Strain identifier
BacDive ID: 5671
Type strain:
Species: Chryseobacterium indologenes
Strain history: CIP <- 1984, NCTC <- R.E. Weaver, CDC: strain 3716, Flavobacterium indologenes
NCBI tax ID(s): 253 (species)
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
@ref | history |
---|---|
6580 | <- CIP <- NCTC <- CDC |
120095 | CIP <- 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
@ref | name | growth | link | composition |
---|---|---|---|---|
6580 | TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) | yes | https://mediadive.dsmz.de/medium/92 | Name: 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 |
34489 | MEDIUM 3 - Columbia agar | yes | Columbia agar (39.000 g);distilled water (1000.000 ml) | |
120095 | CIP Medium 3 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
6580 | positive | growth | 30 | mesophilic |
34489 | positive | growth | 30 | mesophilic |
120095 | positive | growth | 30 | mesophilic |
120095 | no | growth | 41 | thermophilic |
Physiology and metabolism
metabolite utilization
@ref | metabolite | utilization activity | kind of utilization tested | Chebi-ID |
---|---|---|---|---|
68371 | Potassium 5-ketogluconate | - | builds acid from | |
68371 | Potassium 2-ketogluconate | - | builds acid from | |
68371 | gluconate | - | builds acid from | 24265 |
68371 | L-arabitol | - | builds acid from | 18403 |
68371 | D-arabitol | - | builds acid from | 18333 |
68371 | L-fucose | - | builds acid from | 18287 |
68371 | D-fucose | - | builds acid from | 28847 |
68371 | D-tagatose | - | builds acid from | 16443 |
68371 | D-lyxose | - | builds acid from | 62318 |
68371 | turanose | - | builds acid from | 32528 |
68371 | gentiobiose | + | builds acid from | 28066 |
68371 | xylitol | - | builds acid from | 17151 |
68371 | raffinose | - | builds acid from | 16634 |
68371 | melezitose | - | builds acid from | 6731 |
68371 | inulin | - | builds acid from | 15443 |
68371 | trehalose | + | builds acid from | 27082 |
68371 | sucrose | - | builds acid from | 17992 |
68371 | melibiose | - | builds acid from | 28053 |
68371 | lactose | - | builds acid from | 17716 |
68371 | maltose | + | builds acid from | 17306 |
68371 | cellobiose | - | builds acid from | 17057 |
68371 | salicin | - | builds acid from | 17814 |
68371 | esculin | + | builds acid from | 4853 |
68371 | arbutin | - | builds acid from | 18305 |
68371 | N-acetylglucosamine | - | builds acid from | 59640 |
68371 | methyl alpha-D-glucopyranoside | - | builds acid from | 320061 |
68371 | methyl alpha-D-mannoside | - | builds acid from | 43943 |
68371 | D-sorbitol | - | builds acid from | 17924 |
68371 | D-mannitol | - | builds acid from | 16899 |
68371 | myo-inositol | - | builds acid from | 17268 |
68371 | galactitol | - | builds acid from | 16813 |
68371 | L-rhamnose | - | builds acid from | 62345 |
68371 | L-sorbose | - | builds acid from | 17266 |
68371 | D-mannose | + | builds acid from | 16024 |
68371 | D-fructose | - | builds acid from | 15824 |
68371 | D-glucose | + | builds acid from | 17634 |
68371 | D-galactose | - | builds acid from | 12936 |
68371 | methyl beta-D-xylopyranoside | - | builds acid from | 74863 |
68371 | ribitol | - | builds acid from | 15963 |
68371 | L-xylose | - | builds acid from | 65328 |
68371 | D-xylose | - | builds acid from | 65327 |
68371 | D-ribose | - | builds acid from | 16988 |
68371 | L-arabinose | - | builds acid from | 30849 |
68371 | D-arabinose | - | builds acid from | 17108 |
68371 | erythritol | - | builds acid from | 17113 |
68371 | glycerol | - | builds acid from | 17754 |
120095 | esculin | + | hydrolysis | 4853 |
120095 | nitrate | - | reduction | 17632 |
120095 | nitrite | - | reduction | 16301 |
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
@ref | value | activity | ec |
---|---|---|---|
120095 | oxidase | + | |
120095 | beta-galactosidase | + | 3.2.1.23 |
120095 | alcohol dehydrogenase | - | 1.1.1.1 |
120095 | catalase | + | 1.11.1.6 |
120095 | tween esterase | + | |
120095 | lysine decarboxylase | - | 4.1.1.18 |
120095 | ornithine decarboxylase | - | 4.1.1.17 |
120095 | urease | - | 3.5.1.5 |
API 50CHac
@ref | GLY | ERY | DARA | LARA | RIB | DXYL | LXYL | ADO | MDX | GAL | GLU | FRU | MNE | SBE | RHA | DUL | INO | MAN | SOR | MDM | MDG | NAG | AMY | ARB | ESC | SAL | CEL | MAL | LAC | MEL | SAC | TRE | INU | MLZ | RAF | AMD | GLYG | XLT | GEN | TUR | LYX | TAG | DFUC | LFUC | DARL | LARL | GNT | 2KG | 5KG |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
120095 | - | - | - | - | - | - | - | - | - | - | + | - | + | - | - | - | - | - | - | - | - | - | +/- | - | + | - | - | + | - | - | - | + | - | - | - | +/- | +/- | - | + | - | - | - | - | - | - | - | - | - | - |
API biotype100
@ref | GLU | FRU | GAL | TRE | MNE | SBE | MEL | SAC | RAF | MTE | MAL | LAC | LTE | MbGa | MaGa | CEL | GEN | MbGu | ESC | RIB | ARA | XYL | PLE | RHA | FUC | MLZ | DARL | LARL | XLT | DUL | TAG | GLY | INO | MAN | MTL | TUR | SOR | ADO | HBG | LYX | ERY | MDG | 3MDG | SAT | MUC | LTAT | DTAT | MTAT | DMLT | LMLT | CATE | TATE | TTE | CIT | GRT | GAT | 2KG | 5KG | TRY | NAG | GNT | PAC | PAT | pOBE | QAT | GTE | mOBE | BAT | PPAT | CMT | TGE | BET | PCE | ABT | HIN | LAT | CAP | CYT | HIS | SUC | FUM | GRE | GYT | AVT | ETN | TTN | GLN | ITA | 3OBU | APT | GTT | PRO | DALA | LALA | SER | MNT | PROP | TYR | 2KT |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
