Strain identifier

BacDive ID: 5671

Type strain: Yes

Species: Chryseobacterium indologenes

Strain history: CIP <- 1984, NCTC <- R.E. Weaver, CDC: strain 3716, Flavobacterium indologenes

NCBI tax ID(s): 253 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 6580

BacDive-ID: 5671

DSM-Number: 16777

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

description: Chryseobacterium indologenes DSM 16777 is a mesophilic, Gram-negative, rod-shaped human pathogen that was isolated from human, trachea at autopsy.

NCBI tax id

  • NCBI tax id: 253
  • Matching level: species

strain history

@refhistory
6580<- CIP <- NCTC <- CDC
120095CIP <- 1984, NCTC <- R.E. Weaver, CDC: strain 3716, Flavobacterium indologenes

doi: 10.13145/bacdive5671.20230509.8.1

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 indologenes
  • full scientific name: Chryseobacterium indologenes (Yabuuchi et al. 1983) Vandamme et al. 1994
  • synonyms

    • @ref: 20215
    • synonym: Flavobacterium indologenes

@ref: 6580

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Weeksellaceae

genus: Chryseobacterium

species: Chryseobacterium indologenes

full scientific name: Chryseobacterium indologenes (Yabuuchi et al. 1983) Vandamme et al. 1994 emend. Montero-Calasanz et al. 2013

type strain: yes

Morphology

cell morphology

  • @ref: 120095
  • gram stain: negative
  • cell shape: rod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6580TRYPTICASE 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
34489MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
120095CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
6580positivegrowth30mesophilic
34489positivegrowth30mesophilic
120095positivegrowth30mesophilic
120095nogrowth41thermophilic

Physiology and metabolism

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
68371salicin-builds acid from17814
68371esculin+builds acid from4853
68371arbutin-builds acid from18305
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
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
120095esculin+hydrolysis4853
120095nitrate-reduction17632
120095nitrite-reduction16301

antibiotic resistance

  • @ref: 120095
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 120095
  • Chebi-ID: 35581
  • metabolite: indole
  • production: yes

enzymes

@refvalueactivityec
120095oxidase+
120095beta-galactosidase+3.2.1.23
120095alcohol dehydrogenase-1.1.1.1
120095catalase+1.11.1.6
120095tween esterase+
120095lysine decarboxylase-4.1.1.18
120095ornithine decarboxylase-4.1.1.17
120095urease-3.5.1.5

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
120095----------+-+---------+/--+--+---+---+/-+/--+----------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120095++-++----++-----+-+------------+---------------------+-------+---------------------------+++--+----

Isolation, sampling and environmental information

isolation

@refsample typeisolation date
6580human, trachea at autopsy
120095Human, Trachea at autopsy1958

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body-Site#Oral cavity and airways#Trachea

taxonmaps

  • @ref: 69479
  • File name: preview.99_4368.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_76;96_753;97_878;98_1329;99_4368&stattab=map
  • Last taxonomy: Chryseobacterium indologenes
  • 16S sequence: LN681561
  • Sequence Identity:
  • Total samples: 360
  • soil counts: 8
  • aquatic counts: 70
  • animal counts: 270
  • plant counts: 12

Safety information

risk assessment

@refpathogenicity humanpathogenicity animalbiosafety levelbiosafety level comment
6580yesyes2Risk group (German classification)
1200951Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Chryseobacterium indologenes partial 16S rRNA gene, strain LMG 8337AM2328131422ena253
20218Chryseobacterium indologenes strain ATCC 29897 16S-23S ribosomal RNA intergenic spacer, complete sequenceEU014570691ena253
20218Chryseobacterium indologenes 16S ribosomal RNA gene, partial sequenceM587731466ena253
6580Chryseobacterium indologenes partial 16S rRNA gene, type strain DSM 16777TLN6815611469ena1218103

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Chryseobacterium indologenes NCTC10796GCA_900460995contigncbi253
66792Chryseobacterium indologenes DSM 16777GCA_016025055completencbi253
66792Chryseobacterium indologenes strain DSM 16777253.154completepatric253
66792Chryseobacterium indologenes strain DSM 16777253.88wgspatric253
66792Chryseobacterium indologenes strain NCTC10796253.52wgspatric253
66792Chryseobacterium indologenes NCTC 107962816332551draftimg253
66792Chryseobacterium indologenes DSM 167772687453795draftimg253
66792Chryseobacterium indologenes DSM 16777GCA_900113975contigncbi253

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno92.558no
flagellatedno95.915no
gram-positiveno97.613no
anaerobicno99.463no
aerobicyes91.441no
halophileno92.499no
spore-formingno93.363no
glucose-utilyes84.002no
glucose-fermentno93.814no
thermophileno99.753yes

External links

@ref: 6580

culture collection no.: DSM 16777, ATCC 29897, CCUG 14483, CDC 3716, CIP 101026, GIFU 1347, LMG 8337, NCTC 10796

straininfo link

  • @ref: 75153
  • straininfo: 7821

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Pathogenicity11036018Genetic diversity of carbapenem-hydrolyzing metallo-beta-lactamases from Chryseobacterium (Flavobacterium) indologenes.Bellais S, Poirel L, Leotard S, Naas T, Nordmann PAntimicrob Agents Chemother10.1128/AAC.44.11.3028-3034.20002000Amino Acid Sequence, Anti-Bacterial Agents/pharmacology, Carbapenems/metabolism, Flavobacterium/drug effects/enzymology/*genetics, Genetic Variation, Humans, Hydrolysis, Microbial Sensitivity Tests, Molecular Sequence Data, Sequence Homology, Amino Acid, beta-Lactamases/*genetics/metabolismMetabolism
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
Phylogeny21571927Chryseobacterium vietnamense sp. nov., isolated from forest soil.Li Z, Zhu HInt J Syst Evol Microbiol10.1099/ijs.0.027201-02011Bacterial Typing Techniques, Base Composition, Chryseobacterium/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, Pigmentation, Polyenes/chemistry, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Trees/*microbiology, Vietnam, Vitamin K 2/analogs & derivatives/chemistryGenetics
Enzymology22083470Characterization of CIA-1, an Ambler class A extended-spectrum beta-lactamase from Chryseobacterium indologenes.Matsumoto T, Nagata M, Ishimine N, Kawasaki K, Yamauchi K, Hidaka E, Kasuga E, Horiuchi K, Oana K, Kawakami Y, Honda TAntimicrob Agents Chemother10.1128/AAC.05165-112011Amino Acid Sequence, Anti-Bacterial Agents/*administration & dosage, Chromosomes, Bacterial/genetics, Chryseobacterium/drug effects/*genetics/isolation & purification, Cloning, Molecular, Escherichia coli, Flavobacteriaceae Infections/*drug therapy/microbiology, Humans, Microbial Sensitivity Tests, Molecular Sequence Data, Recombinant Proteins/classification/genetics, Sequence Alignment, Sequence Analysis, DNA, Sequence Homology, Amino Acid, *beta-Lactam Resistance, beta-Lactamases/classification/*geneticsPhylogeny
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
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
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
6580Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16777)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16777
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
34489Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/12555
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)
68371Automatically annotated from API 50CH acid
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
75153Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID7821.1StrainInfo: A central database for resolving microbial strain identifiers
120095Curators of the CIPCollection of Institut Pasteur (CIP 101026)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20101026