Strain identifier

BacDive ID: 5667

Type strain: Yes

Species: Chryseobacterium gleum

Strain Designation: F93

Strain history: CIP <- 1987, NCTC <- 1982, B. Holmes, London, UK: strain F93, Flavobacterium gleum

NCBI tax ID(s): 525257 (strain), 250 (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: 6579

BacDive-ID: 5667

DSM-Number: 16776

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

description: Chryseobacterium gleum F93 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from human, high vaginal swab.

NCBI tax id

NCBI tax idMatching level
250species
525257strain

strain history

@refhistory
6579<- CIP <- NCTC <- B. Holmes; F93
67770B. Holmes F93.
119642CIP <- 1987, NCTC <- 1982, B. Holmes, London, UK: strain F93, Flavobacterium gleum

doi: 10.13145/bacdive5667.20230509.8.1

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 gleum
  • full scientific name: Chryseobacterium gleum (Holmes et al. 1984) Vandamme et al. 1994

  • synonyms

    • @ref: 20215
    • synonym: Flavobacterium gleum

@ref: 6579

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Weeksellaceae

genus: Chryseobacterium

species: Chryseobacterium gleum

full scientific name: Chryseobacterium gleum (Holmes et al. 1984) Vandamme et al. 1994 emend. Nguyen et al. 2013 emend. Montero-Calasanz et al. 2014 emend. Hahnke et al. 2016

strain designation: F93

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative99.978
119642negativerod-shapedno

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6579TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
40516MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
119642CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
119642CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
6579positivegrowth30mesophilic
40516positivegrowth30mesophilic
46133positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
46133aerobe
119642obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.996

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose+builds acid from28066
68371xylitol-builds acid from17151
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose+builds acid from27082
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose+builds acid from17306
68371cellobiose-builds acid from17057
68371esculin+builds acid from4853
68371arbutin+builds acid from18305
68371amygdalin+builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose+builds acid from16024
68371D-fructose+builds acid from15824
68371D-glucose+builds acid from17634
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose-builds acid from16988
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
119642nitrate+reduction17632
119642nitrite+reduction16301

metabolite production

  • @ref: 119642
  • Chebi-ID: 35581
  • metabolite: indole
  • production: yes

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
119642oxidase-
119642catalase+1.11.1.6
119642urease-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
119642-+++-++++-++---+++--

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119642+/---+/-------+++---------++++/--+---+---+/-+/--+----------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6579human, high vaginal swabLondonUnited KingdomGBREurope
46133Human vagina,high vaginal swabUnited KingdomGBREurope
67770High vaginal swab
119642Human, High vaginal swabLondonUnited KingdomGBREurope

isolation source categories

Cat1Cat2Cat3
#Infection#Patient#Swab
#Host#Human
#Host Body-Site#Urogenital tract#Vagina

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
65792Risk group (German classification)
1196421Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Chryseobacterium gleum partial 16S rRNA gene, strain CCUG 14555AM2328121438ena250
20218Chryseobacterium gleum 16S ribosomal RNA gene, partial sequenceM587721464ena250
20218F.gleum (NCTC 11432T) gene for 16S rRNAX67852665ena250
6579Chryseobacterium gleum strain LMG 8334 16S ribosomal RNA gene, partial sequenceAY4684491294ena525257

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Chryseobacterium gleum NCTC11432GCA_900636535completencbi250
66792Chryseobacterium gleum ATCC 35910525257.3wgspatric525257
66792Chryseobacterium gleum strain FDAARGOS_1103250.40completepatric250
66792Chryseobacterium gleum strain NCTC11432250.7completepatric250
66792Chryseobacterium gleum F93, ATCC 359102562617092draftimg525257
66792Chryseobacterium gleum ATCC 35910GCA_000143785scaffoldncbi525257

GC content

@refGC-contentmethod
657936.8sequence analysis
6777036.6-38.6thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno95.021no
gram-positiveno97.754no
anaerobicno99.596yes
aerobicyes92.182no
halophileno94.427no
spore-formingno93.982no
thermophileno99.768yes
glucose-utilyes82.697no
motileno89.409no
glucose-fermentno92.415no

