Strain identifier

BacDive ID: 11879

Type strain: Yes

Species: Pseudaminobacter defluvii

Strain Designation: 66

Strain history: CIP <- 2001, IFO, strain: IFO 14570 <- IAM <- Y. Fujimura & H. Kuraishi, THI 051 <- H. Murooka, strain: 66

NCBI tax ID(s): 93380 (species)

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General

@ref: 15814

BacDive-ID: 11879

DSM-Number: 21572

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

description: Pseudaminobacter defluvii 66 is an obligate aerobe, mesophilic, Gram-negative bacterium that was isolated from activated sludge.

NCBI tax id

  • NCBI tax id: 93380
  • Matching level: species

strain history

@refhistory
15814<- NBRC <- IFO <- IAM <- Y. Fujimura and H. Kuraishi; THI 051 <- H. Murooka; 66
67770IAM 12817 <-- Y. Katayama THI 051 <-- H. Murooka 66.
118871CIP <- 2001, IFO, strain: IFO 14570 <- IAM <- Y. Fujimura & H. Kuraishi, THI 051 <- H. Murooka, strain: 66

doi: 10.13145/bacdive11879.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Phyllobacteriaceae
  • genus: Pseudaminobacter
  • species: Pseudaminobacter defluvii
  • full scientific name: Pseudaminobacter defluvii Kämpfer et al. 1999

@ref: 15814

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Phyllobacteriaceae

genus: Pseudaminobacter

species: Pseudaminobacter defluvii

full scientific name: Pseudaminobacter defluvii Kämpfer et al. 1999

strain designation: 66

type strain: yes

Morphology

cell morphology

  • @ref: 118871
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

pigmentation

  • @ref: 118871
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15814R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
33681MEDIUM 127 - for Streptomyces scabiei and Thiobacillus novellusyesDistilled water make up to (1000.000 ml);Magnesium sulphate heptahydrate (0.100 g);Agar (15.000 g);Yeast extract (5.000 g);Potassium di-hydrogen phosphate (1.500 g);Ammonium chloride (0.300 g);Sodium thiosulphate pentahydrate (5.000 g);Di Sodium hydrogen
118871CIP Medium 127yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=127

culture temp

@refgrowthtypetemperaturerange
15814positivegrowth28mesophilic
33681positivegrowth30mesophilic
67770positivegrowth30mesophilic
118871positivegrowth25-37mesophilic
118871nogrowth5psychrophilic
118871nogrowth10psychrophilic
118871nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 118871
  • oxygen tolerance: obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
118871NaClpositivegrowth0-4 %
118871NaClnogrowth6 %
118871NaClnogrowth8 %
118871NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: Q-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11887116947citrate-carbon source
1188714853esculin-hydrolysis
11887117632nitrate-reduction
11887116301nitrite-reduction
11887117632nitrate-respiration

antibiotic resistance

  • @ref: 118871
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 118871
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
118871oxidase+
118871beta-galactosidase-3.2.1.23
118871alcohol dehydrogenase-1.1.1.1
118871gelatinase-
118871amylase-
118871DNase-
118871caseinase-3.4.21.50
118871catalase+1.11.1.6
118871tween esterase+
118871lecithinase+
118871lipase-
118871lysine decarboxylase-4.1.1.18
118871ornithine decarboxylase-4.1.1.17
118871protease-
118871tryptophan deaminase+
118871urease-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
118871-----+--+-----------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
118871----------------------------------------------------------+---+--+------------+-------+------------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
15814activated sludgeJapanJPNAsia
67770Activated sludge
118871Environment, Activated sludge

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Waste
  • Cat3: #Activated sludge

taxonmaps

  • @ref: 69479
  • File name: preview.99_62299.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_220;97_1977;98_12690;99_62299&stattab=map
  • Last taxonomy: Mesorhizobium
  • 16S sequence: D32248
  • Sequence Identity:
  • Total samples: 37
  • soil counts: 9
  • aquatic counts: 12
  • animal counts: 10
  • plant counts: 6

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
158141Risk group (German classification)
1188711Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Pseudaminobacter defluvii gene for 16S rRNA, partial sequence, strain: NBRC 14570AB6806361409ena93380
15814Pseudaminobacter defluvii gene for 16S rRNA, partial sequence, strain: THI 051D322481406ena93380

GC content

  • @ref: 67770
  • GC-content: 62.9
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 15814

culture collection no.: DSM 21572, CIP 107185, IAM 12817, IFO 14570, JCM 20757, NBRC 14570, THI 051, KCTC 2844

straininfo link

  • @ref: 81096
  • straininfo: 62615

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny10319515Description of Pseudaminobacter gen. nov. with two new species, Pseudaminobacter salicylatoxidans sp. nov. and Pseudaminobacter defluvii sp. nov.Kampfer P, Muller C, Mau M, Neef A, Auling G, Busse HJ, Osborn AM, Stolz AInt J Syst Bacteriol10.1099/00207713-49-2-8871999Bacterial Typing Techniques, Base Composition, Biodegradation, Environmental, DNA, Bacterial/analysis/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Gram-Negative Aerobic Bacteria/*classification/cytology/isolation & purification/metabolism, Molecular Sequence Data, Naphthalenesulfonates/*metabolism, Nucleic Acid Hybridization, RNA, Ribosomal, 16S/genetics, Sewage/microbiology, Water MicrobiologyMetabolism
Phylogeny28036252Pseudaminobacter manganicus sp. nov., isolated from sludge of a manganese mine.Li J, Huang J, Liao S, Wang GInt J Syst Evol Microbiol10.1099/ijsem.0.0017652017Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Manganese, *Mining, Nucleic Acid Hybridization, Phospholipids/chemistry, Phyllobacteriaceae/*classification/genetics/isolation & purification, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Spermidine/analogs & derivatives/chemistry, Ubiquinone/chemistryTranscriptome
Phylogeny28752296Pseudaminobacter granuli sp. nov., isolated from granules used in a wastewater treatment plant.Hahn YK, Kim MS, Im WTJ Microbiol10.1007/s12275-017-7257-y2017Aerobiosis, Bacterial Typing Techniques, Base Composition, Cluster Analysis, Culture Media/chemistry, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Locomotion, Microscopy, Electron, Scanning, Nucleic Acid Hybridization, Phospholipids/analysis, Phyllobacteriaceae/*classification/genetics/*isolation & purification/physiology, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Temperature, Waste Water/*microbiologyTranscriptome
Phylogeny30676307Pseudaminobacter arsenicus sp. nov., an arsenic-resistant bacterium isolated from arsenic-rich aquifers.Mu Y, Zhou X, Liu L, Zhou XK, Zeng XC, Li WJInt J Syst Evol Microbiol10.1099/ijsem.0.0032382019*Arsenic, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Groundwater/*microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, Phyllobacteriaceae/*classification/isolation & purification, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
15814Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21572)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21572
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
33681Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4592
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
81096Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID62615.1StrainInfo: A central database for resolving microbial strain identifiers
118871Curators of the CIPCollection of Institut Pasteur (CIP 107185)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107185