Strain identifier
BacDive ID: 2370
Type strain:
Species: Cellulomonas terrae
Strain Designation: DB 5, DB5
Strain history: CIP <- 2005, KCTC <- D. S. An: strain DB5
NCBI tax ID(s): 1305858 (strain), 311234 (species)
General
@ref: 7186
BacDive-ID: 2370
DSM-Number: 17791
keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-positive, rod-shaped
description: Cellulomonas terrae DB 5 is a facultative anaerobe, mesophilic, Gram-positive bacterium that was isolated from garden soil.
NCBI tax id
NCBI tax id | Matching level |
---|---|
311234 | species |
1305858 | strain |
strain history
@ref | history |
---|---|
7186 | <- S.-T. Lee <- D.-S. An; DB 5 |
67770 | NBRC 100819 <-- S.-T. Lee DB5. |
67771 | <- ST Lee, KAIST |
123451 | CIP <- 2005, KCTC <- D. S. An: strain DB5 |
doi: 10.13145/bacdive2370.20230509.8.1
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 terrae
- full scientific name: Cellulomonas terrae An et al. 2005
@ref: 7186
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Cellulomonadaceae
genus: Cellulomonas
species: Cellulomonas terrae
full scientific name: Cellulomonas terrae An et al. 2005
strain designation: DB 5, DB5
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell shape | motility | confidence |
---|---|---|---|---|
31503 | positive | rod-shaped | no | |
67771 | positive | |||
69480 | no | 95.09 | ||
69480 | positive | 100 | ||
123451 | positive | rod-shaped | no |
colony morphology
- @ref: 123451
pigmentation
- @ref: 31503
- production: yes
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
7186 | TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) | yes | https://mediadive.dsmz.de/medium/92 | Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water |
38352 | MEDIUM 72- for trypto casein soja agar | yes | Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g) | |
123451 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
7186 | positive | growth | 28 | mesophilic |
31503 | positive | growth | 04-45 | |
38352 | positive | growth | 30 | mesophilic |
67770 | positive | growth | 28 | mesophilic |
67771 | positive | growth | 30 | mesophilic |
123451 | positive | growth | 15-37 | |
123451 | no | growth | 10 | psychrophilic |
123451 | no | growth | 41 | thermophilic |
123451 | no | growth | 45 | thermophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
31503 | facultative anaerobe |
67771 | aerobe |
123451 | obligate aerobe |
spore formation
- @ref: 69480
- spore formation: no
- confidence: 99.914
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
31503 | NaCl | positive | growth | <4 % |
123451 | NaCl | positive | growth | 0-6 % |
123451 | NaCl | no | growth | 8 % |
123451 | NaCl | no | growth | 10 % |
observation
- @ref: 67770
- observation: quinones: MK-9(H4)
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
31503 | 58143 | 5-dehydro-D-gluconate | + | carbon source |
31503 | 22599 | arabinose | + | carbon source |
31503 | 17057 | cellobiose | + | carbon source |
31503 | 28757 | fructose | + | carbon source |
31503 | 28260 | galactose | + | carbon source |
31503 | 17234 | glucose | + | carbon source |
31503 | 17754 | glycerol | + | carbon source |
31503 | 28087 | glycogen | + | carbon source |
31503 | 17306 | maltose | + | carbon source |
31503 | 37684 | mannose | + | carbon source |
31503 | 28053 | melibiose | + | carbon source |
31503 | 506227 | N-acetylglucosamine | + | carbon source |
31503 | 16634 | raffinose | + | carbon source |
31503 | 26546 | rhamnose | + | carbon source |
31503 | 17992 | sucrose | + | carbon source |
31503 | 27082 | trehalose | + | carbon source |
31503 | 18222 | xylose | + | carbon source |
31503 | 4853 | esculin | + | hydrolysis |
31503 | 17632 | nitrate | + | reduction |
68371 | Potassium 2-ketogluconate | - | builds acid from | |
68371 | 24265 | gluconate | - | builds acid from |
68371 | 18403 | L-arabitol | - | builds acid from |
68371 | 18333 | D-arabitol | - | builds acid from |
68371 | 18287 | L-fucose | - | builds acid from |
68371 | 28847 | D-fucose | - | builds acid from |
68371 | 16443 | D-tagatose | - | builds acid from |
68371 | 62318 | D-lyxose | - | builds acid from |
