Strain identifier

BacDive ID: 2370

Type strain: Yes

Species: Cellulomonas terrae

Strain Designation: DB 5, DB5

Strain history: CIP <- 2005, KCTC <- D. S. An: strain DB5

For citation purpose refer to the digital object identifier (doi) of the current version.
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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 idMatching level
311234species
1305858strain

strain history

@refhistory
7186<- S.-T. Lee <- D.-S. An; DB 5
67770NBRC 100819 <-- S.-T. Lee DB5.
67771<- ST Lee, KAIST
123451CIP <- 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

@refgram staincell shapemotilityconfidence
31503positiverod-shapedno
67771positive
69480no95.09
69480positive100
123451positiverod-shapedno

colony morphology

  • @ref: 123451

pigmentation

  • @ref: 31503
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7186TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: 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
38352MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
123451CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
7186positivegrowth28mesophilic
31503positivegrowth04-45
38352positivegrowth30mesophilic
67770positivegrowth28mesophilic
67771positivegrowth30mesophilic
123451positivegrowth15-37
123451nogrowth10psychrophilic
123451nogrowth41thermophilic
123451nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31503facultative anaerobe
67771aerobe
123451obligate aerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.914

halophily

@refsaltgrowthtested relationconcentration
31503NaClpositivegrowth<4 %
123451NaClpositivegrowth0-6 %
123451NaClnogrowth8 %
123451NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: MK-9(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
31503581435-dehydro-D-gluconate+carbon source
3150322599arabinose+carbon source
3150317057cellobiose+carbon source
3150328757fructose+carbon source
3150328260galactose+carbon source
3150317234glucose+carbon source
3150317754glycerol+carbon source
3150328087glycogen+carbon source
3150317306maltose+carbon source
3150337684mannose+carbon source
3150328053melibiose+carbon source
31503506227N-acetylglucosamine+carbon source
3150316634raffinose+carbon source
3150326546rhamnose+carbon source
3150317992sucrose+carbon source
3150327082trehalose+carbon source
3150318222xylose+carbon source
315034853esculin+hydrolysis
3150317632nitrate+reduction
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
6837117151xylitol-builds acid from
6837128087glycogen+builds acid from
6837128017starch+builds acid from
6837116634raffinose+builds acid from
683716731melezitose+builds acid from
6837115443inulin-builds acid from
6837117992sucrose+builds acid from
6837128053melibiose+builds acid from
6837117716lactose-builds acid from
6837117306maltose+builds acid from
6837117057cellobiose+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
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol+builds acid from
1234514853esculin+hydrolysis
123451606565hippurate+hydrolysis
12345117632nitrate+reduction
12345116301nitrite-reduction
12345117632nitrate-respiration

metabolite production

  • @ref: 123451
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12345115688acetoin-
12345117234glucose+

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
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
123451oxidase-
123451beta-galactosidase+3.2.1.23
123451alcohol dehydrogenase-1.1.1.1
123451gelatinase-
123451amylase+
123451DNase+
123451caseinase+3.4.21.50
123451catalase-1.11.1.6
123451tween esterase-
123451gamma-glutamyltransferase-2.3.2.2
123451lecithinase-
123451lipase-
123451lysine decarboxylase-4.1.1.18
123451ornithine decarboxylase-4.1.1.17
123451phenylalanine ammonia-lyase-4.3.1.24
123451protease-
123451tryptophan deaminase-
123451urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
123451-+++-+----++++-+++--

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
123451+--+-+---+/-+++-------+/-+/-+/-+/-+/-+/-++-+++/--++++-+/-+--------+/-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7186garden soilDaejonRepublic of KoreaKORAsia
67770SoilDaejeonRepublic of KoreaKORAsia
67771From soilRepublic of KoreaKORAsia
123451Environment, SoilYusong, DaejeonRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#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

@refbiosafety levelbiosafety level comment
71861Risk group (German classification)
1234511Risk 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

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Cellulomonas terrae JCM 14899GCA_001314065contigncbi1305858
66792Cellulomonas terrae JCM 148991305858.3wgspatric1305858
66792Cellulomonas terrae strain NBRC 100819311234.4wgspatric311234
66792Cellulomonas terrae JCM 148992734481970draftimg1305858
67770Cellulomonas terrae NBRC 100819GCA_007990265contigncbi311234

GC content

@refGC-contentmethod
718673.9
6777073.9high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno74no
motileno87.225yes
gram-positiveyes90.338yes
anaerobicno97.77yes
halophileno93.021no
spore-formingno93.529no
thermophileno97.652yes
glucose-utilyes88.203no
aerobicyes87.231no
flagellatedno97.681no
glucose-fermentno64.171no

External links

@ref: 7186

culture collection no.: DSM 17791, KCTC 19081, NBRC 100819, JCM 14899, CIP 108880

straininfo link

  • @ref: 71925
  • straininfo: 232311

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16014505Cellulomonas 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 STInt J Syst Evol Microbiol10.1099/ijs.0.63696-02005Bacterial 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/*metabolismMetabolism
Phylogeny30702420Cellulomonas rhizosphaerae sp. nov., a novel actinomycete isolated from soil.Tian Y, Han C, Hu J, Zhao J, Zhang C, Guo X, Wang X, Xiang WInt J Syst Evol Microbiol10.1099/ijsem.0.0032582019Bacterial 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/chemistryTranscriptome
Phylogeny32038002Cellulomonas 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 JInt J Syst Evol Microbiol10.1099/ijsem.0.0039392020Animals, 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/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7186Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17791)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17791
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
31503Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2780128776041
38352Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6558
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
68371Automatically annotated from API 50CH acid
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)
71925Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID232311.1StrainInfo: A central database for resolving microbial strain identifiers
123451Curators of the CIPCollection of Institut Pasteur (CIP 108880)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108880