Strain identifier

BacDive ID: 13065

Type strain: Yes

Species: Pseudomonas synxantha

Strain history: CIP <- 1959, NCIB, Pseudomonas fluorescens <- 1950 ATCC, R.S. Breed, Cornell Univ., New-York, USA, Flavobacterium synthaxum

NCBI tax ID(s): 1215118 (strain), 47883 (species)

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General

@ref: 7789

BacDive-ID: 13065

DSM-Number: 18928

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

description: Pseudomonas synxantha DSM 18928 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from cream.

NCBI tax id

NCBI tax idMatching level
47883species
1215118strain

strain history

@refhistory
7789<- CIP <- NCIB (P. fluorescens) <- ATCC <- R.S. Breed, Cornell Univ. (Flavobacterium synthaxum)
67770IFO 3913 <-- ATCC 9890 <-- R. S. Breed <-- B. W. Hammer.
123400CIP <- 1959, NCIB, Pseudomonas fluorescens <- 1950 ATCC, R.S. Breed, Cornell Univ., New-York, USA, Flavobacterium synthaxum

doi: 10.13145/bacdive13065.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Pseudomonadales
  • family: Pseudomonadaceae
  • genus: Pseudomonas
  • species: Pseudomonas synxantha
  • full scientific name: Pseudomonas synxantha (Ehrenberg 1840) Holland 1920 (Approved Lists 1980)

  • synonyms

    • @ref: 20215
    • synonym: Vibrio synxanthus

@ref: 7789

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pseudomonadales

family: Pseudomonadaceae

genus: Pseudomonas

species: Pseudomonas synxantha

full scientific name: Pseudomonas synxantha (Ehrenberg 1840) Holland 1920

type strain: yes

Morphology

cell morphology

  • @ref: 123400
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7789REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a)yeshttps://mediadive.dsmz.de/medium/1aName: REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
37601MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
123400CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3
123400CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
7789positivegrowth30mesophilic
37601positivegrowth30mesophilic
58786positivegrowth28mesophilic
67770positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
58786aerobe
123400obligate aerobe

spore formation

  • @ref: 123400
  • spore formation: no

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836925115malate+assimilation
6836917128adipate-assimilation
6836927689decanoate+assimilation
6836924265gluconate+assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine+assimilation
6836916899D-mannitol+assimilation
6836916024D-mannose+assimilation
6836930849L-arabinose+assimilation
6836917634D-glucose+assimilation
683695291gelatin+hydrolysis
683694853esculin-hydrolysis
6836916199urea-hydrolysis
6836929016arginine+hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate+reduction
12340017632nitrate+reduction
12340016301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
12340035581indoleyes

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68369cytochrome oxidase+1.9.3.1
68369gelatinase+
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase+3.5.3.6
123400oxidase+
123400catalase+1.11.1.6
123400urease+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
123400-+++-+--+-++--------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
7789+--+--+-+++++-++-++-+
7789+--+--+-+++++-++-++-+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7789creamIowaUSAUSANorth America
58786Cream
67770Cream
123400Food, MilkIowaUnited States of AmericaUSANorth America

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Food production
  • Cat3: #Dairy product

taxonmaps

  • @ref: 69479
  • File name: preview.99_199.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_23;96_61;97_89;98_98;99_199&stattab=map
  • Last taxonomy: Pseudomonas
  • 16S sequence: D84025
  • Sequence Identity:
  • Total samples: 8172
  • soil counts: 874
  • aquatic counts: 1631
  • animal counts: 3216
  • plant counts: 2451

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
77891Risk group (German classification)
1234001Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
7789Pseudomonas synxantha 16S rRNA gene, complete sequenceD840251527ena47883
67770Pseudomonas synxantha gene for 16S rRNA, partial sequence, strain: NBRC 3913AB6801711462ena47883

