Strain identifier

BacDive ID: 12611

Type strain: Yes

Species: Xylanimonas cellulosilytica

Strain Designation: XIL07

Strain history: CIP <- 2003, E. Velazquez, Salamanca, Spain: strain XIL07

NCBI tax ID(s): 446471 (strain), 186189 (species)

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General

@ref: 6172

BacDive-ID: 12611

DSM-Number: 15894

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-positive

description: Xylanimonas cellulosilytica XIL07 is a facultative anaerobe, mesophilic, Gram-positive bacterium that was isolated from decayed tree , sawdust.

NCBI tax id

NCBI tax idMatching level
186189species
446471strain

strain history

@refhistory
6172<- D. Janssens, LMG; XIL07 <- E. Velázquez <- P. Rivas
382602003, E. Velazquez, Salamanca, Spain: strain XIL07
67770CECT 5975 <-- E. Velázquez XIL07 <-- R. Rivas.
117239CIP <- 2003, E. Velazquez, Salamanca, Spain: strain XIL07

doi: 10.13145/bacdive12611.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Promicromonosporaceae
  • genus: Xylanimonas
  • species: Xylanimonas cellulosilytica
  • full scientific name: Xylanimonas cellulosilytica Rivas et al. 2003

@ref: 6172

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Promicromonosporaceae

genus: Xylanimonas

species: Xylanimonas cellulosilytica

full scientific name: Xylanimonas cellulosilytica Rivas et al. 2003

strain designation: XIL07

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480positive100
117239positiveoval-shapedno

colony morphology

@refcolony colorincubation periodmedium used
18398Ivory (1014)10-14 daysISP 2
18398Ivory (1014)10-14 daysISP 3
18398Ivory (1014)10-14 daysISP 4
18398Beige (1001)10-14 daysISP 5
18398Ivory (1014)10-14 daysISP 6
18398Beige (1001)10-14 daysISP 7
117239

multicellular morphology

@refforms multicellular complexmedium name
18398noISP 2
18398noISP 3
18398noISP 4
18398noISP 5
18398noISP 6
18398noISP 7

multimedia

  • @ref: 66793
  • multimedia content: EM_DSM_15894_1.jpg
  • caption: electron microscopic image
  • intellectual property rights: © HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6172TRYPTICASE 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
18398ISP 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
18398ISP 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:
18398ISP 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
18398ISP 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
18398ISP 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
18398ISP 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
38260MEDIUM 567 - for Xylanimonas cellulosilyticayesDistilled water make up to (1000.000 ml);Agar (20.000 g);Yeast extract (3.000 g);Xylan (7.000 g)
117239CIP Medium 567yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=567

culture temp

@refgrowthtypetemperaturerange
6172positivegrowth28mesophilic
18398positiveoptimum28mesophilic
38260positivegrowth30mesophilic
67770positivegrowth28mesophilic
117239positivegrowth10-37
117239nogrowth41thermophilic
117239nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 117239
  • oxygen tolerance: facultative anaerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.559

halophily

@refsaltgrowthtested relationconcentration
117239NaClpositivegrowth0-4 %
117239NaClnogrowth6 %
117239NaClnogrowth8 %
117239NaClnogrowth10 %

murein

  • @ref: 6172
  • murein short key: A11.37
  • type: A4alpha L-Lys-D-Ser-D-Asp

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1839817234glucose+
1839822599arabinose-
1839817992sucrose+
1839818222xylose-
1839817268myo-inositol-
1839829864mannitol+
1839828757fructose+
1839826546rhamnose+
1839816634raffinose-
1839862968cellulose+
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
6837117151xylitol-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
683714853esculin+builds acid from
6837118305arbutin-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
11723916947citrate-carbon source
1172394853esculin+hydrolysis
117239606565hippurate-hydrolysis
11723917632nitrate+reduction
11723916301nitrite-reduction
11723917632nitrate+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: 117239
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 117239
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11723915688acetoin+
11723917234glucose-

enzymes

@refvalueactivityec
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
117239oxidase+
117239beta-galactosidase+3.2.1.23
117239alcohol dehydrogenase-1.1.1.1
117239gelatinase+/-
117239amylase+
117239DNase-
117239caseinase-3.4.21.50
117239catalase-1.11.1.6
117239cellulase-3.2.1.4
117239tween esterase-
117239gamma-glutamyltransferase+2.3.2.2
117239lecithinase-
117239lipase-
117239lysine decarboxylase-4.1.1.18
117239ornithine decarboxylase-4.1.1.17
117239phenylalanine ammonia-lyase-4.3.1.24
117239tryptophan deaminase-
117239urease-3.5.1.5
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
68382alpha-galactosidase+3.2.1.22
68382alpha-glucosidase+3.2.1.20
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
18398+++--+++++-+-+-++++

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
18398-++-+------++++++--
117239+++-+----+++--+-+---

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
117239+/---+-+---++++---------+/--++/-+++-++---++-+++/---------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
117239+++++----+++----+-+-++---------+---+---+--------------+----++--------------+----------+------------

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentisolation date
6172decayed tree (Ulmus nigra), sawdustUlmus nigraSalamancaSpainESPEurope
67770Decayed tree (Ulmus nigra)Ulmus nigraSalamancaSpainESPEurope
117239Sawdust of Ulmus nigraSpainESPEurope2001

