Strain identifier

BacDive ID: 5672

Type strain: Yes

Species: Chryseobacterium indoltheticum

Strain Designation: F37

Strain history: CIP <- 1988, NCIMB, Flavobacterium indoltheticum <- ATCC <- O.B. Weeks: strain F37 <- O.B. Williams

NCBI tax ID(s): 254 (species)

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General

@ref: 6581

BacDive-ID: 5672

DSM-Number: 16778

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic

description: Chryseobacterium indoltheticum F37 is an obligate aerobe, mesophilic bacterium that was isolated from marine mud.

NCBI tax id

  • NCBI tax id: 254
  • Matching level: species

strain history

@refhistory
6581<- CIP <- NCIMB <- ATCC <- O. B. Weeks; F37 <- O. B. Williams
120098CIP <- 1988, NCIMB, Flavobacterium indoltheticum <- ATCC <- O.B. Weeks: strain F37 <- O.B. Williams

doi: 10.13145/bacdive5672.20230509.8.1

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 indoltheticum
  • full scientific name: Chryseobacterium indoltheticum (Campbell and Williams 1951) Vandamme et al. 1994

  • synonyms

    • @ref: 20215
    • synonym: Flavobacterium indoltheticum

@ref: 6581

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Weeksellaceae

genus: Chryseobacterium

species: Chryseobacterium indoltheticum

full scientific name: Chryseobacterium indoltheticum (Campbell and Williams 1951) Vandamme et al. 1994 emend. Wu et al. 2013

strain designation: F37

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no92.206
6948099.978negative
120098nonegativerod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6581TRYPTICASE 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
35499MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
120098CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
120098CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
6581positivegrowth30mesophilic
35499positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 120098
  • oxygen tolerance: obligate 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
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
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
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-fructose-builds acid from15824
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
68369malate-assimilation25115
68369adipate-assimilation17128
68369decanoate-assimilation27689
68369gluconate-assimilation24265
68369maltose-assimilation17306
68369N-acetylglucosamine-assimilation59640
68369D-mannitol-assimilation16899
68369D-mannose-assimilation16024
68369L-arabinose-assimilation30849
68369D-glucose-assimilation17634
68369gelatin+hydrolysis5291
68369esculin+hydrolysis4853
68369urea-hydrolysis16199
68369arginine-hydrolysis29016
68369D-glucose-fermentation17634
68369tryptophan-energy source27897
68369nitrate-reduction17632
120098nitrate-reduction17632
120098nitrite-reduction16301

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
12009835581indoleyes

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

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
68369cytochrome oxidase+1.9.3.1
68369gelatinase+
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
120098oxidase+
120098catalase+1.11.1.6
120098urease-3.5.1.5

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    51524C15:0 ANTEISO514.711
    51524C15:0 ISO35.514.621
    51524C15:0 ISO 3OH316.135
    51524C16:1 ω7c/C15:0 ISO 2OH13.115.85
    51524C17:0 2OH118.249
    51524C17:0 iso 3OH8.218.161
    51524C17:1 ω9c ISO24.116.416
    51524C18:2 ω6,9c/C18:0 ANTE0.817.724
    51524unknown 13.5667.513.566
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
120098-+++-+++++++---+++--

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
51524-----++-------------+

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
120098----------+/--+/----------+/--+-+/-+/--------+/---+/-----------

Isolation, sampling and environmental information

isolation

@refsample type
6581marine mud
51524Marine mud
120098Environment, Marine mud

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Terrestrial#Mud (Sludge)
#Environmental#Aquatic#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_8172.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_76;96_206;97_225;98_254;99_8172&stattab=map
  • Last taxonomy: Chryseobacterium indoltheticum
  • 16S sequence: AY468448
  • Sequence Identity:
  • Total samples: 1798
  • soil counts: 309
  • aquatic counts: 177
  • animal counts: 552
  • plant counts: 760

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
65811Risk group (German classification)
1200981Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Chryseobacterium indoltheticum 16S ribosomal RNA gene, partial sequenceM587741461ena254
6581Chryseobacterium indoltheticum strain LMG 4025 16S ribosomal RNA gene, partial sequenceAY4684481442ena254

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Chryseobacterium indoltheticum ATCC 27950GCA_003815915completencbi254
66792Chryseobacterium indoltheticum ATCC 27950GCA_900156145scaffoldncbi254
66792Chryseobacterium indoltheticum strain ATCC 27950254.4wgspatric254
66792Chryseobacterium indoltheticum DSM 167782681813551draftimg254