External links

@ref: 6579

culture collection no.: DSM 16776, ATCC 35910, CCUG 14555, CIP 103039, JCM 2410, LMG 8334, NCTC 11432, IFO 15054, LMG 12447, NBRC 15054

straininfo link

  • @ref: 75149
  • straininfo: 7824

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Genetics11897576Molecular and biochemical characterization of Ambler class A extended-spectrum beta-lactamase CGA-1 from Chryseobacterium gleum.Bellais S, Naas T, Nordmann PAntimicrob Agents Chemother10.1128/AAC.46.4.966-970.20022002Amino Acid Sequence, Anti-Bacterial Agents/pharmacology, Bacteria/drug effects/*enzymology/genetics, Bacterial Proteins/chemistry, Ceftazidime/pharmacology, Cephalosporins/pharmacology, Clavulanic Acid/pharmacology, Conjugation, Genetic/genetics, Enzyme Induction/drug effects, Escherichia coli/genetics/metabolism, Isoelectric Focusing, Kinetics, Microbial Sensitivity Tests, Molecular Sequence Data, Molecular Weight, Plasmids/genetics, Recombinant Proteins/biosynthesis/chemistry, beta-Lactamases/genetics/*metabolismEnzymology
Enzymology12183230Genetic and biochemical characterization of CGB-1, an Ambler class B carbapenem-hydrolyzing beta-lactamase from Chryseobacterium gleum.Bellais S, Naas T, Nordmann PAntimicrob Agents Chemother10.1128/AAC.46.9.2791-2796.20022002Amino Acid Sequence, Bacteria/drug effects/enzymology/*genetics, Base Sequence, Carbapenems/*pharmacology, Clavulanic Acid/pharmacology, Cloning, Molecular, Conjugation, Genetic, DNA, Bacterial/analysis, DNA, Recombinant/genetics, Drug Resistance, Enzyme Induction/drug effects, Enzyme Inhibitors/pharmacology, In Situ Hybridization, Isoelectric Focusing, Kinetics, Microbial Sensitivity Tests, Molecular Sequence Data, Plasmids/genetics, beta-Lactamases/*geneticsPathogenicity
Phylogeny18319464Chryseobacterium aquifrigidense sp. nov., isolated from a water-cooling system.Park SC, Kim MS, Baik KS, Kim EM, Rhee MS, Seong CNInt J Syst Evol Microbiol10.1099/ijs.0.65475-02008Bacterial Typing Techniques, Base Composition, Chryseobacterium/*classification/genetics/*isolation & purification/physiology, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Fresh Water/*microbiology, Genes, rRNA, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, *Refrigeration, Sequence Analysis, DNA, Species SpecificityGenetics
Phylogeny19749032Chryseobacterium arthrosphaerae sp. nov., isolated from the faeces of the pill millipede Arthrosphaera magna Attems.Kampfer P, Arun AB, Young CC, Chen WM, Sridhar KR, Rekha PDInt J Syst Evol Microbiol10.1099/ijs.0.016840-02009Animals, Arthropods/*microbiology, Chryseobacterium/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Feces/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/geneticsMetabolism
Phylogeny22268076Chryseobacterium viscerum sp. nov., isolated from diseased fish.Zamora L, Vela AI, Palacios MA, Sanchez-Porro C, Svensson-Stadler LA, Dominguez L, Moore ERB, Ventosa A, Fernandez-Garayzabal JFInt J Syst Evol Microbiol10.1099/ijs.0.036699-02012Animals, Bacterial Typing Techniques, Base Composition, Chryseobacterium/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/analysis, Fish Diseases/microbiology, Gills/microbiology, Liver/microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Oncorhynchus mykiss/*microbiology, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/analysisGenetics
Enzymology24885249Cloning, expression and biochemical characterization of the cholesterol oxidase CgChoA from Chryseobacterium gleum.Reiss R, Faccio G, Thony-Meyer L, Richter MBMC Biotechnol10.1186/1472-6750-14-462014Biocatalysis, Cholesterol/metabolism, Cholesterol Oxidase/genetics/*metabolism, Chryseobacterium/classification/*enzymology, Cloning, Molecular, Escherichia coli/metabolism, *Gene Expression Regulation, Bacterial, Genetic Vectors/metabolism, Hydrogen-Ion Concentration, Phylogeny, Recombinant Proteins/biosynthesis/chemistry/isolation & purification, TemperatureMetabolism
