Strain identifier
BacDive ID: 7426
Type strain:
Species: Microbacterium xylanilyticum
Strain Designation: S3-E
Strain history: CIP <- 2005, DSMZ
NCBI tax ID(s): 1302725 (strain), 300018 (species)
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 id | Matching level |
---|---|
1302725 | strain |
300018 | species |
strain history
@ref | history |
---|---|
6639 | <- Kwang Kyu Kim, S3-E |
40064 | 2005, DSMZ |
67770 | KCTC 19079 <-- K. K. Kim S3-E. |
67771 | <- KK Kim, KAIST |
123994 | CIP <- 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
@ref | gram stain | cell shape | motility | confidence |
---|---|---|---|---|
31508 | positive | rod-shaped | no | |
67771 | positive | |||
69480 | positive | 99.72 | ||
123994 | positive | rod-shaped | no |
colony morphology
@ref | colony color | incubation period | medium used |
---|---|---|---|
19743 | Zinc yellow (1018) | 10-14 days | ISP 2 |
19743 | Zinc yellow (1018) | 10-14 days | ISP 3 |
19743 | Zinc yellow (1018) | 10-14 days | ISP 4 |
19743 | Zinc yellow (1018) | 10-14 days | ISP 5 |
19743 | Zinc yellow (1018) | 10-14 days | ISP 6 |
19743 | Zinc yellow (1018) | 10-14 days | ISP 7 |
123994 |
multicellular morphology
@ref | forms multicellular complex | medium name |
---|---|---|
19743 | no | ISP 2 |
19743 | no | ISP 3 |
19743 | no | ISP 4 |
19743 | no | ISP 5 |
19743 | no | ISP 6 |
19743 | no | ISP 7 |
pigmentation
- @ref: 31508
- production: yes
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
6639 | TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) | yes | https://mediadive.dsmz.de/medium/92 | Name: 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 |
19743 | ISP 2 | yes | Name: 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 | |
19743 | ISP 3 | yes | Name: 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: | |
19743 | ISP 4 | yes | Name: 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 | |
19743 | ISP 5 | yes | Name: 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 | |
19743 | ISP 6 | yes | Name: 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 | |
19743 | ISP 7 | yes | Name: 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 | |
40064 | MEDIUM 72- for trypto casein soja agar | yes | Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g) | |
123994 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
6639 | positive | growth | 28 | mesophilic |
19743 | positive | optimum | 28 | mesophilic |
31508 | positive | growth | 25-30 | mesophilic |
31508 | positive | optimum | 27.5 | mesophilic |
40064 | positive | growth | 30 | mesophilic |
67770 | positive | growth | 28 | mesophilic |
67771 | positive | growth | 28 | mesophilic |
culture pH
@ref | ability | type | pH |
---|---|---|---|
31508 | positive | growth | 06-08 |
31508 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
67771 | aerobe |
123994 | facultative anaerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
31508 | no | |
69481 | no | 100 |
69480 | no | 99.997 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
31508 | NaCl | positive | growth | 1-6.5 % |
31508 | NaCl | positive | optimum | 2.5 % |
observation
@ref | observation |
---|---|
31508 | aggregates in clumps |
67770 | quinones: MK-12, MK-11, MK-13 |
67771 | quinones: MK-12, MK-11 |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
19743 | 62968 | cellulose | + | |
19743 | 16634 | raffinose | + | |
19743 | 26546 | rhamnose | - | |
19743 | 28757 | fructose | + | |
19743 | 29864 | mannitol | + | |
19743 | 17268 | myo-inositol | - | |
19743 | 18222 | xylose | - | |
19743 | 17992 | sucrose | + | |
19743 | 22599 | arabinose | + | |
19743 | 17234 | glucose | + | |
31508 | 22599 | arabinose | + | carbon source |
31508 | 17057 | cellobiose | + | carbon source |
