Strain identifier

BacDive ID: 17744

Type strain: Yes

Species: Chitinophaga filiformis

Strain Designation: Fx e1

Strain history: CIP <- 2000, J.F. Bernardet, INRA, Jouy-en-Josas, France <- ATCC <- DSMZ <- H. Reichenbach: strain Fx e1, Flexibacter elegans

NCBI tax ID(s): 104663 (species)

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General

@ref: 125

BacDive-ID: 17744

DSM-Number: 527

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

description: Chitinophaga filiformis Fx e1 is an obligate aerobe, mesophilic, Gram-negative bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 104663
  • Matching level: species

strain history

@refhistory
125<- H. Reichenbach, Fx e1 (Flexibacter elegans)
67770IAM 14320 <-- IFO 15056 <-- DSM 527 ("Myxococcus filiformis") <-- H. Reichenbach Fx e1 ("Flexibacter elegans").
119348CIP <- 2000, J.F. Bernardet, INRA, Jouy-en-Josas, France <- ATCC <- DSMZ <- H. Reichenbach: strain Fx e1, Flexibacter elegans

doi: 10.13145/bacdive17744.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Chitinophagia
  • order: Chitinophagales
  • family: Chitinophagaceae
  • genus: Chitinophaga
  • species: Chitinophaga filiformis
  • full scientific name: Chitinophaga filiformis (Reichenbach 1989 ex Solntseva 1940) Kämpfer et al. 2006

  • synonyms

    • @ref: 20215
    • synonym: Flexibacter filiformis

@ref: 125

domain: Bacteria

phylum: Bacteroidetes

class: Chitinophagia

order: Sphingobacteriales

family: Chitinophagaceae

genus: Chitinophaga

species: Chitinophaga filiformis

full scientific name: Chitinophaga filiformis (Reichenbach 1989) Kämpfer et al. 2006

strain designation: Fx e1

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
125438negative92.065
125439negative91.1
119348negativerod-shapedno

colony morphology

@refincubation period
458321-2 days
119348

pigmentation

  • @ref: 119348
  • production: yes
  • name: Flexirubin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
125EX-LM MEDIUM (DSMZ Medium 1550)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium1550.pdf
40297MEDIUM 342 - for Flexibacter filiformisyesDistilled water make up to (1000.000 ml);Calcium chloride dihydrate (1.360g);Agar (15.000 g);Casitone (3.000 g)
119348CIP Medium 35yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=35

culture temp

@refgrowthtypetemperature
125positivegrowth30
40297positivegrowth30
45832positivegrowth30
67770positivegrowth30
119348positivegrowth15-41
119348nogrowth5
119348nogrowth45

Physiology and metabolism

oxygen tolerance

  • @ref: 119348
  • oxygen tolerance: obligate aerobe

spore formation

  • @ref: 125439
  • spore formation: no
  • confidence: 95.4

compound production

@refcompound
1255 chloroflexirubin
125flexirubin

halophily

@refsaltgrowthtested relationconcentration
119348NaClnogrowth2 %
119348NaClnogrowth4 %
119348NaClnogrowth6 %
119348NaClnogrowth8 %
119348NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1193484853esculin+hydrolysis
11934817632nitrate+reduction
11934816301nitrite-reduction
11934815792malonate-assimilation
11934817632nitrate-respiration

metabolite production

  • @ref: 119348
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11934815688acetoin-
11934817234glucose-

enzymes

@refvalueactivityec
68382alpha-fucosidase+3.2.1.51
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382trypsin+3.4.21.4
68382valine arylamidase+
68382cystine arylamidase+3.4.11.3
68382lipase (C 14)-
68382esterase lipase (C 8)-
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)-
119348beta-galactosidase+3.2.1.23
119348alcohol dehydrogenase-1.1.1.1
119348gelatinase+
119348amylase+
119348DNase-
119348caseinase+3.4.21.50
119348catalase-1.11.1.6
119348tween esterase-
119348gamma-glutamyltransferase+2.3.2.2
119348lecithinase-
119348lipase-
119348lysine decarboxylase-4.1.1.18
119348ornithine decarboxylase-4.1.1.17
119348phenylalanine ammonia-lyase-4.3.1.24
119348protease-
119348tryptophan deaminase-
119348urease-3.5.1.5
68382alpha-mannosidase-3.2.1.24
68382beta-galactosidase+3.2.1.23
68382leucine arylamidase+3.4.11.1

