Strain identifier

BacDive ID: 2360

Type strain: Yes

Species: Cellulomonas hominis

Strain history: CIP <- 1995, G. Funke, Inst. Med. Mikrobiol., Zürich, Switzerland: strain DMMZ 40

NCBI tax ID(s): 1305868 (strain), 156981 (species)

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General

@ref: 3645

BacDive-ID: 2360

DSM-Number: 9581

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, spore-forming, mesophilic, Gram-positive, human pathogen

description: Cellulomonas hominis DSM 9581 is a facultative anaerobe, spore-forming, mesophilic human pathogen that was isolated from cerebrospinal fluid.

NCBI tax id

NCBI tax idMatching level
1305868strain
156981species

strain history

@refhistory
3645<- G. Funke, DMMZ CE40
401521995, G. Funke, Inst. Med. Mikrobiol., Zürich, Switzerland: strain DMMZ 40
67770CCM 4572 <-- G. Funke DMMZ CE40.
119943CIP <- 1995, G. Funke, Inst. Med. Mikrobiol., Zürich, Switzerland: strain DMMZ 40

doi: 10.13145/bacdive2360.20230509.8.1

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 hominis
  • full scientific name: Cellulomonas hominis Funke et al. 1996

@ref: 3645

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Cellulomonadaceae

genus: Cellulomonas

species: Cellulomonas hominis

full scientific name: Cellulomonas hominis Funke et al. 1996

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480positive98.304
119943positiverod-shapedyes

colony morphology

@refcolony colorincubation periodmedium used
20213Colorless10-14 daysISP 2
20213Colorless10-14 daysISP 3

multicellular morphology

@refforms multicellular complexmedium name
20213noISP 2
20213noISP 3

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3645TRYPTICASE 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
20213ISP 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
20213ISP 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:
40152MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
119943CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
20213positiveoptimum37mesophilic
3645positivegrowth37mesophilic
40152positivegrowth37mesophilic
67770positivegrowth37mesophilic
119943positivegrowth37-41

Physiology and metabolism

oxygen tolerance

  • @ref: 119943
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
69481yes100
69480no99.998

halophily

  • @ref: 20213
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 5 %

murein

  • @ref: 3645
  • murein short key: A21.05
  • type: A4ß L-Orn-D-Glu

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2021317234glucose-
2021322599arabinose-
2021317992sucrose-
2021318222xylose-
2021317268myo-inositol-
2021329864mannitol-
2021328757fructose-
2021326546rhamnose-
2021316634raffinose-
2021362968cellulose-
68371Potassium 5-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
6837128066gentiobiose+builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-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
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
1199434853esculin+hydrolysis
11994317632nitrate+reduction
11994316301nitrite-reduction
119943132112sodium thiosulfate-builds gas from

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno
11994335581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin+
6836835581indole-
11994315688acetoin-

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-galactosidase+3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382leucine arylamidase+3.4.11.1
68382esterase lipase (C 8)+
68382esterase (C 4)+
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
119943oxidase+
119943beta-galactosidase+3.2.1.23
119943alcohol dehydrogenase-1.1.1.1
119943gelatinase-
119943caseinase+3.4.21.50
119943catalase+1.11.1.6
119943tween esterase-
119943lecithinase-
119943lysine decarboxylase-4.1.1.18
119943ornithine decarboxylase-4.1.1.17
119943urease-3.5.1.5

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
20213+++++++--+--+++++--
119943-++-+----++-+-++++--

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
20213---------+-

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119943+--++/-+--+++++-+----+-++++++++-++---+/---+++--+--++/-+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119943------------------+--------------------------------------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
3645cerebrospinal fluidSwitzerlandCHEEurope
52317Human cerebrospinal fluid,male patientSwitzerlandCHEEuropeZürich
67770Cerebrospinal fluid
119943Human, Cerebrospinal fluid

isolation source categories

Cat1Cat2Cat3
#Host Body Product#Fluids#Cerebrospinal fluid
#Infection#Patient

taxonmaps

  • @ref: 69479
  • File name: preview.99_27397.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_432;97_493;98_12225;99_27397&stattab=map
  • Last taxonomy: Cellulomonas
  • 16S sequence: X82598
  • Sequence Identity:
  • Total samples: 269
  • soil counts: 123
  • aquatic counts: 24
  • animal counts: 73
  • plant counts: 49

