Strain identifier

BacDive ID: 17748

Type strain: Yes

Species: Chitinophaga skermanii

Strain Designation: CC SG-1B, CC-SG1B

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

NCBI tax ID(s): 331697 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 9.3 (current version):
version 9.2:
version 9.1:
version 9:
version 8.1:
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 9.3 (current version)

General

@ref: 17407

BacDive-ID: 17748

DSM-Number: 23857

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

description: Chitinophaga skermanii CC SG-1B is an aerobe, mesophilic, Gram-negative 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/bacdive17748.20250331.9.3

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 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 SG-1B, CC-SG1B

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
125438negative92.17
125439negative91.7
122639negativerod-shapedno

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

@refgrowthtypetemperature
17407positivegrowth28
34355positivegrowth30
59573positivegrowth30

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
59573aerobe
122639obligate aerobe
125439obligate aerobe97.8

spore formation

  • @ref: 125439
  • spore formation: no
  • confidence: 97.1

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12263917632nitrate-reduction
12263916301nitrite-reduction
6837159640N-acetylglucosamine+builds acid from
6837117754glycerol-builds acid from
68371Potassium 5-ketogluconate+builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose+builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose+builds acid from
6837128066gentiobiose+builds acid from
6837128017starch+builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837128053melibiose+builds acid from
6837117716lactose+builds acid from
6837117306maltose+builds acid from
6837117057cellobiose+builds acid from
6837117814salicin+builds acid from
683714853esculin+builds acid from
6837118305arbutin+builds acid from
6837127613amygdalin+builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose+builds acid from
6837115824D-fructose-builds acid from
6837117634D-glucose+builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837116988D-ribose-builds acid from
6837130849L-arabinose-builds acid from
6837117113erythritol-builds acid from

metabolite production

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

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
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382alpha-galactosidase+3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382cystine arylamidase+3.4.11.3
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382lipase (C 14)-
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382alkaline phosphatase+3.1.3.1
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
68382beta-galactosidase+3.2.1.23
68382trypsin+3.4.21.4

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 magnaTaiwan, Province of ChinaTWNAsia
59573Millipede feces (Arthrosphaera magna)Taiwan, Province of ChinaTWNAsia
122639Faeces, millipede Arthrosphaera magnaTaiwan, Province of ChinaTWNAsia

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

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno92.17no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no98.863yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes89.747yes
125438spore-formingspore-formingAbility to form endo- or exosporesno83.262no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno97.079yes
125438motile2+flagellatedAbility to perform flagellated movementno89.5no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno97.1
125439BacteriaNetmotilityAbility to perform movementno78.1
125439BacteriaNetgram_stainReaction to gram-stainingnegative91.7
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe97.8

External links

@ref: 17407

culture collection no.: DSM 23857, CCUG 52510, CIP 109140

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
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
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