Strain identifier

BacDive ID: 7426

Type strain: Yes

Species: Microbacterium xylanilyticum

Strain Designation: S3-E

Strain history: CIP <- 2005, DSMZ

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 6639

BacDive-ID: 7426

DSM-Number: 16914

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

description: Microbacterium xylanilyticum S3-E is an aerobe, mesophilic, Gram-positive bacterium that was isolated from sludge, biofilm sample.

NCBI tax id

NCBI tax idMatching level
1302725strain
300018species

strain history

@refhistory
6639<- Kwang Kyu Kim, S3-E
400642005, DSMZ
67770KCTC 19079 <-- K. K. Kim S3-E.
67771<- KK Kim, KAIST
123994CIP <- 2005, DSMZ

doi: 10.13145/bacdive7426.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Microbacteriaceae
  • genus: Microbacterium
  • species: Microbacterium xylanilyticum
  • full scientific name: Microbacterium xylanilyticum Kim et al. 2005

@ref: 6639

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Microbacterium

species: Microbacterium xylanilyticum

full scientific name: Microbacterium xylanilyticum Kim et al. 2005

strain designation: S3-E

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
31508positiverod-shapedno
67771positive
69480positive99.72
123994positiverod-shapedno

colony morphology

@refcolony colorincubation periodmedium used
19743Zinc yellow (1018)10-14 daysISP 2
19743Zinc yellow (1018)10-14 daysISP 3
19743Zinc yellow (1018)10-14 daysISP 4
19743Zinc yellow (1018)10-14 daysISP 5
19743Zinc yellow (1018)10-14 daysISP 6
19743Zinc yellow (1018)10-14 daysISP 7
123994

multicellular morphology

@refforms multicellular complexmedium name
19743noISP 2
19743noISP 3
19743noISP 4
19743noISP 5
19743noISP 6
19743noISP 7

pigmentation

  • @ref: 31508
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6639TRYPTICASE 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
19743ISP 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
19743ISP 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:
19743ISP 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
19743ISP 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
19743ISP 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
19743ISP 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
40064MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
123994CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
6639positivegrowth28mesophilic
19743positiveoptimum28mesophilic
31508positivegrowth25-30mesophilic
31508positiveoptimum27.5mesophilic
40064positivegrowth30mesophilic
67770positivegrowth28mesophilic
67771positivegrowth28mesophilic

culture pH

@refabilitytypepH
31508positivegrowth06-08
31508positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
67771aerobe
123994facultative anaerobe

spore formation

@refspore formationconfidence
31508no
69481no100
69480no99.997

halophily

@refsaltgrowthtested relationconcentration
31508NaClpositivegrowth1-6.5 %
31508NaClpositiveoptimum2.5 %

observation

@refobservation
31508aggregates in clumps
67770quinones: MK-12, MK-11, MK-13
67771quinones: MK-12, MK-11

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1974362968cellulose+
1974316634raffinose+
1974326546rhamnose-
1974328757fructose+
1974329864mannitol+
1974317268myo-inositol-
1974318222xylose-
1974317992sucrose+
1974322599arabinose+
1974317234glucose+
3150822599arabinose+carbon source
3150817057cellobiose+carbon source
3150828757fructose+carbon source
3150828260galactose+carbon source
3150817234glucose+carbon source
3150817754glycerol+carbon source
3150828087glycogen+carbon source
3150817716lactose+carbon source
3150817306maltose+carbon source
3150829864mannitol+carbon source
3150837684mannose+carbon source
3150828053melibiose+carbon source
3150826271proline+carbon source
3150816634raffinose+carbon source
3150833942ribose+carbon source
3150817814salicin+carbon source
3150817992sucrose+carbon source
3150826986threonine+carbon source
3150827082trehalose+carbon source
3150818222xylose+carbon source
315084853esculin+hydrolysis
3150817632nitrate+reduction
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-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
6837117151xylitol-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837117814salicin-builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
12399417632nitrate+reduction
12399416301nitrite-reduction
683794853esculin+hydrolysis
6837916199urea-hydrolysis
683795291gelatin-hydrolysis
6837917992sucrose+fermentation

metabolite production

  • @ref: 123994
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
31508catalase+1.11.1.6
31508cytochrome 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
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
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
123994oxidase-
123994catalase+1.11.1.6
123994urease-3.5.1.5

API coryne

@refPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELSAC
19743+-++++-+--+

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
19743+++++++--++++-++-++
123994++--++-+-+-++-++-++-

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
123994+/---+/-+/-+/----+/-+/-+/-+/-----+/---+/----+/--+/-+/-+/-+/-+/-+/---+/-+/-+/--+/-+/-------+/---

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6639sludge, biofilm sampleCheongjuRepublic of KoreaKORAsia
67770Biofilm from a membrane bioreactor for wastewater treatment
67771From sludgeCheongjuRepublic of KoreaKORAsia
123994Biofilm of a membrane bioreactor

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Mud (Sludge)
#Environmental#Biofilm

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
66391Risk group (German classification)
197431Risk group (German classification)
1239941Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6639
  • description: Microbacterium xylanilyticum partial 16S rRNA gene, type strain S3-ET
  • accession: AJ853908
  • length: 1476
  • database: ena
  • NCBI tax ID: 300018

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Microbacterium xylanilyticum JCM 13591GCA_001313345contigncbi1302725
66792Microbacterium xylanilyticum JCM 135911302725.3wgspatric1302725
66792Microbacterium xylanilyticum JCM 135912734481942draftimg1302725

GC content

@refGC-contentmethod
663969.7
6777069.7high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno92.685yes
gram-positiveyes91.312no
anaerobicno98.675yes
halophileno94.401no
spore-formingno95.712yes
thermophileno99.2no
glucose-utilyes89.75yes
aerobicyes96.739yes
flagellatedno97.928yes
glucose-fermentno85.775no

External links

@ref: 6639

culture collection no.: DSM 16914, KCTC 19079, JCM 13591, CIP 108944, IAM 15299, LMG 23366, NCIMB 14334

straininfo link

  • @ref: 76875
  • straininfo: 232309

literature

  • topic: Phylogeny
  • Pubmed-ID: 16166712
  • title: Microbacterium xylanilyticum sp. nov., a xylan-degrading bacterium isolated from a biofilm.
  • authors: Kim KK, Park HY, Park W, Kim IS, Lee ST
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.63706-0
  • year: 2005
  • mesh: Actinomycetales/*classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, Biodegradation, Environmental, Biofilms/*growth & development, *Bioreactors, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Waste Disposal, Fluid/*methods, Xylans/*metabolism
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
6639Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16914)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16914
19743Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM16914.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
31508Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2780528776041
40064Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6630
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/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68371Automatically annotated from API 50CH acid
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
76875Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID232309.1StrainInfo: A central database for resolving microbial strain identifiers
123994Curators of the CIPCollection of Institut Pasteur (CIP 108944)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108944