Strain identifier

BacDive ID: 5678

Type strain: Yes

Species: Chryseobacterium shigense

Strain Designation: GUM-Kaji

Strain history: CIP <- 2005, NCIMB

NCBI tax ID(s): 297244 (species)

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General

@ref: 6773

BacDive-ID: 5678

DSM-Number: 17126

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

description: Chryseobacterium shigense GUM-Kaji is an aerobe, mesophilic, Gram-negative bacterium that was isolated from lactic acid beverage.

NCBI tax id

  • NCBI tax id: 297244
  • Matching level: species

strain history

@refhistory
6773<- NCIMB
383722005, NCIMB
122587CIP <- 2005, NCIMB

doi: 10.13145/bacdive5678.20230509.8.1

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 shigense
  • full scientific name: Chryseobacterium shigense Shimomura et al. 2005

@ref: 6773

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Weeksellaceae

genus: Chryseobacterium

species: Chryseobacterium shigense

full scientific name: Chryseobacterium shigense Shimomura et al. 2005 emend. Montero-Calasanz et al. 2014

strain designation: GUM-Kaji

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
31499negative1.25 µm0.65 µmrod-shapedno
122587negativerod-shapedno

colony morphology

  • @ref: 122587
  • hemolysis ability: 1

pigmentation

  • @ref: 31499
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6773NUTRIENT 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
38372MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
122587CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
6773positivegrowth28mesophilic
31499positivegrowth05-30
31499positiveoptimum25mesophilic
38372positivegrowth30mesophilic
60658positivegrowth30mesophilic

culture pH

@refabilitytypepH
31499positivegrowth05-08
31499positiveoptimum6.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31499aerobe
60658aerobe

observation

  • @ref: 31499
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3149928757fructose+carbon source
3149917234glucose+carbon source
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
6837117306maltose+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
6837117634D-glucose+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
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
12258717632nitrate-reduction
12258716301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
3149935581indoleyes
6836935581indoleyes
12258735581indoleyes

metabolite tests

@refChebi-IDmetaboliteindole test
3149935581indole+
6836935581indole+

enzymes

@refvalueactivityec
31499catalase+1.11.1.6
31499gelatinase+
31499cytochrome oxidase+1.9.3.1
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
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
68382cystine arylamidase-3.4.11.3
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
68369cytochrome oxidase-1.9.3.1
68369gelatinase+
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
122587oxidase+
122587alcohol dehydrogenase-1.1.1.1
122587catalase+1.11.1.6
122587lysine decarboxylase-4.1.1.18
122587ornithine decarboxylase-4.1.1.17
122587urease-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
60658-+++-++-+-++---+++--
122587-+++-+----++---++---

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
60658-+---++--------------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
122587+/----------+++----+----++++-+--++---+/-+/--+----------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
6773lactic acid beverageShiga prefectureJapanJPNAsia
60658Lactic acid beverageJapanJPNAsia2001-05-01
122587Lactic acid beverageShigaJapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Food production#Fermented
#Engineered#Food production#Beverage

taxonmaps

  • @ref: 69479
  • File name: preview.99_3362.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_76;96_753;97_1893;98_2323;99_3362&stattab=map
  • Last taxonomy: Chryseobacterium
  • 16S sequence: HQ630670
  • Sequence Identity:
  • Total samples: 749
  • soil counts: 166
  • aquatic counts: 108
  • animal counts: 434
  • plant counts: 41

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
67731Risk group (German classification)
1225871Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Chryseobacterium shigense strain DSM17126 16S ribosomal RNA gene, partial sequenceHQ6306701429ena297244
6773Chryseobacterium shigense gene for 16S rRNA, partial sequenceAB1931011478ena297244

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Chryseobacterium shigense DSM 17126GCA_900156575contigncbi297244
66792Chryseobacterium shigense DSM 17126GCA_002943655scaffoldncbi297244
66792Chryseobacterium shigense strain DSM 17126297244.4wgspatric297244
66792Chryseobacterium shigense strain DSM 17126297244.9wgspatric297244
66792Chryseobacterium shigense DSM 171262681813504draftimg297244

GC content

  • @ref: 31499
  • GC-content: 36.6

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno95.928yes
gram-positiveno97.626yes
anaerobicno99.547no
aerobicyes92.782no
halophileno95.037no
spore-formingno92.933no
glucose-utilyes88.651no
thermophileno99.881yes
motileno91.836no
glucose-fermentno92.592yes

External links

@ref: 6773

culture collection no.: CCUG 55591, CIP 14047, DSM 17126, NCIMB 14047, BAMY 1001, CIP 108958

straininfo link

  • @ref: 75160
  • straininfo: 265594

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16166686Chryseobacterium shigense sp. nov., a yellow-pigmented, aerobic bacterium isolated from a lactic acid beverage.Shimomura K, Kaji S, Hiraishi AInt J Syst Evol Microbiol10.1099/ijs.0.63690-02005Aerobiosis, Bacterial Typing Techniques, Beverages/*microbiology, Chryseobacterium/*classification/genetics/isolation & purification/physiology, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Lactic Acid, Molecular Sequence Data, Phenotype, Phylogeny, Pigments, Biological/*metabolism, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Phylogeny17684275Chryseobacterium luteum sp. nov., associated with the phyllosphere of grasses.Behrendt U, Ulrich A, Sproer C, Schumann PInt J Syst Evol Microbiol10.1099/ijs.0.65104-02007Chryseobacterium/*classification/genetics/*isolation & purification, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Molecular Sequence Data, Phylogeny, Poaceae/*microbiology, RNA, Ribosomal, 16S/geneticsGenetics
Phylogeny23456810Chryseobacterium carnipullorum sp. nov., isolated from raw chicken.Charimba G, Jooste P, Albertyn J, Hugo CInt J Syst Evol Microbiol10.1099/ijs.0.049445-02013Animals, Bacterial Typing Techniques, Base Composition, Chickens/*microbiology, Chryseobacterium/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/analysis, Food Contamination, *Food Microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, Poultry/microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, South Africa, Vitamin K 2/analogs & derivatives/analysisBiotechnology
Phylogeny32895493Chryseobacterium antibioticum sp. nov. with antimicrobial activity against Gram-negative bacteria, isolated from Arctic soil.Dahal RH, Chaudhary DK, Kim DU, Pandey RP, Kim JJ Antibiot (Tokyo)10.1038/s41429-020-00367-12020Anti-Bacterial Agents/*pharmacology, Arctic Regions, Chryseobacterium/*chemistry/classification/genetics, Classification, Computer Simulation, Genome, Bacterial, Gram-Negative Bacteria/*drug effects, Lipids/chemistry, Microbial Sensitivity Tests, Nucleotides/chemistry, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S, *Soil MicrobiologyGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
6773Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17126)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17126
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
31499Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604127797
38372Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6645
60658Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 55591)https://www.ccug.se/strain?id=55591
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
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
75160Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID265594.1StrainInfo: A central database for resolving microbial strain identifiers
122587Curators of the CIPCollection of Institut Pasteur (CIP 108958)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108958