Strain identifier

BacDive ID: 12581

Type strain: Yes

Species: Cellulosimicrobium funkei

Strain Designation: C8821, W6122

Strain history: CIP <- 2005, J. M. Brown, CDC, Atlanta, USA: strain W6122

NCBI tax ID(s): 1349761 (strain), 264251 (species)

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General

@ref: 6147

BacDive-ID: 12581

DSM-Number: 16025

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

description: Cellulosimicrobium funkei C8821 is an aerobe, mesophilic, Gram-positive human pathogen that was isolated from blood, endocarditis patient.

NCBI tax id

NCBI tax idMatching level
1349761strain
264251species

strain history

@refhistory
6147<- J. M. Brown; W6122 <- University Colorado
349762005, J. M. Brown, CDC, Atlanta, USA: strain W6122
67770DSM 16025 <-- J. M. Brown W6122 <-- Univ. of Colorado, USA.
119494CIP <- 2005, J. M. Brown, CDC, Atlanta, USA: strain W6122

doi: 10.13145/bacdive12581.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Promicromonosporaceae
  • genus: Cellulosimicrobium
  • species: Cellulosimicrobium funkei
  • full scientific name: Cellulosimicrobium funkei Brown et al. 2006

  • synonyms

    • @ref: 20215
    • synonym: Cellulosimicrobium aquatile

@ref: 6147

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Promicromonosporaceae

genus: Cellulosimicrobium

species: Cellulosimicrobium funkei

full scientific name: Cellulosimicrobium funkei Brown et al. 2006

strain designation: C8821, W6122

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31606positive1 µm1 µmrod-shapedyes
69480positive100

colony morphology

@refcolony colorincubation periodmedium used
19738Zinc yellow (1018)10-14 daysISP 2
19738Zinc yellow (1018)10-14 daysISP 3
19738Zinc yellow (1018)10-14 daysISP 4
19738Zinc yellow (1018)10-14 daysISP 5
19738Beige (1001)10-14 daysISP 6
19738Zinc yellow (1018)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
19738noISP 2
19738noISP 3
19738noISP 4
19738noISP 5
19738noISP 6
19738noISP 7

pigmentation

  • @ref: 31606
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6147TRYPTICASE 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
19738ISP 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
19738ISP 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:
19738ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
19738ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
19738ISP 6yesName: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
19738ISP 7yesName: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
34976MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
119494CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
6147positivegrowth28mesophilic
19738positiveoptimum28mesophilic
31606positivegrowth30-35mesophilic
31606nogrowth25mesophilic
34976positivegrowth37mesophilic
58951positivegrowth22-42
67770positivegrowth28mesophilic

culture pH

@refabilitytypepH
31606positivegrowth7
31606positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31606aerobe
58951aerobe

spore formation

@refspore formationconfidence
31606no
69481no95

observation

@refobservation
31606aggregates in chains
67770quinones: MK-9(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3160622599arabinose+carbon source
3160617057cellobiose+carbon source
3160628757fructose+carbon source
3160628260galactose+carbon source
3160617234glucose+carbon source
3160617754glycerol+carbon source
3160617716lactose+carbon source
3160617306maltose+carbon source
3160637684mannose+carbon source
3160617814salicin+carbon source
3160617992sucrose+carbon source
3160627082trehalose+carbon source
3160618222xylose+carbon source
6837917632nitrate+reduction
683794853esculin+hydrolysis
683795291gelatin+hydrolysis
6837917634D-glucose+fermentation
6837916988D-ribose-fermentation
6837965327D-xylose+fermentation
6837916899D-mannitol-fermentation
6837917306maltose+fermentation
6837917716lactose-fermentation
6837917992sucrose+fermentation
6837928087glycogen+fermentation

enzymes

@refvalueactivityec
31606catalase+1.11.1.6
68379gelatinase+
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
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase+3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
19738++++-+++++/-++-+-+-++