31508 | 28757 | fructose | + | carbon source |
31508 | 28260 | galactose | + | carbon source |
31508 | 17234 | glucose | + | carbon source |
31508 | 17754 | glycerol | + | carbon source |
31508 | 28087 | glycogen | + | carbon source |
31508 | 17716 | lactose | + | carbon source |
31508 | 17306 | maltose | + | carbon source |
31508 | 29864 | mannitol | + | carbon source |
31508 | 37684 | mannose | + | carbon source |
31508 | 28053 | melibiose | + | carbon source |
31508 | 26271 | proline | + | carbon source |
31508 | 16634 | raffinose | + | carbon source |
31508 | 33942 | ribose | + | carbon source |
31508 | 17814 | salicin | + | carbon source |
31508 | 17992 | sucrose | + | carbon source |
31508 | 26986 | threonine | + | carbon source |
31508 | 27082 | trehalose | + | carbon source |
31508 | 18222 | xylose | + | carbon source |
31508 | 4853 | esculin | + | hydrolysis |
31508 | 17632 | nitrate | + | reduction |
68371 | Potassium 5-ketogluconate | - | builds acid from | |
68371 | Potassium 2-ketogluconate | - | builds acid from | |
68371 | 18403 | L-arabitol | - | builds acid from |
68371 | 18333 | D-arabitol | - | builds acid from |
68371 | 18287 | L-fucose | - | builds acid from |
68371 | 28847 | D-fucose | - | builds acid from |
68371 | 16443 | D-tagatose | - | builds acid from |
68371 | 62318 | D-lyxose | - | builds acid from |
68371 | 17151 | xylitol | - | builds acid from |
68371 | 6731 | melezitose | - | builds acid from |
68371 | 15443 | inulin | - | builds acid from |
68371 | 17814 | salicin | - | builds acid from |
68371 | 18305 | arbutin | - | builds acid from |
68371 | 27613 | amygdalin | - | builds acid from |
68371 | 59640 | N-acetylglucosamine | - | builds acid from |
68371 | 43943 | methyl alpha-D-mannoside | - | builds acid from |
68371 | 17924 | D-sorbitol | - | builds acid from |
68371 | 17268 | myo-inositol | - | builds acid from |
68371 | 16813 | galactitol | - | builds acid from |
68371 | 62345 | L-rhamnose | - | builds acid from |
68371 | 17266 | L-sorbose | - | builds acid from |
68371 | 74863 | methyl beta-D-xylopyranoside | - | builds acid from |
68371 | 15963 | ribitol | - | builds acid from |
68371 | 65328 | L-xylose | - | builds acid from |
68371 | 17108 | D-arabinose | - | builds acid from |
68371 | 17113 | erythritol | - | builds acid from |
123994 | 17632 | nitrate | + | reduction |
123994 | 16301 | nitrite | - | reduction |
68379 | 4853 | esculin | + | hydrolysis |
68379 | 16199 | urea | - | hydrolysis |
68379 | 5291 | gelatin | - | hydrolysis |
68379 | 17992 | sucrose | + | fermentation |
metabolite production
- @ref: 123994
- Chebi-ID: 35581
- metabolite: indole
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
31508 | catalase | + | 1.11.1.6 |
31508 | cytochrome oxidase | + | 1.9.3.1 |
68382 | alpha-fucosidase | + | 3.2.1.51 |
68382 | alpha-mannosidase | + | 3.2.1.24 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | beta-glucosidase | + | 3.2.1.21 |
68382 | alpha-glucosidase | + | 3.2.1.20 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | beta-galactosidase | + | 3.2.1.23 |
68382 | alpha-galactosidase | + | 3.2.1.22 |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | valine arylamidase | + | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | esterase (C 4) | + | |
68382 | alkaline phosphatase | + | 3.1.3.1 |
68379 | gelatinase | - | |
68379 | urease | - | 3.5.1.5 |
68379 | beta-glucosidase | + | 3.2.1.21 |
68379 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68379 | alpha-glucosidase | + | 3.2.1.20 |
68379 | beta-galactosidase | + | 3.2.1.23 |
68379 | beta-glucuronidase | + | 3.2.1.31 |
68379 | alkaline phosphatase | + | 3.1.3.1 |
68379 | pyrrolidonyl arylamidase | - | 3.4.19.3 |