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudomonas synxantha NCTC10696GCA_901482615completencbi47883
66792Pseudomonas synxantha NBRC 3913 strain NBRC 39131215118.3wgspatric1215118
66792Pseudomonas synxantha strain DSM 1892847883.4wgspatric47883
66792Pseudomonas synxantha strain LMG 219047883.6completepatric47883
66792Pseudomonas synxantha strain NCTC1069647883.23completepatric47883
66792Pseudomonas synxantha LMG 21902667527385draftimg47883
66792Pseudomonas synxantha DSM 189282660238513draftimg47883
67770Pseudomonas synxantha NBRC 3913GCA_002091795contigncbi1215118
67770Pseudomonas synxantha DSM 18928GCA_001439725contigncbi47883
67770Pseudomonas synxantha LMG 2190GCA_900105675chromosomencbi47883

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedyes77.303no
gram-positiveno97.98no
anaerobicno98.205yes
aerobicyes92.012no
halophileno93.344no
spore-formingno94.495no
thermophileno99.896yes
glucose-utilyes94.396no
motileyes90.056no
glucose-fermentno90.575yes

External links

@ref: 7789

culture collection no.: DSM 18928, ATCC 9890, CIP 59.22, LMG 2335, NCDO 757, NCIMB 8178, NCTC 10969, CCUG 50208, NCTC 10696, LMG 2190, NRRL B-780, JCM 11599, CCEB 293, IAM 12356, IFO 3913, NBRC 3913

straininfo link

  • @ref: 82275
  • straininfo: 92404

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Metabolism17578676Regulation of pyrimidine nucleotide biosynthesis in Pseudomonas synxantha.West TPAntonie Van Leeuwenhoek10.1007/s10482-007-9164-42007Aspartate Carbamoyltransferase/metabolism, Dihydroorotase/metabolism, Dihydroorotate Dehydrogenase, *Gene Expression Regulation, Bacterial, Inorganic Pyrophosphatase/pharmacology, Mutation, Orotate Phosphoribosyltransferase/genetics/*metabolism, Orotidine-5'-Phosphate Decarboxylase/metabolism, Oxidoreductases Acting on CH-CH Group Donors/metabolism, Pseudomonas/genetics/*metabolism, Pyrimidine Nucleotides/*biosynthesis, Succinic Acid/metabolism, Uracil/metabolismEnzymology
Phylogeny31922466Pseudomonas carnis sp. nov., isolated from meat.Lick S, Krockel L, Wibberg D, Winkler A, Blom J, Bantleon A, Goesmann A, Kalinowski JInt J Syst Evol Microbiol10.1099/ijsem.0.0039282020Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Food Microbiology, Genes, Bacterial, Germany, Meat/*microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Poultry, Pseudomonas/*classification/isolation & purification, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Swine, Ubiquinone/chemistryBiotechnology
Phylogeny32043958Pseudomonas haemolytica sp. nov., isolated from raw milk and skimmed milk concentrate.Hofmann K, Huptas C, Doll EV, Scherer S, Wenning MInt J Syst Evol Microbiol10.1099/ijsem.0.0040432020Animals, Bacterial Typing Techniques, Base Composition, Cattle, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Food Microbiology, Genes, Bacterial, Milk/*microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pseudomonas/*classification/isolation & purification, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryBiotechnology
Phylogeny34309505Pseudomonas lactucae sp. nov., a pathogen causing bacterial rot of lettuce in Japan.Sawada H, Fujikawa T, Satou MInt J Syst Evol Microbiol10.1099/ijsem.0.0049172021Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Japan, Lettuce/*microbiology, Nucleic Acid Hybridization, *Phylogeny, Plant Diseases/*microbiology, Pseudomonas/*classification/isolation & purification, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome

Reference

@idauthorscataloguedoi/urltitle
7789Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18928)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18928
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
37601Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/9762
58786Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 50208)https://www.ccug.se/strain?id=50208
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68369Automatically annotated from API 20NE
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
82275Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID92404.1StrainInfo: A central database for resolving microbial strain identifiers
123400Curators of the CIPCollection of Institut Pasteur (CIP 59.22)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2059.22