Strain identifier

BacDive ID: 5688

Type strain: Yes

Species: Chryseobacterium gregarium

Strain Designation: P 461/12

Strain history: CIP <- 2010, DSMZ <- U. Behrendt, ZALF, Müncheberg, Germany: strain P 461/12

NCBI tax ID(s): 1121287 (strain), 456299 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 7896

BacDive-ID: 5688

DSM-Number: 19109

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

description: Chryseobacterium gregarium P 461/12 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from decaying plant material, litter layer.

NCBI tax id

NCBI tax idMatching level
456299species
1121287strain

strain history

@refhistory
7896<- U. Behrendt, Leibniz-Centre Agricult. Landscape Res. (ZALF), Inst. Landscape Matter Dynamics, Müncheberg; P 461/12
119735CIP <- 2010, DSMZ <- U. Behrendt, ZALF, Müncheberg, Germany: strain P 461/12

doi: 10.13145/bacdive5688.20230509.8.1

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 gregarium
  • full scientific name: Chryseobacterium gregarium Behrendt et al. 2008

@ref: 7896

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Weeksellaceae

genus: Chryseobacterium

species: Chryseobacterium gregarium

full scientific name: Chryseobacterium gregarium Behrendt et al. 2008 emend. Montero-Calasanz et al. 2013 emend. Loch and Faisal 2014

strain designation: P 461/12

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32474negative1.85 µm0.7 µmrod-shapedno
69480no90.697
69480negative99.982
119735negativerod-shaped

pigmentation

  • @ref: 32474
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7896NUTRIENT 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
33350MEDIUM 328- for nutrient agaryesDistilled water make up to (1000.000 ml);Agar (15.000 g);Peptone (5.000g);Beef extract (3.000 g)
119735CIP Medium 328yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=328

culture temp

@refgrowthtypetemperaturerange
7896positivegrowth21-30
32474positivegrowth04-30
32474positiveoptimum25mesophilic
33350positivegrowth25mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32474aerobe
119735obligate aerobe

spore formation

@refspore formationconfidence
32474no
69481no100
69480no99.995

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3247422599arabinose+carbon source
3247417234glucose+carbon source
3247417306maltose+carbon source
3247437684mannose+carbon source
3247433942ribose+carbon source
3247417814salicin+carbon source
3247417992sucrose+carbon source
3247427082trehalose+carbon source
324744853esculin+hydrolysis
11973517632nitrate-reduction
11973516301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
3247435581indoleyes
11973535581indoleyes

metabolite tests

  • @ref: 32474
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: +

enzymes

@refvalueactivityec
32474acid phosphatase+3.1.3.2
32474alkaline phosphatase+3.1.3.1
32474catalase+1.11.1.6
32474gelatinase+
32474cytochrome oxidase+1.9.3.1
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
119735oxidase+
119735catalase+1.11.1.6
119735urease-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
119735-+++-++-+-++----++--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7896decaying plant material, litter layerBrandenburg, Havelland, PaulinenaueGermanyDEUEurope
119735Decaying plant material, litter layerBrandenburgGermanyDEUEurope

isolation source categories

  • Cat1: #Host
  • Cat2: #Plants
  • Cat3: #Decomposing plant

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
78961Risk group (German classification)
1197351Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7896
  • description: Chryseobacterium gregarium partial 16S rRNA gene, type strain DSM 19109T
  • accession: AM773820
  • length: 1462
  • database: ena
  • NCBI tax ID: 1121287

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Chryseobacterium gregarium DSM 19109GCA_000430845scaffoldncbi1121287
66792Chryseobacterium gregarium DSM 191091121287.4wgspatric1121287
66792Chryseobacterium gregarium DSM 191092523533548draftimg1121287

GC content

  • @ref: 7896
  • GC-content: 38.4

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno90.568yes
flagellatedno96.804yes
gram-positiveno97.991yes
anaerobicno99.465yes
aerobicyes91.698yes
halophileno93.706no
spore-formingno95.453yes
glucose-utilyes88.384yes
thermophileno99.312no
glucose-fermentno91.529no

External links

@ref: 7896

culture collection no.: DSM 19109, LMG 24052, CIP 110171

straininfo link

  • @ref: 75170
  • straininfo: 353997

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18450690Chryseobacterium gregarium sp. nov., isolated from decaying plant material.Behrendt U, Ulrich A, Schumann PInt J Syst Evol Microbiol10.1099/ijs.0.65544-02008Bacterial Typing Techniques, Chryseobacterium/*classification/genetics/*isolation & purification/physiology, DNA, Bacterial/analysis, Genes, rRNA, Genotype, Molecular Sequence Data, Phenotype, Phylogeny, Poaceae/*metabolism/*microbiology, RNA, Ribosomal, 16S/genetics, Ribotyping, Sequence Analysis, DNA, Species SpecificityGenetics
Phylogeny24480907Chryseobacterium aahli sp. nov., isolated from lake trout (Salvelinus namaycush) and brown trout (Salmo trutta), and emended descriptions of Chryseobacterium ginsenosidimutans and Chryseobacterium gregarium.Loch TP, Faisal MInt J Syst Evol Microbiol10.1099/ijs.0.052373-02014Animals, Bacterial Typing Techniques, Base Composition, Bayes Theorem, Chryseobacterium/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Lakes, Michigan, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Trout/*microbiologyGenetics
Phylogeny26573006Chryseobacterium panacis sp. nov., isolated from ginseng soil.Singh P, Kim YJ, Farh Mel-A, Dan WD, Kang CH, Yang DCAntonie Van Leeuwenhoek10.1007/s10482-015-0620-22015Base Composition, Chryseobacterium/classification/genetics/*isolation & purification/metabolism, Fatty Acids/chemistry/metabolism, Molecular Sequence Data, Panax/*growth & development, Phylogeny, Republic of Korea, *Soil MicrobiologyMetabolism

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7896Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19109)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19109
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
32474Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2869528776041
33350Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/8000
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)
68382Automatically annotated from API zym
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
75170Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID353997.1StrainInfo: A central database for resolving microbial strain identifiers
119735Curators of the CIPCollection of Institut Pasteur (CIP 110171)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110171