Strain identifier

BacDive ID: 2368

Type strain: Yes

Species: Cellulomonas xylanilytica

Strain Designation: XIL11, CIL11

Strain history: CIP <- 2004, CECT <- E. Velaquez <- R. Rivas, Salamanca, Spain: strain CIL11

NCBI tax ID(s): 1305856 (strain), 233583 (species)

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General

@ref: 6653

BacDive-ID: 2368

DSM-Number: 16933

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

description: Cellulomonas xylanilytica XIL11 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from decayed wood of an elm tree.

NCBI tax id

NCBI tax idMatching level
233583species
1305856strain

strain history

@refhistory
6653<- M. Trujillo <- R. Rivas; XIL11
67770CECT 5729 <-- E. Velázquez XIL11.
123993CIP <- 2004, CECT <- E. Velaquez <- R. Rivas, Salamanca, Spain: strain CIL11

doi: 10.13145/bacdive2368.20230509.8.1

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 xylanilytica
  • full scientific name: Cellulomonas xylanilytica Rivas et al. 2004

@ref: 6653

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Cellulomonadaceae

genus: Cellulomonas

species: Cellulomonas xylanilytica

full scientific name: Cellulomonas xylanilytica Rivas et al. 2004

strain designation: XIL11, CIL11

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30038positive2.4 µm1.4 µmrod-shapedno
69480no93.068
69480positive100
123993positiverod-shapedno

colony morphology

  • @ref: 123993

pigmentation

  • @ref: 30038
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6653XED-AGAR (DSMZ Medium 1026)yeshttps://mediadive.dsmz.de/medium/1026Name: XED-AGAR (DSMZ Medium 1026) Composition: Agar 18.0 g/l Xylan 7.0 g/l Yeast extract 3.0 g/l Distilled water
6653CORYNEBACTERIUM AGAR (DSMZ Medium 53)yeshttps://mediadive.dsmz.de/medium/53Name: 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 water
33231MEDIUM 595 - for Cellulomonas xylanilyticayesDistilled water make up to (1000.000 ml);Magnesium sulphate heptahydrate (0.500 g);Agar (20.000 g);Yeast extract (10.000 g);Di Potassium monohydrogenophosphate (1.000 g);Xylan (5.000 g)
123993CIP Medium 595yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=595

culture temp

@refgrowthtypetemperaturerange
6653positivegrowth28mesophilic
30038positivegrowth28mesophilic
30038positiveoptimum30mesophilic
33231positivegrowth30mesophilic
67770positivegrowth28mesophilic
123993positivegrowth25-30mesophilic
123993nogrowth10psychrophilic
123993nogrowth15psychrophilic
123993nogrowth37mesophilic
123993nogrowth41thermophilic
123993nogrowth45thermophilic

culture pH

  • @ref: 30038
  • ability: positive
  • type: optimum
  • pH: 7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
30038aerobe
123993facultative anaerobe

spore formation

@refspore formationconfidence
30038no
69481no96
69480no99.385

halophily

@refsaltgrowthtested relationconcentration
123993NaClpositivegrowth0-4 %
123993NaClnogrowth6 %
123993NaClnogrowth8 %
123993NaClnogrowth10 %

murein

  • @ref: 6653
  • murein short key: A21.05
  • type: A4ß L-Orn-D-Glu

observation

  • @ref: 67770
  • observation: quinones: MK-9(H4), MK-8(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3003822599arabinose+carbon source
3003817716lactose+carbon source
3003817306maltose+carbon source
3003837684mannose+carbon source
30038506227N-acetylglucosamine+carbon source
3003826546rhamnose+carbon source
300384853esculin+hydrolysis
3003817632nitrate+reduction
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
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837117151xylitol-builds acid from
6837116634raffinose+builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837117716lactose-builds acid from
6837117306maltose-builds acid from
6837117814salicin-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
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-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
12399316947citrate-carbon source
1239934853esculin+hydrolysis
123993606565hippurate+hydrolysis
12399317632nitrate+reduction
12399316301nitrite-reduction
12399317632nitrate+respiration

antibiotic resistance

  • @ref: 123993
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 123993
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12399315688acetoin-
12399317234glucose+

enzymes

@refvalueactivityec
30038catalase+1.11.1.6
30038cytochrome oxidase+1.9.3.1
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
123993oxidase+
123993beta-galactosidase+3.2.1.23
123993alcohol dehydrogenase-1.1.1.1
123993gelatinase+
123993amylase+
123993DNase+
123993caseinase+3.4.21.50
123993catalase+1.11.1.6
123993cellulase-3.2.1.4
123993tween esterase-
123993gamma-glutamyltransferase+2.3.2.2
123993lecithinase-
123993lipase-
123993lysine decarboxylase-4.1.1.18
123993ornithine decarboxylase-4.1.1.17
123993phenylalanine ammonia-lyase-4.3.1.24
123993tryptophan deaminase-
123993urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
123993-+++-+----+-+++++++-