68371 | 32528 | turanose | + | builds acid from |
68371 | 17151 | xylitol | - | builds acid from |
68371 | 28087 | glycogen | + | builds acid from |
68371 | 28017 | starch | + | builds acid from |
68371 | 16634 | raffinose | + | builds acid from |
68371 | 6731 | melezitose | + | builds acid from |
68371 | 15443 | inulin | - | builds acid from |
68371 | 17992 | sucrose | + | builds acid from |
68371 | 28053 | melibiose | + | builds acid from |
68371 | 17716 | lactose | - | builds acid from |
68371 | 17306 | maltose | + | builds acid from |
68371 | 17057 | cellobiose | + | builds acid from |
68371 | 43943 | methyl alpha-D-mannoside | - | builds acid from |
68371 | 17924 | D-sorbitol | - | builds acid from |
68371 | 16899 | D-mannitol | - | builds acid from |
68371 | 17268 | myo-inositol | - | builds acid from |
68371 | 16813 | galactitol | - | builds acid from |
68371 | 62345 | L-rhamnose | - | builds acid from |
68371 | 17266 | L-sorbose | - | builds acid from |
68371 | 16024 | D-mannose | + | builds acid from |
68371 | 15824 | D-fructose | + | builds acid from |
68371 | 17634 | D-glucose | + | builds acid from |
68371 | 74863 | methyl beta-D-xylopyranoside | - | builds acid from |
68371 | 15963 | ribitol | - | builds acid from |
68371 | 65328 | L-xylose | - | builds acid from |
68371 | 65327 | D-xylose | + | builds acid from |
68371 | 16988 | D-ribose | - | builds acid from |
68371 | 30849 | L-arabinose | + | builds acid from |
68371 | 17108 | D-arabinose | - | builds acid from |
68371 | 17113 | erythritol | - | builds acid from |
68371 | 17754 | glycerol | + | builds acid from |
123451 | 4853 | esculin | + | hydrolysis |
123451 | 606565 | hippurate | + | hydrolysis |
123451 | 17632 | nitrate | + | reduction |
123451 | 16301 | nitrite | - | reduction |
123451 | 17632 | nitrate | - | respiration |
metabolite production
- @ref: 123451
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
@ref | Chebi-ID | metabolite | voges-proskauer-test | methylred-test |
---|---|---|---|---|
123451 | 15688 | acetoin | - | |
123451 | 17234 | glucose | + |
enzymes
@ref | value | activity | ec |
---|---|---|---|
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 |
123451 | oxidase | - | |
123451 | beta-galactosidase | + | 3.2.1.23 |
123451 | alcohol dehydrogenase | - | 1.1.1.1 |
123451 | gelatinase | - | |
123451 | amylase | + | |
123451 | DNase | + | |
123451 | caseinase | + | 3.4.21.50 |
123451 | catalase | - | 1.11.1.6 |
123451 | tween esterase | - | |
123451 | gamma-glutamyltransferase | - | 2.3.2.2 |
123451 | lecithinase | - | |
123451 | lipase | - | |
123451 | lysine decarboxylase | - | 4.1.1.18 |
123451 | ornithine decarboxylase | - | 4.1.1.17 |
123451 | phenylalanine ammonia-lyase | - | 4.3.1.24 |
123451 | protease | - | |
123451 | tryptophan deaminase | - | |
123451 | urease | - | 3.5.1.5 |
API zym
@ref | Control | 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
123451 | - | + | + | + | - | + | - | - | - | - | + | + | + | + | - | + | + | + | - | - |
API 50CHac
@ref | GLY | ERY | DARA | LARA | RIB | DXYL | LXYL | ADO | MDX | GAL | GLU | FRU | MNE | SBE | RHA | DUL | INO | MAN | SOR | MDM | MDG | NAG | AMY | ARB | ESC | SAL | CEL | MAL | LAC | MEL | SAC | TRE | INU | MLZ | RAF | AMD | GLYG | XLT | GEN | TUR | LYX | TAG | DFUC | LFUC | DARL | LARL | GNT | 2KG | 5KG |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
123451 | + | - | - | + | - | + | - | - | - | +/- | + | + | + | - | - | - | - | - | - | - | +/- | +/- | +/- | +/- | +/- | +/- | + | + | - | + | + | +/- | - | + | + | + | + | - | +/- | + | - | - | - | - | - | - | - | - | +/- |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
7186 | garden soil | Daejon | Republic of Korea | KOR | Asia |
67770 | Soil | Daejeon | Republic of Korea | KOR | Asia |
67771 | From soil | Republic of Korea | KOR | Asia | |
123451 | Environment, Soil | Yusong, Daejeon | Republic of Korea | KOR | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Terrestrial | #Soil |
#Engineered | #Agriculture | #Garden |
taxonmaps
- @ref: 69479
- File name: preview.99_7325.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_432;97_1685;98_2637;99_7325&stattab=map