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
19738+++-+----++-+-+++--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
6147blood, endocarditis patientColoradoUSAUSANorth America
67770Blood of an endocarditis patient
119494Human, BloodDenver, ColoradoUnited States of AmericaUSANorth America1975

isolation source categories

Cat1Cat2Cat3
#Infection#Patient
#Host Body Product#Fluids#Blood

taxonmaps

  • @ref: 69479
  • File name: preview.99_256.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_179;97_195;98_218;99_256&stattab=map
  • Last taxonomy: Cellulosimicrobium
  • 16S sequence: AY501364
  • Sequence Identity:
  • Total samples: 5475
  • soil counts: 1873
  • aquatic counts: 417
  • animal counts: 1680
  • plant counts: 1505

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
6147yes, in single cases1Risk group (German classification)
197382Risk group
1194941Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6147
  • description: Cellulosimicrobium funkei strain W6122 16S small subunit ribosomal RNA gene, partial sequence
  • accession: AY501364
  • length: 1444
  • database: ena
  • NCBI tax ID: 264251

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Cellulosimicrobium funkei NBRC 1041181349761.3wgspatric1349761
66792Cellulosimicrobium funkei strain JCM 14302264251.7wgspatric264251
66792Cellulosimicrobium funkei NBRC 1041182731957606draftimg1349761
67770Cellulosimicrobium funkei NBRC 104118GCA_001570825contigncbi1349761
67770Cellulosimicrobium funkei JCM 14302GCA_004519295contigncbi264251

GC content

@refGC-contentmethod
614774.5
6777074.5thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno95no
motileyes66.59no
gram-positiveyes86.753yes
anaerobicno98.426yes
halophileno93.256no
spore-formingno85.42yes
glucose-utilyes89.714yes
aerobicyes89.139no
flagellatedno91.95no
thermophileno98.665yes
glucose-fermentno65.324yes

External links

@ref: 6147

culture collection no.: DSM 16025, ATCC BAA 886, CCUG 50705, JCM 14302, CIP 108915, NBRC 104118, VTT E-072700

straininfo link

  • @ref: 81795
  • straininfo: 389461

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16585698Characterization of clinical isolates previously identified as Oerskovia turbata: proposal of Cellulosimicrobium funkei sp. nov. and emended description of the genus Cellulosimicrobium.Brown JM, Steigerwalt AG, Morey RE, Daneshvar MI, Romero LJ, McNeil MMInt J Syst Evol Microbiol10.1099/ijs.0.63882-02006Actinomycetales Infections/*microbiology, *Bacterial Typing Techniques, Cellulomonas/chemistry/*classification/genetics/isolation & purification, DNA, Ribosomal/analysis, Humans, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/analysis/geneticsPathogenicity
Phylogeny26373417Cellulosimicrobium aquatile sp. nov., isolated from Panagal reservoir, Nalgonda, India.Sultanpuram VR, Mothe T, Chintalapati S, Chintalapati VRAntonie Van Leeuwenhoek10.1007/s10482-015-0588-y2015Actinobacteria/*classification/genetics/*isolation & purification/physiology, Aerobiosis, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, India, Lysine/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analysisGenetics
Phylogeny35348452Cellulosimicrobium protaetiae sp. nov., isolated from the gut of the larva of Protaetia brevitarsis seulensis.Le Han H, Nguyen TTH, Li Z, Shin NR, Kim SGInt J Syst Evol Microbiol10.1099/ijsem.0.0052962022Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, *Fatty Acids/chemistry, Larva/microbiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
6147Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16025)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16025
19738Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM16025.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
31606Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2789428776041
34976Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6598
58951Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 50705)https://www.ccug.se/strain?id=50705
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/
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
81795Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID389461.1StrainInfo: A central database for resolving microbial strain identifiers
119494Curators of the CIPCollection of Institut Pasteur (CIP 108915)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108915