Strain identifier

BacDive ID: 5679

Type strain: Yes

Species: Chryseobacterium formosense

Strain Designation: CC-H3-2

Strain history: CIP <- 2004, P. Kämpfer, Giessen, Germany: strain CC-H3-2

NCBI tax ID(s): 236814 (species)

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General

@ref: 6992

BacDive-ID: 5679

DSM-Number: 17452

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

description: Chryseobacterium formosense CC-H3-2 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from rhizosphere of Lactuca sativa L. .

NCBI tax id

  • NCBI tax id: 236814
  • Matching level: species

strain history

@refhistory
6992<- P. Kämpfer, Giessen, Germany <- A. B. Arun; CC-H3-2
119426CIP <- 2004, P. Kämpfer, Giessen, Germany: strain CC-H3-2

doi: 10.13145/bacdive5679.20230509.8.1

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 formosense
  • full scientific name: Chryseobacterium formosense Young et al. 2005

@ref: 6992

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Weeksellaceae

genus: Chryseobacterium

species: Chryseobacterium formosense

full scientific name: Chryseobacterium formosense Young et al. 2005 emend. Hahnke et al. 2016

strain designation: CC-H3-2

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative99.991
119426negativerod-shapedno

colony morphology

  • @ref: 119426

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6992NUTRIENT 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
38272MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
119426CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
6992positivegrowth28mesophilic
38272positivegrowth30mesophilic
58489positivegrowth30-37mesophilic
119426positivegrowth15-30
119426nogrowth5psychrophilic
119426nogrowth37mesophilic
119426nogrowth41thermophilic
119426nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
58489aerobe
119426obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.994

halophily

@refsaltgrowthtested relationconcentration
119426NaClpositivegrowth0-2 %
119426NaClnogrowth4 %
119426NaClnogrowth6 %
119426NaClnogrowth8 %
119426NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1194264853esculin+hydrolysis
119426606565hippurate-hydrolysis
11942617632nitrate-builds gas from
11942617632nitrate-reduction
11942616301nitrite-builds gas from
11942616301nitrite-reduction
11942615792malonate-assimilation
11942617632nitrate-respiration

antibiotic resistance

  • @ref: 119426
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 119426
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11942615688acetoin-
11942617234glucose-

enzymes

@refvalueactivityec
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
119426oxidase+
119426beta-galactosidase+3.2.1.23
119426alcohol dehydrogenase-1.1.1.1
119426gelatinase+/-
119426amylase+
119426DNase+
119426caseinase+3.4.21.50
119426catalase+1.11.1.6
119426tween esterase+
119426gamma-glutamyltransferase+2.3.2.2
119426lecithinase+
119426lipase+
119426lysine decarboxylase-4.1.1.18
119426ornithine decarboxylase-4.1.1.17
119426phenylalanine ammonia-lyase-4.3.1.24
119426protease+
119426tryptophan deaminase-
119426urease-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
119426-+++-++++-++----+---

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinentgeographic location
6992rhizosphere of Lactuca sativa L. (garden lettuce)Lactuca sativaTaiwanTWNAsia
58489Rhizosphere of Lactuca sativa (garden lettuce)TaiwanTWNAsiaTaichung county,Koshing,R.O.C.
119426Environment, Rhizosphere of Lactuca saliva L. (garden lettuce)TaiwanTWNAsia

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Rhizosphere

taxonmaps

  • @ref: 69479
  • File name: preview.99_824.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_76;96_206;97_225;98_657;99_824&stattab=map
  • Last taxonomy: Chryseobacterium formosense
  • 16S sequence: AY315443
  • Sequence Identity:
  • Total samples: 173
  • soil counts: 27
  • aquatic counts: 44
  • animal counts: 76
  • plant counts: 26

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
69921Risk group (German classification)
1194261Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6992
  • description: Chryseobacterium formosense strain CC-H3-2 16S ribosomal RNA gene, partial sequence
  • accession: AY315443
  • length: 1455
  • database: ena
  • NCBI tax ID: 236814

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Chryseobacterium formosense DSM 17452GCA_900116415contigncbi236814
66792Chryseobacterium formosense strain DSM 17452236814.8wgspatric236814
66792Chryseobacterium formosense DSM 174522684622901draftimg236814

GC content

  • @ref: 6992
  • GC-content: 34.8
  • method: sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno90.528no
gram-positiveno98.124no
anaerobicno99.142no
aerobicyes89.485no
halophileno92.835no
spore-formingno96.282no
glucose-utilyes88.559no
flagellatedno97.038no
thermophileno99.015yes
glucose-fermentno91.193no

External links

@ref: 6992

culture collection no.: DSM 17452, CCUG 49271, CIP 108367, KCTC 12435

straininfo link

  • @ref: 75161
  • straininfo: 135107

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15653912Chryseobacterium formosense sp. nov., isolated from the rhizosphere of Lactuca sativa L. (garden lettuce).Young CC, Kampfer P, Shen FT, Lai WA, Arun ABInt J Syst Evol Microbiol10.1099/ijs.0.63331-02005Bacterial Typing Techniques, Chryseobacterium/chemistry/*classification/genetics/isolation & purification, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Lettuce/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, TaiwanGenetics
Phylogeny29264617Chryseobacterium chungangensis sp. nov., a bacterium isolated from soil of sweet gourd garden.Huq MAArch Microbiol10.1007/s00203-017-1469-82017Base Composition, Chryseobacterium/cytology/*genetics/isolation & purification/metabolism, Cucurbitaceae, DNA, Bacterial/genetics, Fatty Acids/metabolism, Gardens, Molecular Typing, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil Microbiology, Vitamin K 2/analogs & derivatives/metabolismMetabolism

Reference

@idauthorscataloguedoi/urltitle
6992Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17452)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17452
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
38272Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5981
58489Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 49271)https://www.ccug.se/strain?id=49271
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
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
75161Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID135107.1StrainInfo: A central database for resolving microbial strain identifiers
119426Curators of the CIPCollection of Institut Pasteur (CIP 108367)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108367