Strain identifier

BacDive ID: 2357

Type strain: Yes

Species: Cellulomonas uda

Strain Designation: 136, NRS-136

Strain history: CIP <- 1986, DSM <- ATCC <- N.R. Smith: strain NRS-136

NCBI tax ID(s): 1714 (species)

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General

@ref: 8532

BacDive-ID: 2357

DSM-Number: 20107

keywords: genome sequence, 16S sequence, Bacteria, spore-forming, mesophilic

description: Cellulomonas uda 136 is a spore-forming, mesophilic bacterium that was isolated from compost.

NCBI tax id

  • NCBI tax id: 1714
  • Matching level: species

strain history

@refhistory
8532<- ATCC <- N.R. Smith, 136
67770K. Suzuki CNF 200 <-- AJ 1568 <-- ATCC 491 <-- N. R. Smith NRS 136.
123708CIP <- 1986, DSM <- ATCC <- N.R. Smith: strain NRS-136

doi: 10.13145/bacdive2357.20230509.8.1

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 uda
  • full scientific name: Cellulomonas uda (Kellerman et al. 1913) Bergey et al. 1923 (Approved Lists 1980)

  • synonyms

    • @ref: 20215
    • synonym: Bacterium udum

@ref: 8532

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Cellulomonadaceae

genus: Cellulomonas

species: Cellulomonas uda

full scientific name: Cellulomonas uda (Kellerman et al. 1913) Bergey et al. 1923

strain designation: 136, NRS-136

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no92.337
69480100positive

colony morphology

@refcolony colorincubation periodmedium used
19788Light ivory (1015)10-14 daysISP 2
19788Light ivory (1015)10-14 daysISP 3

multicellular morphology

@refforms multicellular complexmedium name
19788noISP 2
19788noISP 3

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
19788ISP 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
19788ISP 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:
8532CORYNEBACTERIUM AGAR (DSMZ Medium 53)yesName: CORYNEBACTERIUM AGAR (DSMZ Medium 53) Composition: Agar 15.0 g/l Casein peptone 10.0 g/l NaCl 5.0 g/l Glucose 5.0 g/l Yeast extract 5.0 g/l Distilled waterhttps://mediadive.dsmz.de/medium/53
40354MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
123708CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
19788positiveoptimum28mesophilic
8532positivegrowth30mesophilic
40354positivegrowth30mesophilic
67770positivegrowth30mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481yes97
69480no99.923

halophily

  • @ref: 19788
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 5 %

murein

  • @ref: 8532
  • murein short key: A21.05
  • type: A4ß L-Orn-D-Glu

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1978862968cellulose-
1978816634raffinose-
1978826546rhamnose-
1978828757fructose-
1978829864mannitol-
1978817268myo-inositol-
1978818222xylose-
1978817992sucrose-
1978822599arabinose-
1978817234glucose-
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis
6837917632nitrate-reduction
683794853esculin+hydrolysis
6837916199urea+hydrolysis
683795291gelatin+hydrolysis
6837917634D-glucose+fermentation
6837916988D-ribose+fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol+fermentation
6837917306maltose+fermentation
6837917716lactose+fermentation
6837917992sucrose+fermentation
6837928087glycogen-fermentation

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin-
6836835581indole-

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
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
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease-3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase-3.5.3.6
68368beta-galactosidase+3.2.1.23

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
19788--+-+++++++++-++++-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
19788+-+-+++++++++-+++--

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19788+----------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
8532compost
67770Compost from ArlingtonVAUSAUSANorth America
123708Environment, Compost

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Biodegradation
  • Cat3: #Composting

taxonmaps

  • @ref: 69479
  • File name: preview.99_23238.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_432;97_4150;98_5311;99_23238&stattab=map
  • Last taxonomy: Cellulomonas uda
  • 16S sequence: X79457
  • Sequence Identity:
  • Total samples: 39
  • soil counts: 10
  • aquatic counts: 8
  • animal counts: 17
  • plant counts: 4