68379 | pyrazinamidase | + | 3.5.1.B15 |
123994 | oxidase | - | |
123994 | catalase | + | 1.11.1.6 |
123994 | urease | - | 3.5.1.5 |
API coryne
@ref | PYZ | PYRA | PAL | beta GUR | beta GAL | alpha GLU | beta NAG | ESC | URE | GEL | SAC |
---|---|---|---|---|---|---|---|---|---|---|---|
19743 | + | - | + | + | + | + | - | + | - | - | + |
API zym
@ref | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase | Control |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
19743 | + | + | + | + | + | + | + | - | - | + | + | + | + | - | + | + | - | + | + | |
123994 | + | + | - | - | + | + | - | + | - | + | - | + | + | - | + | + | - | + | + | - |
API 50CHac
@ref | GLY | ERY | DARA | LARA | RIB | DXYL | LXYL | ADO | MDX | GAL | GLU | FRU | MNE | SBE | RHA | DUL | INO | MAN | SOR | MDM | MDG | NAG | AMY | ARB | ESC | SAL | CEL | MAL | LAC | MEL | SAC | TRE | INU | MLZ | RAF | AMD | GLYG | XLT | GEN | TUR | LYX | TAG | DFUC | LFUC | DARL | LARL | GNT | 2KG | 5KG |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
123994 | +/- | - | - | +/- | +/- | +/- | - | - | - | +/- | +/- | +/- | +/- | - | - | - | - | +/- | - | - | +/- | - | - | - | +/- | - | +/- | +/- | +/- | +/- | +/- | +/- | - | - | +/- | +/- | +/- | - | +/- | +/- | - | - | - | - | - | - | +/- | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
6639 | sludge, biofilm sample | Cheongju | Republic of Korea | KOR | Asia |
67770 | Biofilm from a membrane bioreactor for wastewater treatment | ||||
67771 | From sludge | Cheongju | Republic of Korea | KOR | Asia |
123994 | Biofilm of a membrane bioreactor |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Terrestrial | #Mud (Sludge) |
#Environmental | #Biofilm |
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
6639 | 1 | Risk group (German classification) |
19743 | 1 | Risk group (German classification) |
123994 | 1 | Risk 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
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Microbacterium xylanilyticum JCM 13591 | GCA_001313345 | contig | ncbi | 1302725 |
66792 | Microbacterium xylanilyticum JCM 13591 | 1302725.3 | wgs | patric | 1302725 |
66792 | Microbacterium xylanilyticum JCM 13591 | 2734481942 | draft | img | 1302725 |
GC content
@ref | GC-content | method |
---|---|---|
6639 | 69.7 | |
67770 | 69.7 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | no | 92.685 | yes |
gram-positive | yes | 91.312 | no |
anaerobic | no | 98.675 | yes |
halophile | no | 94.401 | no |
spore-forming | no | 95.712 | yes |
thermophile | no | 99.2 | no |
glucose-util | yes | 89.75 | yes |
aerobic | yes | 96.739 | yes |
flagellated | no | 97.928 | yes |
glucose-ferment | no | 85.775 | no |
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
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
6639 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16914) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-16914 | |||
19743 | Wink, J. | http://www.dsmz.de/microorganisms/wink_pdf/DSM16914.pdf | Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
31508 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 27805 | 28776041 | |
40064 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/6630 | ||||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | ||||
68371 | Automatically annotated from API 50CH acid | |||||
68379 | Automatically annotated from API Coryne | |||||
68382 | Automatically annotated from API zym | |||||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
76875 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID232309.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
123994 | Curators of the CIP | Collection of Institut Pasteur (CIP 108944) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108944 |