Strain identifier

BacDive ID: 5707

Type strain: Yes

Species: Chryseobacterium solincola

Strain Designation: 1YB-R12

Strain history: CIP <- 2010, M-L Fardeau, Provence and Méd. Univ., Marseille, France: strain 1YB-R12

NCBI tax ID(s): 510955 (species)

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General

@ref: 16355

BacDive-ID: 5707

DSM-Number: 22468

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

description: Chryseobacterium solincola 1YB-R12 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from hydrocarbon-polluted soil.

NCBI tax id

  • NCBI tax id: 510955
  • Matching level: species

strain history

@refhistory
16355<- M. L. Fardeau, Lab. Microbiol. de l'IRD/ESIL, Univ. de Provence et de la Méditerranée, Marseille, France; 1YB-R12 <- Y. Benmalek
122672CIP <- 2010, M-L Fardeau, Provence and Méd. Univ., Marseille, France: strain 1YB-R12

doi: 10.13145/bacdive5707.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Weeksellaceae
  • genus: Chryseobacterium
  • species: Chryseobacterium solincola
  • full scientific name: Chryseobacterium solincola Benmalek et al. 2010

  • synonyms

    • @ref: 20215
    • synonym: Kaistella solincola

@ref: 16355

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Weeksellaceae

genus: Chryseobacterium

species: Chryseobacterium solincola

full scientific name: Chryseobacterium solincola Benmalek et al. 2010 emend. Hahnke et al. 2016

strain designation: 1YB-R12

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29207negative0.9-4 µm0.5-1 µmovoid-shapedno
69480no92.281
69480negative99.968
122672negativerod-shapedno

pigmentation

  • @ref: 29207
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16355LB (Luria-Bertani) MEDIUM (DSMZ Medium 381)yeshttps://mediadive.dsmz.de/medium/381Name: LB (Luria-Bertani) MEDIUM (DSMZ Medium 381) Composition: Agar 20.0 g/l NaCl 10.0 g/l Tryptone 10.0 g/l Yeast extract 5.0 g/l Distilled water
37579MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
122672CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
16355positivegrowth28mesophilic
29207positivegrowth04-37
29207positiveoptimum28-30mesophilic
37579positivegrowth30mesophilic
60666positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
29207positivegrowth05-11alkaliphile
29207positiveoptimum7.3-8

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29207aerobe
60666aerobe
122672obligate aerobe

spore formation

@refspore formationconfidence
29207no
69481no100
69480no99.993
122672no

halophily

@refsaltgrowthtested relationconcentration
29207NaClpositivegrowth0-6 %
29207NaClpositiveoptimum4 %

observation

  • @ref: 29207
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2920717234glucose+carbon source
2920717632nitrate+reduction
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837117992sucrose-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117057cellobiose-builds acid from
6837117814salicin-builds acid from
683714853esculin-builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose-builds acid from
6837115824D-fructose-builds acid from
6837112936D-galactose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837116988D-ribose-builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
12267217632nitrate-reduction
12267216301nitrite-reduction

metabolite production

  • @ref: 122672
  • Chebi-ID: 35581
  • metabolite: indole
  • production: yes

enzymes

@refvalueactivityec
29207urease+3.5.1.5
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
122672oxidase-
122672catalase+1.11.1.6
122672urease-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
122672-+++++++-+++---+----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
122672----------+/-----------------+/--------+/-+/-------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling dateisolation date
16355hydrocarbon-polluted soilWestern Algeria, Meftah cityAlgeriaDZAAfrica
60666Soil of petrol stationMefteh CityAlgeriaDZAAfrica2006-04-01
122672Environment, SoilWesternAlgeriaDZAAfrica2006

isolation source categories

Cat1Cat2Cat3
#Engineered#Contamination
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_6762.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_76;96_1132;97_1328;98_4988;99_6762&stattab=map
  • Last taxonomy: Kaistella
  • 16S sequence: EU516352
  • Sequence Identity:
  • Total samples: 1593
  • soil counts: 196
  • aquatic counts: 491
  • animal counts: 807
  • plant counts: 99

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
163551Risk group (German classification)
1226721Risk group (French classification)

Sequence information

16S sequences

  • @ref: 16355
  • description: Chryseobacterium solincola strain 1YB-R12 16S ribosomal RNA gene, partial sequence
  • accession: EU516352
  • length: 1473
  • database: ena
  • NCBI tax ID: 510955

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Kaistella solincola DSM 22468GCA_000812875contigncbi510955
66792Chryseobacterium solincola DSM 22468510955.4wgspatric510955
66792Chryseobacterium solincola DSM 224682634166404draftimg510955

GC content

@refGC-contentmethod
1635540.9high performance liquid chromatography (HPLC)
2920740.9
1635539.5sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno98.357yes
anaerobicno99.114no
halophileno81.795no
spore-formingno96.518no
glucose-utilyes85.746yes
aerobicyes88.436no
thermophileno99.165no
motileno91.596yes
flagellatedno96.981yes
glucose-fermentno93.54no

External links

@ref: 16355

culture collection no.: DSM 22468, CCUG 55604, DSM 1183, CIP 110201

straininfo link

  • @ref: 75189
  • straininfo: 370342

literature

  • topic: Phylogeny
  • Pubmed-ID: 19767354
  • title: Chryseobacterium solincola sp. nov., isolated from soil.
  • authors: Benmalek Y, Cayol JL, Bouanane NA, Hacene H, Fauque G, Fardeau ML
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.008631-0
  • year: 2009
  • mesh: Chryseobacterium/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
16355Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22468)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22468
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
29207Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2562828776041
37579Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/8034
60666Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 55604)https://www.ccug.se/strain?id=55604
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 updates33211880Nucleic Acids Res. 49: D498-D508 2020
68371Automatically annotated from API 50CH acid
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
75189Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID370342.1StrainInfo: A central database for resolving microbial strain identifiers
122672Curators of the CIPCollection of Institut Pasteur (CIP 110201)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110201