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno97.26no
gram-positiveno98.323no
anaerobicno99.318no
aerobicyes90.155no
halophileno92.871no
spore-formingno96.362no
thermophileno99.129yes
glucose-utilyes87.697no
motileno89.912no
glucose-fermentno93.899yes

External links

@ref: 6581

culture collection no.: DSM 16778, ATCC 27950, CCUG 33445, CIP 103168, LMG 4025, NCIMB 2220

straininfo link

  • @ref: 75154
  • straininfo: 2825

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Pathogenicity16903830Influence of lipopolysaccharides and lipids A from some marine bacteria on spontaneous and Escherichia coli LPS-induced TNF-alpha release from peripheral human blood cells.Vorobeva EV, Krasikova IN, Solov'eva TFBiochemistry (Mosc)10.1134/s000629790607008x2006Animals, Dose-Response Relationship, Drug, Endotoxins/antagonists & inhibitors, Enzyme-Linked Immunosorbent Assay, Escherichia coli/cytology/metabolism, Gram-Negative Bacteria/cytology/*metabolism, Humans, Leukocytes, Mononuclear/drug effects/*immunology, Lipid A/chemistry/*pharmacology/toxicity, Lipopolysaccharides/antagonists & inhibitors/*pharmacology/toxicity, Mice, Tumor Necrosis Factor-alpha/*metabolismMetabolism
Phylogeny18319450Chryseobacterium aquaticum sp. nov., isolated from a water reservoir.Kim KK, Lee KC, Oh HM, Lee JSInt J Syst Evol Microbiol10.1099/ijs.0.65491-02008Bacterial Typing Techniques, Chryseobacterium/*classification/genetics/isolation & purification/physiology, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Fresh Water/*microbiology, Genes, rRNA, Genotype, Korea, Molecular Sequence Data, Phenotype, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species SpecificityGenetics
Phylogeny20656821Chryseobacterium ginsenosidimutans sp. nov., a bacterium with ginsenoside-converting activity isolated from soil of a Rhus vernicifera-cultivated field.Im WT, Yang JE, Kim SY, Yi THInt J Syst Evol Microbiol10.1099/ijs.0.023614-02010Aerobiosis, Base Composition, Chryseobacterium/*classification/genetics/*isolation & purification/physiology, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Ginsenosides/*metabolism, Hydrogen-Ion Concentration, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Rhus/growth & development, Sequence Analysis, DNA, Sodium Chloride/metabolism, *Soil Microbiology, Temperature, beta-Glucosidase/metabolismMetabolism
Phylogeny23378110Chryseobacterium ginsengisoli sp. nov., isolated from the rhizosphere of ginseng and emended description of Chryseobacterium gleum.Nguyen NL, Kim YJ, Hoang VA, Yang DCInt J Syst Evol Microbiol10.1099/ijs.0.045427-02013Bacterial Typing Techniques, Base Composition, Chryseobacterium/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Molecular Sequence Data, Nucleic Acid Hybridization, Panax/*microbiology, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Rhizosphere, Sequence Analysis, DNA, Soil Microbiology, Vitamin K 2/analogs & derivatives/analysisGenetics
Phylogeny25878202Chryseobacterium solani sp. nov., isolated from field-grown eggplant rhizosphere soil.Du J, Ngo HTT, Won K, Kim KY, Jin FX, Yi THInt J Syst Evol Microbiol10.1099/ijs.0.0002662015Bacterial Typing Techniques, Base Composition, Chryseobacterium/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Solanum melongena/*microbiology, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny26210236Chryseobacterium formosus sp. nov., a bacterium isolated from an ancient tree trunk.Akter S, NGO HT, Du J, Won K, Singh H, Yin CS, Kook M, Yi THArch Microbiol10.1007/s00203-015-1137-92015Bacterial Typing Techniques, Base Composition, Chryseobacterium/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Species Specificity, Trees/*microbiologyGenetics
Phylogeny31424383Chryseobacterium mulctrae sp. nov., isolated from raw cow's milk.Yoon SH, Lee JE, Han RH, Kwon M, Kim GBInt J Syst Evol Microbiol10.1099/ijsem.0.0036472019Animals, Bacterial Typing Techniques, Base Composition, Cattle, Chryseobacterium/*classification/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Female, Milk/*microbiology, Nucleic Acid Hybridization, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6581Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16778)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16778
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
35499Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/14936
51524Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 33445)https://www.ccug.se/strain?id=33445
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
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
75154Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID2825.1StrainInfo: A central database for resolving microbial strain identifiers
120098Curators of the CIPCollection of Institut Pasteur (CIP 103168)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103168