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
123993-----+/----+/-+++-----------+/--+/---+/-+/---+/-++/-+/--+/-----------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123993+++++-++++++++-++-+-++---+-----+--++------------------+----++------------------+---+--+-------+----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
6653decayed wood of an elm treeSalamancaSpainESPEurope
67770Decade wood of an elm tree
123993Plant, From decayed wood elm treeSalamancaSpainESPEurope2001

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Decomposing plant
#Host#Plants#Tree
#Host Body Product#Plant#Timber

taxonmaps

  • @ref: 69479
  • File name: preview.99_3436.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_432;97_1685;98_2637;99_3436&stattab=map
  • Last taxonomy: Cellulomonas
  • 16S sequence: AY303668
  • Sequence Identity:
  • Total samples: 5905
  • soil counts: 3471
  • aquatic counts: 607
  • animal counts: 1257
  • plant counts: 570

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
66531Risk group (German classification)
1239931Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6653
  • description: Cellulomonas xylanilytica 16S ribosomal RNA gene, complete sequence
  • accession: AY303668
  • length: 1516
  • database: ena
  • NCBI tax ID: 233583

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Cellulomonas xylanilytica JCM 14281GCA_001314025contigncbi1305856
66792Cellulomonas xylanilytica JCM 142811305856.3wgspatric1305856
66792Cellulomonas xylanilytica strain NBRC 101102233583.3wgspatric233583
66792Cellulomonas xylanilytica JCM 142812681813035draftimg1305856
67770Cellulomonas xylanilytica NBRC 101102GCA_007989805contigncbi233583

GC content

@refGC-contentmethod
665373
6777073thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno96no
motileno88.295yes
gram-positiveyes89.257yes
anaerobicno98.477yes
halophileno91.458no
spore-formingno94.526yes
thermophileno98.681yes
glucose-utilyes90.708no
aerobicyes90.278yes
flagellatedno97.376yes
glucose-fermentno65.378no

External links

@ref: 6653

culture collection no.: DSM 16933, CECT 5729, LMG 21723, JCM 14281, CIP 108340, NBRC 101102

straininfo link

  • @ref: 71923
  • straininfo: 89018

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15023971Cellulomonas xylanilytica sp. nov., a cellulolytic and xylanolytic bacterium isolated from a decayed elm tree.Rivas R, Trujillo ME, Mateos PF, Martinez-Molina E, Velazquez EInt J Syst Evol Microbiol10.1099/ijs.0.02866-02004Base Composition, Cellulomonas/*classification/genetics/growth & development/isolation & purification, Cellulose/metabolism, DNA, Bacterial/chemistry/genetics, Molecular Sequence Data, Phylogeny, Ulmus/*microbiology, Xylans/metabolismMetabolism
Phylogeny16014505Cellulomonas terrae sp. nov., a cellulolytic and xylanolytic bacterium isolated from soil.An DS, Im WT, Yang HC, Kang MS, Kim KK, Jin L, Kim MK, Lee STInt J Syst Evol Microbiol10.1099/ijs.0.63696-02005Bacterial Typing Techniques, Cellulomonas/*classification/genetics/isolation & purification/physiology, Cellulose/*metabolism, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species Specificity, Xylans/*metabolismMetabolism
Phylogeny30702420Cellulomonas rhizosphaerae sp. nov., a novel actinomycete isolated from soil.Tian Y, Han C, Hu J, Zhao J, Zhang C, Guo X, Wang X, Xiang WInt J Syst Evol Microbiol10.1099/ijsem.0.0032582019Bacterial Typing Techniques, Base Composition, Cellulomonas/*classification/isolation & purification, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Multilocus Sequence Typing, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/chemistryTranscriptome
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/urltitleID_cross_referencepubmed
6653Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16933)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16933
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
30038Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2639928776041
33231Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5952
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/
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
71923Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID89018.1StrainInfo: A central database for resolving microbial strain identifiers
123993Curators of the CIPCollection of Institut Pasteur (CIP 108340)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108340