Phylogeny24958763Chryseobacterium artocarpi sp. nov., isolated from the rhizosphere soil of Artocarpus integer.Venil CK, Nordin N, Zakaria ZA, Ahmad WAInt J Syst Evol Microbiol10.1099/ijs.0.063594-02014Artocarpus/*microbiology, Bacterial Typing Techniques, Base Composition, Chryseobacterium/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Malaysia, Molecular Sequence Data, Nucleic Acid Hybridization, Phosphatidylethanolamines/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny27902284Chryseobacterium cucumeris sp. nov., an endophyte isolated from cucumber (Cucumis sativus L.) root, and emended description of Chryseobacterium arthrosphaerae.Jeong JJ, Lee DW, Park B, Sang MK, Choi IG, Kim KDInt J Syst Evol Microbiol10.1099/ijsem.0.0016702017Bacterial Typing Techniques, Base Composition, Chryseobacterium/*classification/genetics/isolation & purification, Cucumis sativus/*microbiology, DNA, Bacterial/genetics, Endophytes/classification/genetics/isolation & purification, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pigmentation, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryEnzymology
Phylogeny31150322Chryseobacterium pennipullorum sp. nov., isolated from poultry feather waste.Oosthuizen L, Charimba G, Hitzeroth A, Nde AL, Steyn L, Newman J, Hugo CInt J Syst Evol Microbiol10.1099/ijsem.0.0034912019Animals, Bacterial Typing Techniques, Base Composition, Chryseobacterium/*classification/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Feathers/*microbiology, Nucleic Acid Hybridization, Phosphatidylethanolamines/chemistry, *Phylogeny, Poultry/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, South Africa, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny31535961Chryseobacterium candidae sp. nov., isolated from a yeast (Candida tropicalis).B I, G K, N S, A S, Ch S, Ch V RInt J Syst Evol Microbiol10.1099/ijsem.0.0037162020Bacterial Typing Techniques, Base Composition, *Candida tropicalis, Chryseobacterium/*classification/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, India, Nucleic Acid Hybridization, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Pathogenicity35476918Identification and Biosynthesis of Pro-Inflammatory Sulfonolipids from an Opportunistic Pathogen Chryseobacterium gleum.Hou L, Tian HY, Wang L, Ferris ZE, Wang J, Cai M, Older EA, Raja MRK, Xue D, Sun W, Nagarkatti P, Nagarkatti M, Chen H, Fan D, Tang X, Li JACS Chem Biol10.1021/acschembio.2c001412022Acyltransferases, Animals, Chryseobacterium, *Cysteic Acid/metabolism, Lipids, Mice, *SphingolipidsMetabolism
Phylogeny35511036Polar lipid characterization and description of Chryseobacterium capnotolerans sp. nov., isolated from high CO2-containing atmosphere and emended descriptions of the genus Chryseobacterium, and the species C. balustinum, C. daecheongense, C. formosense, C. gleum, C. indologenes, C. joostei, C. scophthalmum and C. ureilyticum.Heidler von Heilborn D, Nover LL, Weber M, Holzl G, Gisch N, Waldhans C, Mittler M, Kreyenschmidt J, Woehle C, Huttel B, Lipski AInt J Syst Evol Microbiol10.1099/ijsem.0.0053722022Atmosphere/analysis, Bacterial Typing Techniques, Base Composition, Carbon Dioxide, *Chryseobacterium, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycine/genetics, Lipids/analysis, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6579Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16776)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16776
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
40516Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/14792
46133Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 14555)https://www.ccug.se/strain?id=14555
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
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
75149Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID7824.1StrainInfo: A central database for resolving microbial strain identifiers
119642Curators of the CIPCollection of Institut Pasteur (CIP 103039)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103039