Strain identifier

BacDive ID: 2369

Type strain: Yes

Species: Cellulomonas bogoriensis

Strain Designation: 69B4

Strain history: CIP <- 2005, DSMZ <- B.E. Jones, Genencor Int., Leiden, The Netherlands: strain 69B4

NCBI tax ID(s): 1386082 (strain), 301388 (species)

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General

@ref: 6592

BacDive-ID: 2369

DSM-Number: 16987

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, spore-forming, mesophilic, Gram-positive, motile, rod-shaped

description: Cellulomonas bogoriensis 69B4 is a facultative anaerobe, spore-forming, mesophilic bacterium that was isolated from sediment and water.

NCBI tax id

NCBI tax idMatching level
1386082strain
301388species

strain history

@refhistory
6592<- B.E.Jones, A. Kramer, strain 69B4
67770CIP 108683 <-- DSM 16987 <-- B. E. Jones; Genencor Int., B.V., Netherlands; 69B4.
116830CIP <- 2005, DSMZ <- B.E. Jones, Genencor Int., Leiden, The Netherlands: strain 69B4

doi: 10.13145/bacdive2369.20230509.8.1

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 bogoriensis
  • full scientific name: Cellulomonas bogoriensis Jones et al. 2005

  • synonyms

    • @ref: 20215
    • synonym: Actinotalea bogoriensis

@ref: 6592

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Cellulomonadaceae

genus: Cellulomonas

species: Cellulomonas bogoriensis

full scientific name: Cellulomonas bogoriensis Jones et al. 2005

strain designation: 69B4

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell shapemotilityconfidence
31481positive0.6 µmrod-shapedyes
69480positive100
116830positiverod-shapedno

colony morphology

@refincubation periodmedium usedcolony color
1974510-14 daysISP 2
1974510-14 daysISP 3Zinc yellow (1018)
116830

multicellular morphology

@refforms multicellular complexmedium name
19745noISP 2
19745noISP 3

pigmentation

  • @ref: 31481
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6592BOGORIELLA MEDIUM (DSMZ Medium 785)yeshttps://mediadive.dsmz.de/medium/785Name: BOGORIELLA MEDIUM (DSMZ Medium 785) Composition: NaCl 40.0 g/l Glucose 10.0 g/l Na2CO3 10.0 g/l Yeast extract 5.0 g/l Peptone 5.0 g/l KH2PO4 1.0 g/l MgSO4 x 7 H2O 0.2 g/l Distilled water
19745ISP 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
19745ISP 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:
36769MEDIUM 6 - Columbia agar with 10 % horse bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
116830CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
116830CIP Medium 6yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6

culture temp

@refgrowthtypetemperaturerange
19745positiveoptimum28mesophilic
6592positivegrowth28mesophilic
31481positivegrowth20-37
31481positiveoptimum33.5mesophilic
36769positivegrowth30mesophilic
67770positivegrowth28mesophilic
116830positivegrowth25-45
116830nogrowth10psychrophilic
116830nogrowth15psychrophilic

culture pH

@refabilitytypepHPH range
31481positivegrowth6.0-10.5alkaliphile
31481positiveoptimum9.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31481facultative anaerobe
116830obligate aerobe

spore formation

@refspore formationconfidence
69481yes99
69480no98.464

halophily

@refsaltgrowthtested relationconcentration
31481NaClpositivegrowth<8.0 %
116830NaClnogrowth0 %
116830NaClnogrowth2 %
116830NaClnogrowth4 %
116830NaClnogrowth6 %
116830NaClnogrowth8 %
116830NaClnogrowth10 %