120095 | + | + | - | + | + | - | - | - | - | + | + | - | - | - | - | - | + | - | + | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | + | + | - | - | + | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | isolation date |
---|---|---|
6580 | human, trachea at autopsy | |
120095 | Human, Trachea at autopsy | 1958 |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | pathogenicity human | pathogenicity animal | biosafety level | biosafety level comment |
---|---|---|---|---|
6580 | yes | yes | 2 | Risk group (German classification) |
120095 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Chryseobacterium indologenes partial 16S rRNA gene, strain LMG 8337 | AM232813 | 1422 | ena | 253 |
20218 | Chryseobacterium indologenes strain ATCC 29897 16S-23S ribosomal RNA intergenic spacer, complete sequence | EU014570 | 691 | ena | 253 |
20218 | Chryseobacterium indologenes 16S ribosomal RNA gene, partial sequence | M58773 | 1466 | ena | 253 |
6580 | Chryseobacterium indologenes partial 16S rRNA gene, type strain DSM 16777T | LN681561 | 1469 | ena | 1218103 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Chryseobacterium indologenes NCTC10796 | GCA_900460995 | contig | ncbi | 253 |
66792 | Chryseobacterium indologenes DSM 16777 | GCA_016025055 | complete | ncbi | 253 |
66792 | Chryseobacterium indologenes strain DSM 16777 | 253.154 | complete | patric | 253 |
66792 | Chryseobacterium indologenes strain DSM 16777 | 253.88 | wgs | patric | 253 |
66792 | Chryseobacterium indologenes strain NCTC10796 | 253.52 | wgs | patric | 253 |
66792 | Chryseobacterium indologenes NCTC 10796 | 2816332551 | draft | img | 253 |
66792 | Chryseobacterium indologenes DSM 16777 | 2687453795 | draft | img | 253 |
66792 | Chryseobacterium indologenes DSM 16777 | GCA_900113975 | contig | ncbi | 253 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | no | 92.558 | no |
flagellated | no | 95.915 | no |
gram-positive | no | 97.613 | no |
anaerobic | no | 99.463 | no |
aerobic | yes | 91.441 | no |
halophile | no | 92.499 | no |
spore-forming | no | 93.363 | no |
glucose-util | yes | 84.002 | no |
glucose-ferment | no | 93.814 | no |
thermophile | no | 99.753 | yes |
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
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Pathogenicity | 11036018 | Genetic diversity of carbapenem-hydrolyzing metallo-beta-lactamases from Chryseobacterium (Flavobacterium) indologenes. | Bellais S, Poirel L, Leotard S, Naas T, Nordmann P | Antimicrob Agents Chemother | 10.1128/AAC.44.11.3028-3034.2000 | 2000 | Amino 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/metabolism | Metabolism |
Phylogeny | 18319464 | Chryseobacterium aquifrigidense sp. nov., isolated from a water-cooling system. | Park SC, Kim MS, Baik KS, Kim EM, Rhee MS, Seong CN | Int J Syst Evol Microbiol | 10.1099/ijs.0.65475-0 | 2008 | Bacterial 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 Specificity | Genetics |
Phylogeny | 21571927 | Chryseobacterium vietnamense sp. nov., isolated from forest soil. | Li Z, Zhu H | Int J Syst Evol Microbiol | 10.1099/ijs.0.027201-0 | 2011 | Bacterial 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/chemistry | Genetics |
Enzymology | 22083470 | Characterization 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 T | Antimicrob Agents Chemother | 10.1128/AAC.05165-11 | 2011 | Amino 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/*genetics | Phylogeny |
Phylogeny | 22268076 | Chryseobacterium 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 JF | Int J Syst Evol Microbiol | 10.1099/ijs.0.036699-0 | 2012 | Animals, 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/analysis | Genetics |
Phylogeny | 27902284 | Chryseobacterium 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 KD | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001670 | 2017 | Bacterial 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/chemistry | Enzymology |
Phylogeny | 35511036 | Polar 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 A | Int J Syst Evol Microbiol | 10.1099/ijsem.0.005372 | 2022 | Atmosphere/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, DNA | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
6580 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16777) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-16777 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
34489 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/12555 | ||||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
68371 | Automatically annotated from API 50CH acid | |||||
69479 | João 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 | |||
75153 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID7821.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
120095 | Curators of the CIP | Collection of Institut Pasteur (CIP 101026) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20101026 |