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
3645yes, in single cases1Risk group (German classification)
202131
1199431Risk group (French classification)

Sequence information

16S sequences

  • @ref: 3645
  • description: Cellulomonas hominis 16S rRNA gene
  • accession: X82598
  • length: 1406
  • database: ena
  • NCBI tax ID: 156981

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Cellulomonas hominis DSM 9581GCA_014201095contigncbi156981
66792Cellulomonas hominis JCM 12133GCA_001315265contigncbi1305868
66792Cellulomonas hominis JCM 121331305868.3wgspatric1305868
66792Cellulomonas hominis strain ATCC 51964156981.6wgspatric156981
66792Cellulomonas hominis strain DSM 9581156981.9wgspatric156981
66792Cellulomonas hominis strain NBRC 16055156981.5wgspatric156981
66792Cellulomonas hominis JCM 121332734481979draftimg1305868
66792Cellulomonas hominis DSM 95812856438371draftimg156981
67770Cellulomonas hominis NBRC 16055GCA_007989225contigncbi156981
67770Cellulomonas hominis ATCC 51964GCA_012396105contigncbi156981

GC content

  • @ref: 3645
  • GC-content: 76
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno75.333no
gram-positiveyes65.918no
anaerobicno95.81no
halophileno79.006no
spore-formingno96.022no
thermophileno97.691yes
glucose-utilyes86.345yes
aerobicno50no
flagellatedno91.425no
glucose-fermentyes68.24no

External links

@ref: 3645

culture collection no.: DSM 9581, CCUG 34783, ATCC 51964, LMG 17240, CIP 104574, NBRC 16055, JCM 12133, DMMZ CE40, CCM 4572, IFM 10516, IFO 16055, KCTC 9982, DMMZ 40

straininfo link

  • @ref: 71915
  • straininfo: 8222

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny7559954Identification of some clinical strains of CDC coryneform group A-3 and A-4 bacteria as Cellulomonas species and proposal of Cellulomonas hominis sp. nov. for some group A-3 strains.Funke G, Ramos CP, Collins MDJ Clin Microbiol10.1128/jcm.33.8.2091-2097.19951995Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Sequence, DNA Primers/genetics, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Drug Resistance, Microbial, Genes, Bacterial, Humans, Molecular Sequence Data, Phenotype, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Homology, Nucleic Acid, Species SpecificityPathogenicity
Phylogeny15814993Phenotypic and genetic characterization of clinical isolates of CDC coryneform group A-3: proposal of a new species of Cellulomonas, Cellulomonas denverensis sp. nov.Brown JM, Frazier RP, Morey RE, Steigerwalt AG, Pellegrini GJ, Daneshvar MI, Hollis DG, McNeil MMJ Clin Microbiol10.1128/JCM.43.4.1732-1737.20052005Actinomycetales Infections/microbiology, *Bacterial Typing Techniques, Cellulomonas/chemistry/*classification/*genetics/isolation & purification, DNA, Ribosomal/analysis, Fatty Acids/analysis, Humans, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAPathogenicity
Phylogeny35779121Cellulomonas triticagri sp. nov., isolated from the rhizosphere soil of wheat (Triticum aestivum L.).Han C, Zhang Y, Yu B, Shan Q, Zhao J, Shi H, Tian Y, Zhang Y, Zhu C, Xiang WArch Microbiol10.1007/s00203-022-03036-z2022Bacterial Typing Techniques, *Cellulomonas/genetics, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, Soil/chemistry, Soil Microbiology, TriticumTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3645Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 9581)https://www.dsmz.de/collection/catalogue/details/culture/DSM-9581
20213Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM9581.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
40152Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16497
52317Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 34783)https://www.ccug.se/strain?id=34783
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
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
71915Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID8222.1StrainInfo: A central database for resolving microbial strain identifiers
119943Curators of the CIPCollection of Institut Pasteur (CIP 104574)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104574