Strain identifier

BacDive ID: 2372

Type strain: Yes

Species: Cellulomonas chitinilytica

Strain Designation: XBU-b

Strain history: <- ST Lee, KAIST

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 7248

BacDive-ID: 2372

DSM-Number: 17922

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-positive, rod-shaped

description: Cellulomonas chitinilytica XBU-b is a facultative anaerobe, mesophilic, Gram-positive bacterium that was isolated from compost, cattle farm.

NCBI tax id

NCBI tax idMatching level
1305865strain
398759species

strain history

@refhistory
7248<- Sung-Taik Lee; Xbu-b
67770W.-T. Im X.bu-b.
67771<- ST Lee, KAIST

doi: 10.13145/bacdive2372.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Cellulomonadaceae
  • genus: Cellulomonas
  • species: Cellulomonas chitinilytica
  • full scientific name: Cellulomonas chitinilytica Yoon et al. 2008

@ref: 7248

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Cellulomonadaceae

genus: Cellulomonas

species: Cellulomonas chitinilytica

full scientific name: Cellulomonas chitinilytica Yoon et al. 2008

strain designation: XBU-b

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31988positive1.5-2.2 µm0.4-0.6 µmrod-shapedno
67771positive
69480positive100

colony morphology

@refcolony colorincubation periodmedium used
18317Rapeseed yellow (1021)10-14 daysISP 2
18317Rapeseed yellow (1021)10-14 daysISP 3
18317Rapeseed yellow (1021)10-14 daysISP 4
18317Beige (1001)10-14 daysISP 5
18317Rapeseed yellow (1021)10-14 daysISP 6
18317Beige (1001)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
18317noISP 2
18317noISP 3
18317noISP 4
18317noISP 5
18317noISP 6
18317noISP 7

pigmentation

  • @ref: 31988
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7248R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
18317ISP 2yesName: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
18317ISP 3yesName: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
18317ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
18317ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
18317ISP 6yesName: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
18317ISP 7yesName: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes

culture temp

@refgrowthtypetemperaturerange
18317positiveoptimum28mesophilic
7248positivegrowth28mesophilic
31988positivegrowth04-30
31988positiveoptimum25mesophilic
67770positivegrowth28mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
31988positivegrowth5-8.5alkaliphile
31988positiveoptimum6.9-7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31988facultative anaerobe
67771aerobe

spore formation

@refspore formationconfidence
31988no
69481yes98
69480no99.396

halophily

  • @ref: 31988
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-2 %

murein

  • @ref: 7248
  • murein short key: A21.05
  • type: A4ß L-Orn-D-Glu

observation

@refobservation
31988aggregates in chains
67770quinones: MK-9(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3198830089acetate+carbon source
3198817057cellobiose+carbon source
3198828757fructose+carbon source
3198824265gluconate+carbon source
3198817234glucose+carbon source
3198829987glutamate+carbon source
3198817754glycerol+carbon source
3198828087glycogen+carbon source
3198817716lactose+carbon source
3198815792malonate+carbon source
3198829864mannitol+carbon source
3198837684mannose+carbon source
31988506227N-acetylglucosamine+carbon source
3198818401phenylacetate+carbon source
3198815361pyruvate+carbon source
3198816634raffinose+carbon source
3198817814salicin+carbon source
3198830911sorbitol+carbon source
3198818222xylose+carbon source
3198817632nitrate+reduction
6837917632nitrate+reduction
683794853esculin+hydrolysis
6837916199urea-hydrolysis
683795291gelatin+hydrolysis
6837917634D-glucose+fermentation
6837916988D-ribose-fermentation
6837965327D-xylose+fermentation
6837916899D-mannitol-fermentation
6837917306maltose+fermentation
6837917992sucrose+fermentation

enzymes

@refvalueactivityec
31988catalase+1.11.1.6
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
68379gelatinase+
68379urease-3.5.1.5
68379beta-glucosidase+3.2.1.21
68379N-acetyl-beta-glucosaminidase+3.2.1.52
68379alpha-glucosidase+3.2.1.20
68379beta-galactosidase+3.2.1.23
68379beta-glucuronidase+3.2.1.31
68379alkaline phosphatase-3.1.3.1
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase-3.5.1.B15

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
18317+---+++++-++-+-++/-++/-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
18317-++-++--+++++++++--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7248compost, cattle farmnear DaejeonRepublic of KoreaKORAsia
67770Compost at a cattle farm near DaejeonRepublic of KoreaKORAsia
67771From compost at a cattle farmDaejeonRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture#Livestock (Husbandry)
#Engineered#Biodegradation#Composting
#Host#Mammals#Bovinae (Cow, Cattle)

taxonmaps

  • @ref: 69479
  • File name: preview.99_127742.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_432;97_1685;98_4020;99_127742&stattab=map
  • Last taxonomy: Cellulomonas chitinilytica
  • 16S sequence: AB268586
  • Sequence Identity:
  • Total samples: 207
  • soil counts: 182
  • aquatic counts: 10
  • animal counts: 9
  • plant counts: 6

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
183171German classification
72481Risk group (German classification)

Sequence information

16S sequences

  • @ref: 7248
  • description: Cellulomonas chitinilytica gene for 16S rRNA, partial sequence
  • accession: AB268586
  • length: 1460
  • database: ena
  • NCBI tax ID: 1305865

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Cellulomonas chitinilytica NBRC 110799GCA_016862675contigncbi398759
66792Cellulomonas chitinilytica JCM 16927GCA_001314205contigncbi1305865
66792Cellulomonas chitinilytica JCM 169271305865.3wgspatric1305865
66792Cellulomonas chitinilytica strain NBRC 110799398759.3wgspatric398759
66792Cellulomonas chitinilytica JCM 169272734481976draftimg1305865

GC content

@refGC-contentmethod
724873.6
6777073.6high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes98no
motileno77.459yes
gram-positiveyes67.874no
anaerobicno94.799yes
halophileno90.975no
spore-formingno94.01yes
thermophileno96.644yes
glucose-utilyes92.151yes
flagellatedno93.614no
aerobicyes82.085no
glucose-fermentyes53.574yes

External links

@ref: 7248

culture collection no.: DSM 17922, KCTC 19133, JCM 16927, NBRC 110799

straininfo link

  • @ref: 71927
  • straininfo: 397709

literature

  • topic: Phylogeny
  • Pubmed-ID: 18676473
  • title: Cellulomonas chitinilytica sp. nov., a chitinolytic bacterium isolated from cattle-farm compost.
  • authors: Yoon MH, Ten LN, Im WT, Lee ST
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.64768-0
  • year: 2008
  • mesh: *Animal Husbandry, Animals, Bacterial Typing Techniques, Base Composition, Cattle, Cellulomonas/*classification/genetics/isolation & purification/physiology, Chitin/*metabolism, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species Specificity
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7248Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17922)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17922
18317Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM17922.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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
31988Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2824228776041
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/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68379Automatically annotated from API Coryne
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
71927Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID397709.1StrainInfo: A central database for resolving microbial strain identifiers