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Decomposing plant
#Host#Plants#Tree

taxonmaps

  • @ref: 69479
  • File name: preview.99_4830.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_1778;97_2128;98_3616;99_4830&stattab=map
  • Last taxonomy: Xylanimonas cellulosilytica subclade
  • 16S sequence: AF403541
  • Sequence Identity:
  • Total samples: 137
  • soil counts: 73
  • aquatic counts: 14
  • animal counts: 30
  • plant counts: 20

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
183981German classification
61721Risk group (German classification)
1172391Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6172
  • description: Xylanomonas cellulosilytica 16S ribosomal RNA gene, partial sequence
  • accession: AF403541
  • length: 1518
  • database: ena
  • NCBI tax ID: 446471

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Xylanimonas cellulosilytica DSM 15894GCA_000024965completencbi446471
66792Xylanimonas cellulosilytica DSM 15894446471.16plasmidpatric446471
66792Xylanimonas cellulosilytica DSM 15894446471.6completepatric446471
66792Xylanimonas cellulosilytica XIL07, DSM 15894646311968completeimg446471

GC content

@refGC-contentmethod
617273
6777073thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno57no
motileno88.545no
flagellatedno98.008no
gram-positiveyes91.898no
anaerobicno98.054no
aerobicyes80.091no
halophileno92.762no
spore-formingno82.292no
glucose-utilyes88.196yes
thermophileno97.747yes
glucose-fermentno69.506no

External links

@ref: 6172

culture collection no.: DSM 15894, CECT 5975, LMG 20990, JCM 12276, KCTC 9989, NBRC 107835, CIP 108193

straininfo link

  • @ref: 81825
  • straininfo: 85151

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12656159Xylanimonas cellulosilytica gen. nov., sp. nov., a xylanolytic bacterium isolated from a decayed tree (Ulmus nigra).Rivas R, Sanchez M, Trujillo ME, Zurdo-Pineiro JL, Mateos PF, Martinez-Molina E, Velazquez EInt J Syst Evol Microbiol10.1099/ijs.0.02207-02003Actinomycetales/*classification/genetics/*isolation & purification/metabolism, Base Composition, Base Sequence, Carbohydrates/analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Lipids/analysis, Microscopy, Electron, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Trees/microbiology, Xylans/metabolismMetabolism
Phylogeny15143008Reclassification of Cellulosimicrobium variabile Bakalidou et al. 2002 as Isoptericola variabilis gen. nov., comb. nov.Stackebrandt E, Schumann P, Cui XLInt J Syst Evol Microbiol10.1099/ijs.0.02878-02004Actinomycetales/*classification/genetics/metabolism, Amino Acid Sequence, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Peptidoglycan/chemistry, Phospholipids/chemistry, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Terminology as TopicMetabolism
Genetics21304672Complete genome sequence of Xylanimonas cellulosilytica type strain (XIL07).Foster B, Pukall R, Abt B, Nolan M, Glavina Del Rio T, Chen F, Lucas S, Tice H, Pitluck S, Cheng JF, Chertkov O, Brettin T, Han C, Detter JC, Bruce D, Goodwin L, Ivanova N, Mavromatis K, Pati A, Mikhailova N, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Chain P, Rohde M, Goker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus AStand Genomic Sci10.4056/sigs.5711022010
Phylogeny31976851Xylanimonas allomyrinae sp. nov. isolated from the gut of larva of Allomyrina dichotoma, reclassification of Xylanibacterium ulmi as Xylanimonas ulmi comb. nov. and Xylanimicrobium pachnodae as Xylanimonas pachnodae comb. nov., and emendation of the genus Xylanimonas.Heo J, Cho H, Hamada M, Kim JS, Hong SB, Kim SJ, Kwon SWInt J Syst Evol Microbiol10.1099/ijsem.0.0040012020Actinobacteria/*classification/isolation & purification, Animals, Bacterial Typing Techniques, Base Composition, Coleoptera/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gastrointestinal Tract/*microbiology, Larva/microbiology, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNATranscriptome
Phylogeny32306134Lactococcus protaetiae sp. nov. and Xylanimonas protaetiae sp. nov., isolated from gut of larvae of Protaetia brevitarsis seulensis.Heo J, Kim SJ, Kim MA, Tamura T, Saitou S, Hamada M, Kim JS, Hong SB, Kwon SWAntonie Van Leeuwenhoek10.1007/s10482-020-01413-62020Actinobacteria/*classification/genetics/*isolation & purification, Actinomycetales/classification, Animals, Bacterial Typing Techniques, Base Composition, Coleoptera/*microbiology, DNA, Bacterial/genetics, Fatty Acids/analysis, *Gastrointestinal Microbiome, Lactococcus/*classification/genetics/*isolation & purification, Larva/*microbiology, Peptidoglycan, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAEnzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6172Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15894)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15894
18398Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM15894.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
38260Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5788
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)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life 35: 676-683 201728604660
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/
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)
81825Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID85151.1StrainInfo: A central database for resolving microbial strain identifiers
117239Curators of the CIPCollection of Institut Pasteur (CIP 108193)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108193