- Last taxonomy: Cellulomonas terrae
- 16S sequence: AY884570
- Sequence Identity:
- Total samples: 896
- soil counts: 628
- aquatic counts: 80
- animal counts: 97
- plant counts: 91
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
7186 | 1 | Risk group (German classification) |
123451 | 1 | Risk group (French classification) |
Sequence information
16S sequences
- @ref: 7186
- description: Cellulomonas terrae 16S ribosomal RNA gene, partial sequence
- accession: AY884570
- length: 1475
- database: ena
- NCBI tax ID: 311234
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Cellulomonas terrae JCM 14899 | GCA_001314065 | contig | ncbi | 1305858 |
66792 | Cellulomonas terrae JCM 14899 | 1305858.3 | wgs | patric | 1305858 |
66792 | Cellulomonas terrae strain NBRC 100819 | 311234.4 | wgs | patric | 311234 |
66792 | Cellulomonas terrae JCM 14899 | 2734481970 | draft | img | 1305858 |
67770 | Cellulomonas terrae NBRC 100819 | GCA_007990265 | contig | ncbi | 311234 |
GC content
@ref | GC-content | method |
---|---|---|
7186 | 73.9 | |
67770 | 73.9 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 74 | no |
motile | no | 87.225 | yes |
gram-positive | yes | 90.338 | yes |
anaerobic | no | 97.77 | yes |
halophile | no | 93.021 | no |
spore-forming | no | 93.529 | no |
thermophile | no | 97.652 | yes |
glucose-util | yes | 88.203 | no |
aerobic | yes | 87.231 | no |
flagellated | no | 97.681 | no |
glucose-ferment | no | 64.171 | no |
External links
@ref: 7186
culture collection no.: DSM 17791, KCTC 19081, NBRC 100819, JCM 14899, CIP 108880
straininfo link
- @ref: 71925
- straininfo: 232311
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 16014505 | Cellulomonas terrae sp. nov., a cellulolytic and xylanolytic bacterium isolated from soil. | An DS, Im WT, Yang HC, Kang MS, Kim KK, Jin L, Kim MK, Lee ST | Int J Syst Evol Microbiol | 10.1099/ijs.0.63696-0 | 2005 | Bacterial Typing Techniques, Cellulomonas/*classification/genetics/isolation & purification/physiology, Cellulose/*metabolism, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species Specificity, Xylans/*metabolism | Metabolism |
Phylogeny | 30702420 | Cellulomonas rhizosphaerae sp. nov., a novel actinomycete isolated from soil. | Tian Y, Han C, Hu J, Zhao J, Zhang C, Guo X, Wang X, Xiang W | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003258 | 2019 | Bacterial Typing Techniques, Base Composition, Cellulomonas/*classification/isolation & purification, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Multilocus Sequence Typing, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/chemistry | Transcriptome |
Phylogeny | 32038002 | Cellulomonas shaoxiangyii sp. nov., isolated from faeces of Tibetan antelope (Pantholops hodgsonii) on the Qinghai-Tibet Plateau. | Tian Z, Lu S, Jin D, Yang J, Pu J, Lai XH, Ren ZH, Wu XM, Li J, Wang S, Xu J | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003939 | 2020 | Animals, Antelopes/*microbiology, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, Cellulomonas/*classification/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Feces/*microbiology, Nucleic Acid Hybridization, Ornithine/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Tibet, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
7186 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17791) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-17791 | |||
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 | |||
31503 | 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 | 27801 | 28776041 | |
38352 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/6558 | ||||
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 | ||||
68371 | Automatically annotated from API 50CH acid | |||||
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) | |||
71925 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID232311.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
123451 | Curators of the CIP | Collection of Institut Pasteur (CIP 108880) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108880 |