Strain identifier

BacDive ID: 22941

Type strain: Yes

Species: Paenochrobactrum gallinarii

Strain Designation: Sa-25

Strain history: <- P. Kämpfer; Sa-25 <- E. Martin

NCBI tax ID(s): 643673 (species)

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General

@ref: 19102

BacDive-ID: 22941

DSM-Number: 22336

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

description: Paenochrobactrum gallinarii Sa-25 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from air of a duck barn.

NCBI tax id

  • NCBI tax id: 643673
  • Matching level: species

strain history

  • @ref: 19102
  • history: <- P. Kämpfer; Sa-25 <- E. Martin

doi: 10.13145/bacdive22941.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Brucellaceae
  • genus: Paenochrobactrum
  • species: Paenochrobactrum gallinarii
  • full scientific name: Paenochrobactrum gallinarii Kämpfer et al. 2010

@ref: 19102

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Brucellaceae

genus: Paenochrobactrum

species: Paenochrobactrum gallinarii

full scientific name: Paenochrobactrum gallinarii Kämpfer et al. 2010

strain designation: Sa-25

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell shapemotilityconfidence
29559negative2 µmrod-shapedno
69480negative99.824

colony morphology

@refincubation period
191021-2 days
614341 day

Culture and growth conditions

culture medium

  • @ref: 19102
  • name: CASO AGAR (MERCK 105458) (DSMZ Medium 220)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/220
  • composition: Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
19102positivegrowth28mesophilic
29559positivegrowth25-30mesophilic
61434positivegrowth30-37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29559aerobe
61434aerobe

spore formation

@refspore formationconfidence
29559no
69481no100
69480no99.996

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2955916449alanine+carbon source
2955917234glucose+carbon source
2955924996lactate+carbon source
2955917272propionate+carbon source
6836925115malate-assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
683695291gelatin-hydrolysis
683694853esculin-hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

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

enzymes

@refvalueactivityec
19102cytochrome-c oxidase+1.9.3.1
29559cytochrome oxidase+1.9.3.1
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
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
61434-----+--+-----------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
19102--------------------+
61434--------+--+--+----++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
19102air of a duck barnBerlinGermanyDEUEurope
61434Air,duck barnBerlinGermanyDEUEurope

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture#Livestock (Husbandry)
#Environmental#Air#Indoor Air
#Host#Birds

taxonmaps

  • @ref: 69479
  • File name: preview.99_72500.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_14385;97_17544;98_21800;99_72500&stattab=map
  • Last taxonomy: Paenochrobactrum
  • 16S sequence: FN391023
  • Sequence Identity:
  • Total samples: 37
  • soil counts: 4
  • aquatic counts: 10
  • animal counts: 14
  • plant counts: 9

Safety information

risk assessment

  • @ref: 19102
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 19102
  • description: Paenochrobactrum gallinarii partial 16S rRNA gene, type strain Sa25T
  • accession: FN391023
  • length: 1345
  • database: ena
  • NCBI tax ID: 643673

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paenochrobactrum gallinarii DSM 22336GCA_014205685scaffoldncbi643673
66792Paenochrobactrum gallinarii strain DSM 22336643673.3wgspatric643673
66792Paenochrobactrum gallinarii DSM 223362828294024draftimg643673

GC content

@refGC-contentmethod
1910249.7high performance liquid chromatography (HPLC)
2955949.7

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno96.55yes
gram-positiveno97.94no
anaerobicno97.812yes
aerobicyes92.323yes
halophileno83.979no
spore-formingno96.624no
glucose-utilyes86.928yes
thermophileno90.037yes
motileno89.293yes
glucose-fermentno91.681yes

External links

@ref: 19102

culture collection no.: DSM 22336, CCM 7656, CCUG 57736

straininfo link

  • @ref: 87189
  • straininfo: 403298

literature

  • topic: Phylogeny
  • Pubmed-ID: 19684318
  • title: Paenochrobactrum gallinarii gen. nov., sp. nov., isolated from air of a duck barn, and reclassification of Pseudochrobactrum glaciei as Paenochrobactrum glaciei comb. nov.
  • authors: Kampfer P, Martin E, Lodders N, Jackel U, Huber BE, Schumann P, Langer S, Busse HJ, Scholz H
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.015842-0
  • year: 2009
  • mesh: Agriculture, *Air Microbiology, Animals, Base Sequence, Brucellaceae/*classification/genetics/isolation & purification/physiology, Ducks, Fatty Acids/analysis, Molecular Sequence Data, Ochrobactrum/classification, Phylogeny, RNA, Ribosomal, 16S/genetics
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
19102Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22336)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22336
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
29559Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2595428776041
61434Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 57736)https://www.ccug.se/strain?id=57736
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)
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
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
87189Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID403298.1StrainInfo: A central database for resolving microbial strain identifiers