Strain identifier

BacDive ID: 2352

Type strain: Yes

Species: Cellulomonas fimi

Strain Designation: 133, NRS-133

Strain history: CIP <- 1986, DSM <- ATCC <- N.R. Smith: strain NRS-133

NCBI tax ID(s): 590998 (strain), 1708 (species)

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General

@ref: 8538

BacDive-ID: 2352

DSM-Number: 20113

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, motile, rod-shaped

description: Cellulomonas fimi 133 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from soil.

NCBI tax id

NCBI tax idMatching level
1708species
590998strain

strain history

@refhistory
8538<- ATCC <- N.R. Smith, 133
67770K. Suzuki CNF 025 <-- AJ 1571 <-- ATCC 484 <-- N. R. Smith NRS 133.
119351CIP <- 1986, DSM <- ATCC <- N.R. Smith: strain NRS-133

doi: 10.13145/bacdive2352.20230509.8.1

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 fimi
  • full scientific name: Cellulomonas fimi (McBeth and Scales 1913) Bergey et al. 1923 (Approved Lists 1980)

  • synonyms

    • @ref: 20215
    • synonym: Bacterium fimi

@ref: 8538

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Cellulomonadaceae

genus: Cellulomonas

species: Cellulomonas fimi

full scientific name: Cellulomonas fimi (McBeth and Scales 1913) Bergey et al. 1923 emend. Nouioui et al. 2018

strain designation: 133, NRS-133

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
43361positiverod-shapedyes
69480positive100
119351positiverod-shapedyes

colony morphology

@refcolony colorincubation periodmedium usedcolony size
18304Colorless10-14 daysISP 2
18304Colorless10-14 daysISP 3
43361white or yellowyeast extract glucose agar5 mm

multicellular morphology

@refforms multicellular complexmedium name
18304noISP 2
18304noISP 3

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
18304ISP 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
18304ISP 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:
8538CORYNEBACTERIUM 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
40361MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
43361yeast extract glucose agaryespeptone 1%, yeast extract 0.5%, glucose 0.5%, agar 1%
119351CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
18304positiveoptimum28mesophilic
8538positivegrowth30mesophilic
40361positivegrowth30mesophilic
67770positivegrowth28mesophilic
119351positivegrowth30-41

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
43361aerobe
119351facultative anaerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.56

halophily

  • @ref: 18304
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0 %

murein

  • @ref: 8538
  • murein short key: A21.05
  • type: A4ß L-Orn-D-Glu

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4336116651(S)-lactate+assimilation
4336130089acetate-assimilation
4336162968cellulose+degradation
4336124265gluconate-assimilation
4336117632nitrate+reduction
4336116634raffinose-assimilation
4336133942ribose-assimilation
68371Potassium 5-ketogluconate-builds acid from
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
6837132528turanose+builds acid from
6837128066gentiobiose+builds acid from
6837128087glycogen+builds acid from
6837128017starch+builds acid from
6837116634raffinose+builds acid from
683716731melezitose+builds acid from
6837115443inulin-builds acid from
6837127082trehalose+builds acid from
6837117992sucrose+builds acid from
6837128053melibiose+builds acid from
6837117716lactose+builds acid from
6837117306maltose+builds acid from
6837117057cellobiose+builds acid from
6837117814salicin+builds acid from
683714853esculin+builds acid from
6837118305arbutin+builds acid from
6837127613amygdalin+builds acid from
6837159640N-acetylglucosamine+builds acid from
68371320061methyl alpha-D-glucopyranoside+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
6837112936D-galactose+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
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis
1193514853esculin+hydrolysis
119351606565hippurate-hydrolysis
11935117632nitrate+reduction
11935116301nitrite-reduction
11935117234glucose+degradation
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-
11935115688acetoin-

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
119351oxidase-
119351beta-galactosidase+3.2.1.23
119351alcohol dehydrogenase-1.1.1.1
119351gelatinase-
119351amylase+
119351caseinase+3.4.21.50
119351catalase+1.11.1.6
119351lecithinase-
119351lysine decarboxylase-4.1.1.18
119351ornithine decarboxylase-4.1.1.17
119351urease-3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
18304--+-+++--++++-+++--

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
18304--+-+++--++++-+++--

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
18304+----------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119351+--+-+---++++-+-----++++++++++++-+++++/-+++/---------