murein

  • @ref: 6592
  • murein short key: A21.04
  • type: A4ß L-Orn-D-Asp

observation

@refobservation
31481aggregates in clumps
67770quinones: MK-9(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
31481581435-dehydro-D-gluconate+carbon source
3148122599arabinose+carbon source
3148117057cellobiose+carbon source
3148128757fructose+carbon source
314815291gelatin+carbon source
3148117234glucose+carbon source
3148117306maltose+carbon source
3148137684mannose+carbon source
3148126546rhamnose+carbon source
3148117814salicin+carbon source
3148117992sucrose+carbon source
3148118222xylose+carbon source
11683016947citrate-carbon source
1168304853esculin+hydrolysis
116830606565hippurate+hydrolysis
11683017632nitrate-reduction
11683016301nitrite-reduction
11683017632nitrate-respiration
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

antibiotic resistance

  • @ref: 116830
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 116830
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11683015688acetoin-
11683017234glucose-

enzymes

@refvalueactivityec
31481catalase+1.11.1.6
31481gelatinase+
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
116830oxidase-
116830beta-galactosidase+3.2.1.23
116830alcohol dehydrogenase-1.1.1.1
116830gelatinase-
116830amylase+
116830DNase-
116830caseinase+3.4.21.50
116830catalase+1.11.1.6
116830cellulase-3.2.1.4
116830tween esterase-
116830gamma-glutamyltransferase-2.3.2.2
116830lecithinase-
116830lipase-
116830lysine decarboxylase-4.1.1.18
116830ornithine decarboxylase-4.1.1.17
116830phenylalanine ammonia-lyase-4.3.1.24
116830tryptophan deaminase-
116830urease-3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
19745+-----+-++-+-+-----

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
19745-+--+------+--++---

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
6592sediment and waterLake BogoriaKenyaKENAfrica
67770The littoral zone of Lake BogoriaKenyaKENAfrica
116830Environment, Sediment and waterBogoria lakeKenyaKENAfrica1988

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic
#Environmental#Terrestrial#Sediment

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
65921Risk group (German classification)
197451Risk group (German classification)
1168301Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
6592Cellulomonas bogoriensis 16S rRNA gene, type strain 69B4TX921521458ena301388
67770Cellulomonas bogoriaensis 16S rRNA gene, strain 69B4AJ8631641506ena301388

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Cellulomonas bogoriensis 69B4 = DSM 169871386082.3wgspatric1386082
66792Cellulomonas bogoriensis 69B42651869835draftimg1386082
67770Cellulomonas bogoriensis 69B4 = DSM 16987GCA_000767165contigncbi1386082

GC content

@refGC-contentmethod
659271.5
6777071.5high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes99no
motileyes79.362no
gram-positiveyes92.467yes
anaerobicno97.799yes
halophileno66.198yes
spore-formingno76.648no
glucose-utilyes88.15yes
thermophileno97.598no
aerobicyes69.203yes
flagellatedno87.356no
glucose-fermentno61.56yes

External links

@ref: 6592

culture collection no.: DSM 16987, CIP 108683, JCM 30720

straininfo link

  • @ref: 71924
  • straininfo: 265389

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16014506Cellulomonas bogoriensis sp. nov., an alkaliphilic cellulomonad.Jones BE, Grant WD, Duckworth AW, Schumann P, Weiss N, Stackebrandt EInt J Syst Evol Microbiol10.1099/ijs.0.63646-02005Bacterial Typing Techniques, Base Composition, Cellulomonas/*classification/genetics/growth & development/metabolism, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Fresh Water/*microbiology, Genes, rRNA, Geologic Sediments/*microbiology, Hydrogen-Ion Concentration, Kenya, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, *Sodium ChlorideGenetics
Genetics26587181Draft genome sequence of Cellulomonas carbonis T26(T) and comparative analysis of six Cellulomonas genomes.Zhuang W, Zhang S, Xia X, Wang GStand Genomic Sci10.1186/s40793-015-0096-82015

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
6592Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16987)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16987
19745Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM16987.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
31481Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2777928776041
36769Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6338
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 updates33211880Nucleic Acids Res. 49: D498-D508 2020
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
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
71924Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID265389.1StrainInfo: A central database for resolving microbial strain identifiers
116830Curators of the CIPCollection of Institut Pasteur (CIP 108683)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108683