Strain identifier

BacDive ID: 17748

Type strain: Yes

Species: Chitinophaga skermanii

Strain Designation: CC-SG1B

Strain history: CIP <- 2006, P. Kämpfer, Justus Liebig Univ., Giessen, Germany: strain CC-SG1B

NCBI tax ID(s): 331697 (species)

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General

@ref: 17407

BacDive-ID: 17748

DSM-Number: 23857

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

description: Chitinophaga skermanii CC-SG1B is an aerobe, mesophilic bacterium that was isolated from faeces of the millipede .

NCBI tax id

  • NCBI tax id: 331697
  • Matching level: species

strain history

@refhistory
17407<- CCUG <- P. Kämpfer, Univ. Giessen, Germany
122639CIP <- 2006, P. Kämpfer, Justus Liebig Univ., Giessen, Germany: strain CC-SG1B

doi: 10.13145/bacdive17748.20230509.8.1

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 skermanii
  • full scientific name: Chitinophaga skermanii Kämpfer et al. 2006

@ref: 17407

domain: Bacteria

phylum: Bacteroidetes

class: Chitinophagia

order: Sphingobacteriales

family: Chitinophagaceae

genus: Chitinophaga

species: Chitinophaga skermanii

full scientific name: Chitinophaga skermanii Kämpfer et al. 2006

strain designation: CC-SG1B

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no93.59
6948099.97negative
122639nonegativerod-shaped

colony morphology

  • @ref: 122639
  • hemolysis ability: 1

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
17407TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545)yeshttps://mediadive.dsmz.de/medium/545Name: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545) Composition: Casein peptone 17.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l D(+)-Glucose 2.5 g/l K2HPO4 2.5 g/l Distilled water
34355MEDIUM 328- for nutrient agaryesDistilled water make up to (1000.000 ml);Agar (15.000 g);Peptone (5.000g);Beef extract (3.000 g)
122639CIP Medium 328yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=328

culture temp

@refgrowthtypetemperaturerange
17407positivegrowth28mesophilic
34355positivegrowth30mesophilic
59573positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
59573aerobe
122639obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.973

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
68371starch+builds acid from28017
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
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
68371amygdalin+builds acid from27613
68371N-acetylglucosamine+builds acid from59640
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
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
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
122639nitrate-reduction17632
122639nitrite-reduction16301

metabolite production

  • @ref: 122639
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
122639oxidase+
122639alcohol dehydrogenase-1.1.1.1
122639catalase+1.11.1.6
122639lysine decarboxylase-4.1.1.18
122639ornithine decarboxylase-4.1.1.17
122639urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase+3.4.11.3
68382trypsin+3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase+3.2.1.22
68382beta-galactosidase+3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase+3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
122639-+++-++++-++++-+++-+

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
122639--+/-------+/-+-+-------+/-++++++++++/-+/---+/-++/-+/-++---+----+

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinent
17407faeces of the millipede (Arthrosphaera magna)Arthrosphaera magnaTaiwanTWNAsia
59573Millipede feces (Arthrosphaera magna)TaiwanTWNAsia
122639Faeces, millipede Arthrosphaera magnaTaiwanTWNAsia

isolation source categories

Cat1Cat2Cat3
#Host#Arthropoda#Insecta
#Host Body Product#Gastrointestinal tract#Feces (Stool)

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
174071Risk group (German classification)
1226391Risk group (French classification)

Sequence information

16S sequences

  • @ref: 17407
  • accession: CIP109140
  • database: ena

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Chitinophaga skermanii DSM 23857GCA_003259335scaffoldncbi331697
66792Chitinophaga skermanii strain DSM 23857331697.3wgspatric331697
66792Chitinophaga skermanii DSM 238572593339293draftimg331697

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno93.907no
flagellatedno97.957no
gram-positiveno97.927no
anaerobicno99.123no
aerobicyes92.221yes
halophileno94.517no
spore-formingno92.865no
glucose-utilyes87.143no
thermophileno97.333yes
glucose-fermentno82.981no

External links

@ref: 17407

culture collection no.: DSM 23857, CCUG 52510, CIP 109140, CC SG-1B

straininfo link

  • @ref: 86739
  • straininfo: 297146

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16957125Transfer of [Flexibacter] sancti, [Flexibacter] filiformis, [Flexibacter] japonensis and [Cytophaga] arvensicola to the genus Chitinophaga and description of Chitinophaga skermanii sp. nov.Kampfer P, Young CC, Sridhar KR, Arun AB, Lai WA, Shen FT, Rekha PDInt J Syst Evol Microbiol10.1099/ijs.0.64359-02006Bacteroides/*classification, Cytophaga/*classification, DNA, Bacterial/*analysis, DNA, Ribosomal/analysis, Flexibacter/*classification, Molecular Sequence Data, RNA, Ribosomal, 16S/*analysis/geneticsGenetics
Phylogeny29749924Chitinophaga caeni sp. nov., isolated from activated sludge.Jin D, Kong X, Wang J, Sun J, Yu X, Zhuang X, Deng Y, Bai ZInt J Syst Evol Microbiol10.1099/ijsem.0.0028112018Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, Beijing, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
17407Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23857)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23857
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
34355Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6848
59573Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 52510)https://www.ccug.se/strain?id=52510
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
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
86739Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297146.1StrainInfo: A central database for resolving microbial strain identifiers
122639Curators of the CIPCollection of Institut Pasteur (CIP 109140)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109140