Isolation, sampling and environmental information

isolation

@refsample type
8538soil
47916Soil
67770Soil
119351Environment, Soil

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_3465.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_432;97_1685;98_2660;99_3465&stattab=map
  • Last taxonomy: Cellulomonas
  • 16S sequence: X79460
  • Sequence Identity:
  • Total samples: 959
  • soil counts: 529
  • aquatic counts: 122
  • animal counts: 233
  • plant counts: 75

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
183041Hazard group
85381Risk group (German classification)
1193511Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218C.fimi DSM 20113 16S rDNAX794601486ena590998
20218C.fimi 16S rRNA geneX838031452ena590998

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Cellulomonas fimi ATCC 484GCA_000212695completencbi590998
66792Cellulomonas fimi NCTC7547GCA_900637695completencbi1708
66792Cellulomonas fimi ATCC 484590998.5completepatric590998
66792Cellulomonas fimi strain NCTC75471708.3completepatric1708
66792Cellulomonas fimi NRS 133, ATCC 4842505679089completeimg590998

GC content

@refGC-contentmethod
853871.7
4336171.3thermal denaturation, midpoint method (Tm)
6777071.7thermal denaturation, midpoint method (Tm)
6777074.7genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes76no
motileyes81.349yes
flagellatedno92.921no
gram-positiveyes90.6yes
anaerobicno98.852yes
aerobicyes83.471yes
halophileno95.739yes
spore-formingno80.732no
thermophileno97.822yes
glucose-utilyes87.314no
glucose-fermentno66.768no

External links

@ref: 8538

culture collection no.: DSM 20113, ATCC 484, NCIB 8980, NCTC 7547, CCUG 24087, JCM 1341, BCRC 14867, CECT 4283, CFBP 4254, CGMCC 1.1900, CIP 102114, HAMBI 93, IAM 12107, IFO 15513, IMET 10687, KCTC 1436, LMG 16345, NBRC 15513, NCAIM B.01386, NCCB 29016, NCIMB 11341, NCIMB 8980, VKM Ac-1411, VTT E-93020