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
197881Hazard group
85321Risk group (German classification)
1237081Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218C.uda 16S rRNA geneX838011500ena1714
20218C.uda NCIMB 8200 16S rDNAX794571444ena1714

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Cellulomonas uda CECT 4284GCA_011759685scaffoldncbi1714
66792Cellulomonas uda strain CECT 42841714.4wgspatric1714
66792Cellulomonas uda strain NBRC 37471714.3wgspatric1714
66792Cellulomonas uda CECT 42842824343141draftimg1714
67770Cellulomonas uda NBRC 3747GCA_006538705contigncbi1714

GC content

@refGC-contentmethod
853272.0
6777072thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes97no
motileno88.035no
flagellatedno97.093no
gram-positiveyes92.84no
anaerobicno98.687no
aerobicyes79.521no
halophileno92.868no
spore-formingno88.711no
glucose-utilyes78.118yes
thermophileno97.097yes
glucose-fermentno66.938no

External links

@ref: 8532

culture collection no.: DSM 20107, ATCC 491, NCIB 8200, JCM 1492, BCRC 14868, CCUG 24088, CECT 4284, CFBP 4256, CGMCC 1.1916, CIP 102089, IAM 12111, IFO 3747, KCCM 12156, KCTC 1441, LMG 16327, NBRC 3747, NCAIM B.01382, NCIMB 8200, NRRL B-404, VKM Ac-1140

straininfo link

  • @ref: 71912
  • straininfo: 311059

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17551039Cellulomonas composti sp. nov., a cellulolytic bacterium isolated from cattle farm compost.Kang MS, Im WT, Jung HM, Kim MK, Goodfellow M, Kim KK, Yang HC, An DS, Lee STInt J Syst Evol Microbiol10.1099/ijs.0.63974-02007Aerobiosis, Anaerobiosis, Animals, Bacterial Typing Techniques, Carbohydrates/analysis, Cattle, Cell Wall/chemistry, Cellulase/analysis, Cellulomonas/chemistry/*classification/*isolation & purification/physiology, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Genes, rRNA, Korea, Lipids/analysis, Locomotion, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/analysis, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Soil Microbiology, Vitamin K 2/analysis, beta-Glucosidase/analysisGenetics
Phylogeny32877326Cellulomonas citrea sp. nov., isolated from paddy soil.Lee HJ, Kim SY, Whang KSInt J Syst Evol Microbiol10.1099/ijsem.0.0044092020Bacterial Typing Techniques, Base Composition, Cellulomonas/*classification/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, *Oryza, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny35100105Cellulomonas fulva sp. nov., isolated from oil-contaminated soil.Dahal RH, Kim J, Kim DU, Dong K, Hong Y, Chaudhary DKInt J Syst Evol Microbiol10.1099/ijsem.0.0052092022Bacterial Typing Techniques, Base Composition, *Cellulomonas/classification/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, *Petroleum Pollution, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Soil PollutantsTranscriptome
Phylogeny35960648Cellulomonas palmilyticum sp. nov., from earthworm soil biofertilizer with the potential to degrade oil palm empty fruit bunch.Siriatcharanon AK, Sutheeworapong S, Waeonukul R, Pason P, Uke A, Kosugi A, Ratanakhanokchai K, Tachaapaikoon CInt J Syst Evol Microbiol10.1099/ijsem.0.0054942022Animals, Bacterial Typing Techniques, Base Composition, *Cellulomonas, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Fruit, *Oligochaeta, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil, Soil MicrobiologyTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8532Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20107)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20107
19788Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM20107.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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
40354Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/13736
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/
68368Automatically annotated from API 20E
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
71912Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID311059.1StrainInfo: A central database for resolving microbial strain identifiers
123708Curators of the CIPCollection of Institut Pasteur (CIP 102089)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20102089