Strain identifier
BacDive ID: 2372
Type strain:
Species: Cellulomonas chitinilytica
Strain Designation: XBU-b
Strain history: <- ST Lee, KAIST
NCBI tax ID(s): 1305865 (strain), 398759 (species)
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 id | Matching level |
---|---|
1305865 | strain |
398759 | species |
strain history
@ref | history |
---|---|
7248 | <- Sung-Taik Lee; Xbu-b |
67770 | W.-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
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
31988 | positive | 1.5-2.2 µm | 0.4-0.6 µm | rod-shaped | no | |
67771 | positive | |||||
69480 | positive | 100 |
colony morphology
@ref | colony color | incubation period | medium used |
---|---|---|---|
18317 | Rapeseed yellow (1021) | 10-14 days | ISP 2 |
18317 | Rapeseed yellow (1021) | 10-14 days | ISP 3 |
18317 | Rapeseed yellow (1021) | 10-14 days | ISP 4 |
18317 | Beige (1001) | 10-14 days | ISP 5 |
18317 | Rapeseed yellow (1021) | 10-14 days | ISP 6 |
18317 | Beige (1001) | 10-14 days | ISP 7 |
multicellular morphology
@ref | forms multicellular complex | medium name |
---|---|---|
18317 | no | ISP 2 |
18317 | no | ISP 3 |
18317 | no | ISP 4 |
18317 | no | ISP 5 |
18317 | no | ISP 6 |
18317 | no | ISP 7 |
pigmentation
- @ref: 31988
- production: yes
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
7248 | R2A MEDIUM (DSMZ Medium 830) | yes | https://mediadive.dsmz.de/medium/830 | Name: 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 |
18317 | ISP 2 | yes | Name: 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 | |
18317 | ISP 3 | yes | Name: 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: | |
18317 | ISP 4 | yes | Name: 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 | |
18317 | ISP 5 | yes | Name: 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 | |
18317 | ISP 6 | yes | Name: 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 | |
18317 | ISP 7 | yes | Name: 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
@ref | growth | type | temperature | range |
---|---|---|---|---|
18317 | positive | optimum | 28 | mesophilic |
7248 | positive | growth | 28 | mesophilic |
31988 | positive | growth | 04-30 | |
31988 | positive | optimum | 25 | mesophilic |
67770 | positive | growth | 28 | mesophilic |
67771 | positive | growth | 30 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
31988 | positive | growth | 5-8.5 | alkaliphile |
31988 | positive | optimum | 6.9-7.5 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
31988 | facultative anaerobe |
67771 | aerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
31988 | no | |
69481 | yes | 98 |
69480 | no | 99.396 |
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
@ref | observation |
---|---|
31988 | aggregates in chains |
67770 | quinones: MK-9(H4) |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
31988 | 30089 | acetate | + | carbon source |
31988 | 17057 | cellobiose | + | carbon source |
31988 | 28757 | fructose | + | carbon source |
31988 | 24265 | gluconate | + | carbon source |
31988 | 17234 | glucose | + | carbon source |
31988 | 29987 | glutamate | + | carbon source |
31988 | 17754 | glycerol | + | carbon source |
31988 | 28087 | glycogen | + | carbon source |
31988 | 17716 | lactose | + | carbon source |
31988 | 15792 | malonate | + | carbon source |
31988 | 29864 | mannitol | + | carbon source |
31988 | 37684 | mannose | + | carbon source |
31988 | 506227 | N-acetylglucosamine | + | carbon source |
31988 | 18401 | phenylacetate | + | carbon source |
31988 | 15361 | pyruvate | + | carbon source |
31988 | 16634 | raffinose | + | carbon source |
31988 | 17814 | salicin | + | carbon source |
31988 | 30911 | sorbitol | + | carbon source |
31988 | 18222 | xylose | + | carbon source |
31988 | 17632 | nitrate | + | reduction |
68379 | 17632 | nitrate | + | reduction |
68379 | 4853 | esculin | + | hydrolysis |
68379 | 16199 | urea | - | hydrolysis |
68379 | 5291 | gelatin | + | hydrolysis |
68379 | 17634 | D-glucose | + | fermentation |
68379 | 16988 | D-ribose | - | fermentation |
68379 | 65327 | D-xylose | + | fermentation |