straininfo link

  • @ref: 71907
  • straininfo: 92513

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19060084Cellulomonas aerilata sp. nov., isolated from an air sample.Lee CM, Weon HY, Hong SB, Jeon YA, Schumann P, Kroppenstedt RM, Kwon SW, Stackebrandt EInt J Syst Evol Microbiol10.1099/ijs.0.2008/002253-02008*Air Microbiology, Cellulomonas/chemistry/*classification/genetics/*physiology, Fatty Acids/analysis, Korea, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Species SpecificityGenetics
Phylogeny20729313Cellulomonas phragmiteti sp. nov., a cellulolytic bacterium isolated from reed (Phragmites australis) periphyton in a shallow soda pond.Rusznyak A, Toth EM, Schumann P, Sproer C, Makk J, Szabo G, Vladar P, Marialigeti K, Borsodi AKInt J Syst Evol Microbiol10.1099/ijs.0.022608-02010Bacterial Typing Techniques, Base Composition, Cellulomonas/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hungary, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, *Phylogeny, Poaceae/*microbiology, Ponds, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny23342046The genome sequences of Cellulomonas fimi and "Cellvibrio gilvus" reveal the cellulolytic strategies of two facultative anaerobes, transfer of "Cellvibrio gilvus" to the genus Cellulomonas, and proposal of Cellulomonas gilvus sp. nov.Christopherson MR, Suen G, Bramhacharya S, Jewell KA, Aylward FO, Mead D, Brumm PJPLoS One10.1371/journal.pone.00539542013Cellulomonas/classification/*genetics/*metabolism, Cellulose/*metabolism, Cellvibrio/classification/*genetics/*metabolism, Energy Metabolism/genetics, Fermentation/genetics, Genome, Bacterial/*genetics, Hydrolysis, Phylogeny, Polysaccharides/metabolism, Sequence Homology, Nucleic AcidMetabolism
Metabolism23793636Saccharification of cellulose by recombinant Rhodococcus opacus PD630 strains.Hetzler S, Broker D, Steinbuchel AAppl Environ Microbiol10.1128/AEM.01214-132013Cellobiose/*metabolism, Cellulases/*biosynthesis/genetics, Cellulose/*metabolism, Gene Expression, Hydrolysis, *Metabolic Engineering, Plasmids, Recombinant Proteins/biosynthesis/genetics, Rhodococcus/*enzymology/genetics/*metabolismEnzymology
Enzymology25225266Characterization of five beta-glycoside hydrolases from Cellulomonas fimi ATCC 484.Gao J, Wakarchuk WJ Bacteriol10.1128/JB.02194-142014Cellulomonas/*enzymology/genetics, Cloning, Molecular, Escherichia coli/genetics, Gene Expression, Glucosides/*metabolism, Glycoside Hydrolases/genetics/*isolation & purification/*metabolism, Recombinant Proteins/genetics/isolation & purification/metabolism, Substrate SpecificityMetabolism
Metabolism25797391Novel alpha-L-arabinofuranosidase from Cellulomonas fimi ATCC 484 and its substrate-specificity analysis with the aid of computer.Yang Y, Zhang L, Guo M, Sun J, Matsukawa S, Xie J, Wei DJ Agric Food Chem10.1021/jf50596832015Amino Acid Sequence, Bacterial Proteins/*chemistry/genetics/metabolism, Cellulomonas/chemistry/*enzymology/genetics, Cloning, Molecular, Computational Biology, Glycoside Hydrolases/*chemistry/genetics/metabolism, Molecular Docking Simulation, Molecular Sequence Data, Oligosaccharides/chemistry/metabolism, Sequence Alignment, Substrate Specificity, Xylans/chemistry/metabolismEnzymology
Metabolism26950732Proteomic Analysis of the Secretome of Cellulomonas fimi ATCC 484 and Cellulomonas flavigena ATCC 482.Wakarchuk WW, Brochu D, Foote S, Robotham A, Saxena H, Erak T, Kelly JPLoS One10.1371/journal.pone.01511862016Carboxymethylcellulose Sodium/metabolism, Cellulomonas/enzymology/*metabolism, *Proteomics, Species Specificity, Xylans/metabolismPhylogeny
Enzymology28982013Characterization of a thermostable endoglucanase from Cellulomonas fimi ATCC484.Saxena H, Hsu B, de Asis M, Zierke M, Sim L, Withers SG, Wakarchuk WBiochem Cell Biol10.1139/bcb-2017-01502017Biomass, Cell Wall/metabolism, Cellulase/chemistry/*metabolism, Cellulomonas/*enzymology, Enzyme Stability, Hydrolysis, Protein Denaturation, *TemperatureMetabolism
Phenotype29557768Genetic variation during long-term preservation of bacteria in public culture collections.Sakurai K, Kawasaki HInt J Syst Evol Microbiol10.1099/ijsem.0.0027172018Bacteria/*genetics, Bacterial Typing Techniques, *Biological Specimen Banks, DNA, Bacterial/genetics, Exons, Introns, Phenotype, *Polymorphism, Single Nucleotide, Sequence Analysis, DNATranscriptome
Metabolism31147220Direct electron transfer of Cellulomonas fimi and microbial fuel cells fueled by cellulose.Khawdas W, Watanabe K, Karatani H, Aso Y, Tanaka T, Ohara HJ Biosci Bioeng10.1016/j.jbiosc.2019.05.0012019Bioelectric Energy Sources, Cellulomonas/*metabolism, Cellulose/metabolism, Electrodes, Electron Transport, Oxidation-Reduction
Phylogeny31218500Cellulomonas aurantiaca sp. nov., isolated from a soil sample from a tangerine field.Kim SK, Kook M, Yan ZF, Trinh H, Zheng SD, Yang JE, Park SY, Yi THAntonie Van Leeuwenhoek10.1007/s10482-019-01288-22019Cellulomonas/*classification/genetics/*isolation & purification, *Citrus, Genome, Bacterial, Genomics/methods, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Soil, *Soil MicrobiologyGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8538Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20113)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20113
18304Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM20113.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
40361Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/13765
43361Erko Stackenbrandt, Otto Kandler10.1099/00207713-29-4-273Taxonomy of the Genus Cellulomonas, Based on Phenotypic Characters and Deoxyribonucleic Acid-Deoxyribonucleic Acid Homology, and Proposal of Seven Neotype StrainsIJSEM 29: 273-282 1979
47916Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 24087)https://www.ccug.se/strain?id=24087
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68368Automatically annotated from API 20E
68371Automatically annotated from API 50CH acid
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)
71907Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID92513.1StrainInfo: A central database for resolving microbial strain identifiers
119351Curators of the CIPCollection of Institut Pasteur (CIP 102114)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20102114