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
119348-+---++++-++-+-+++-+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119348+++++-+++++++++++++-+-++-+--------++-----+------------+-+--++-------------------------+--+++-------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
125soilSamoa, Upolu, Apia
45832SoilApia,UpoluSamoaWSMAustralia and Oceania
67770Soil on the island of UpoluSamoaWSMAustralia and Oceania
119348Environment, SoilUpolu, ApiaSamoaWSMAustralia and Oceania1966

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_113675.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_334;96_3064;97_3763;98_14597;99_113675&stattab=map
  • Last taxonomy: Chitinophaga
  • 16S sequence: AB680761
  • Sequence Identity:
  • Total samples: 392
  • soil counts: 315
  • aquatic counts: 4
  • animal counts: 15
  • plant counts: 58

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
1251Risk group (German classification)
1193481Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Flexibacter elegans 16S ribosomal RNAM587821481nuccore997
20218Flexibacter filiformis gene for 16S rRNA, strain:IFO 15056AB0780491481nuccore104663
20218Chitinophaga filiformis gene for 16S rRNA, partial sequence, strain: NBRC 15056AB6807611451nuccore104663
124043Chitinophaga filiformis partial 16S rRNA gene, strain HAMBI 1966LT8999411507nuccore104663

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Chitinophaga filiformis strain DSM 527104663.4wgspatric104663
66792Chitinophaga filiformis DSM 5272634166296draftimg104663
67770Chitinophaga filiformis DSM 527GCA_900102545scaffoldncbi104663

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno92.065no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.881yes
125438spore-formingspore-formingAbility to form endo- or exosporesno68.521no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes88.835yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno95.972yes
125438motile2+flagellatedAbility to perform flagellated movementno89.25no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno95.4
125439BacteriaNetmotilityAbility to perform movementno68.2
125439BacteriaNetgram_stainReaction to gram-stainingnegative91.1
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthfacultative aerobe78.3

External links

@ref: 125

culture collection no.: CCUG 12809, CIP 106401, DSM 527, ATCC 29495, IAM 14320, IFO 15056, NBRC 15056, JCM 21160, HAMBI 1966, LMG 23482, NCIMB 13250, VKM B-1400

straininfo link

  • @ref: 86735
  • straininfo: 10279

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny22307507Chitinophaga oryziterrae sp. nov., isolated from the rhizosphere soil of rice (Oryza sativa L.).Chung EJ, Park TS, Jeon CO, Chung YRInt J Syst Evol Microbiol10.1099/ijs.0.036442-02012Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Oryza/*microbiology, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/analysis, Vitamin K 2/analogs & derivatives/analysisGenetics
Phylogeny33063169Chitinophaga agri sp. nov., a bacterium isolated from soil of reclaimed land.Lee SA, Heo J, Kim TW, Sang MK, Song J, Kwon SW, Weon HYArch Microbiol10.1007/s00203-020-02066-92020Bacteroidetes/classification/genetics, Base Composition, Gammaproteobacteria/*classification/genetics, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Species Specificity

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
125Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 527)https://www.dsmz.de/collection/catalogue/details/culture/DSM-527
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
40297Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18527
45832Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 12809)https://www.ccug.se/strain?id=12809
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/
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
86735Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID10279.1StrainInfo: A central database for resolving microbial strain identifiers
119348Curators of the CIPCollection of Institut Pasteur (CIP 106401)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106401
124043Isabel Schober, Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1