68379 | 16899 | D-mannitol | - | fermentation |
68379 | 17306 | maltose | + | fermentation |
68379 | 17992 | sucrose | + | fermentation |
enzymes
@ref | value | activity | ec |
---|---|---|---|
31988 | catalase | + | 1.11.1.6 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 |
68382 | beta-glucosidase | + | 3.2.1.21 |
68382 | alpha-glucosidase | + | 3.2.1.20 |
68382 | beta-glucuronidase | + | 3.2.1.31 |
68382 | beta-galactosidase | + | 3.2.1.23 |
68382 | alpha-galactosidase | + | 3.2.1.22 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | alpha-chymotrypsin | + | 3.4.21.1 |
68382 | trypsin | - | 3.4.21.4 |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | valine arylamidase | + | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | lipase (C 14) | - | |
68382 | esterase lipase (C 8) | + | |
68382 | esterase (C 4) | + | |
68382 | alkaline phosphatase | - | 3.1.3.1 |
68379 | gelatinase | + | |
68379 | urease | - | 3.5.1.5 |
68379 | beta-glucosidase | + | 3.2.1.21 |
68379 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 |
68379 | alpha-glucosidase | + | 3.2.1.20 |
68379 | beta-galactosidase | + | 3.2.1.23 |
68379 | beta-glucuronidase | + | 3.2.1.31 |
68379 | alkaline phosphatase | - | 3.1.3.1 |
68379 | pyrrolidonyl arylamidase | - | 3.4.19.3 |
68379 | pyrazinamidase | - | 3.5.1.B15 |
API coryne
@ref | NIT | PYZ | PYRA | PAL | beta GUR | beta GAL | alpha GLU | beta NAG | ESC | URE | GEL | GLU | RIB | XYL | MAN | MAL | LAC | SAC | GLYG |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
18317 | + | - | - | - | + | + | + | + | + | - | + | + | - | + | - | + | +/- | + | +/- |
API zym
@ref | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
18317 | - | + | + | - | + | + | - | - | + | + | + | + | + | + | + | + | + | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
7248 | compost, cattle farm | near Daejeon | Republic of Korea | KOR | Asia |
67770 | Compost at a cattle farm near Daejeon | Republic of Korea | KOR | Asia | |
67771 | From compost at a cattle farm | Daejeon | Republic of Korea | KOR | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | biosafety level | biosafety level comment |
---|---|---|
18317 | 1 | German classification |
7248 | 1 | Risk 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
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Cellulomonas chitinilytica NBRC 110799 | GCA_016862675 | contig | ncbi | 398759 |
66792 | Cellulomonas chitinilytica JCM 16927 | GCA_001314205 | contig | ncbi | 1305865 |
66792 | Cellulomonas chitinilytica JCM 16927 | 1305865.3 | wgs | patric | 1305865 |
66792 | Cellulomonas chitinilytica strain NBRC 110799 | 398759.3 | wgs | patric | 398759 |
66792 | Cellulomonas chitinilytica JCM 16927 | 2734481976 | draft | img | 1305865 |
GC content
@ref | GC-content | method |
---|---|---|
7248 | 73.6 | |
67770 | 73.6 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 98 | no |
motile | no | 77.459 | yes |
gram-positive | yes | 67.874 | no |
anaerobic | no | 94.799 | yes |
halophile | no | 90.975 | no |
spore-forming | no | 94.01 | yes |
thermophile | no | 96.644 | yes |
glucose-util | yes | 92.151 | yes |
flagellated | no | 93.614 | no |
aerobic | yes | 82.085 | no |
glucose-ferment | yes | 53.574 | yes |
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
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
7248 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17922) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-17922 | |||
18317 | Wink, J. | http://www.dsmz.de/microorganisms/wink_pdf/DSM17922.pdf | Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
31988 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 28242 | 28776041 | |
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | ||||
68379 | Automatically annotated from API Coryne | |||||
68382 | Automatically annotated from API zym | |||||
69479 | João 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 | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
71927 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID397709.1 | StrainInfo: A central database for resolving microbial strain identifiers |