila gene for 16S rRNA, partial sequence, strain: NBRC 103037AB6819171449ena304

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pelomonas saccharophila strain DSM 654304.35wgspatric304
66792Pelomonas saccharophila DSM 6542802428851draftimg304
67770Pelomonas saccharophila DSM 654GCA_004342485scaffoldncbi304

GC content

@refGC-contentmethod
24668.9
6777069.1high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
gram-positiveno98.592no
anaerobicno98.222no
halophileno97.515no
spore-formingno93.978no
glucose-utilyes85.205no
motileyes88.515no
flagellatedyes81.297no
aerobicyes84.203no
thermophileno98.596yes
glucose-fermentno87.541no

External links

@ref: 246

culture collection no.: DSM 654, ATCC 15946, CFBP 2433, CIP 59.18, HAMBI 373, IAM 14368, JCM 15912, LMG 2256, NCCB 46053, VKM B-902, CCUG 32988, BUCSAV 293, CCM 1980, CCUG 15839, IAM 1504, JCM 21181, LMG 7831, NBRC 103037, NCDO 1936, NCIMB 8570, NRRL B-1492, JCM 13309

straininfo link

  • @ref: 72503
  • straininfo: 100388

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16280506Reclassification of Alcaligenes latus strains IAM 12599T and IAM 12664 and Pseudomonas saccharophila as Azohydromonas lata gen. nov., comb. nov., Azohydromonas australica sp. nov. and Pelomonas saccharophila gen. nov., comb. nov., respectively.Xie CH, Yokota AInt J Syst Evol Microbiol10.1099/ijs.0.63733-02005Alcaligenes/*classification/genetics/isolation & purification/physiology, Base Composition, Comamonadaceae/*classification/genetics/isolation & purification/physiology, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Fatty Acids/analysis/isolation & purification, Molecular Sequence Data, Nitrogen Fixation, Nucleic Acid Hybridization, Phenazines, Phylogeny, Pseudomonas/*classification/genetics/isolation & purification, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/analysis/genetics, Sequence Analysis, DNAEnzymology
Phylogeny17978231Description of Pelomonas aquatica sp. nov. and Pelomonas puraquae sp. nov., isolated from industrial and haemodialysis water.Gomila M, Bowien B, Falsen E, Moore ERB, Lalucat JInt J Syst Evol Microbiol10.1099/ijs.0.65149-02007Bacterial Proteins/genetics, Bacterial Typing Techniques, Betaproteobacteria/*classification/genetics/*isolation & purification/physiology, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, DNA, Ribosomal Spacer/analysis, Fatty Acids/analysis, Genotype, *Industry, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, *Renal Dialysis, Sequence Analysis, DNA, *Water MicrobiologyGenetics
Phylogeny28671521Paucibacter oligotrophus sp. nov., isolated from fresh water, and emended description of the genus Paucibacter.Pheng S, Lee JJ, Eom MK, Lee KH, Kim SGInt J Syst Evol Microbiol10.1099/ijsem.0.0019312017Bacterial Typing Techniques, Base Composition, Burkholderiaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fresh Water/*microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
246Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 654)https://www.dsmz.de/collection/catalogue/details/culture/DSM-654
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
37699Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/9758
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)
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
72503Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID100388.1StrainInfo: A central database for resolving microbial strain identifiers
122338Curators of the CIPCollection of Institut Pasteur (CIP 59.18)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2059.18