Strain identifier
BacDive ID: 7414
Type strain:
Species: Microbacterium paraoxydans
Strain Designation: CF36
Strain history: CIP <- 2003, DSMZ <- G. Wauters: strain CF36 <- J. Gigi
NCBI tax ID(s): 1223529 (strain), 199592 (species)
General
@ref: 5670
BacDive-ID: 7414
DSM-Number: 15019
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, motile, rod-shaped, human pathogen
description: Microbacterium paraoxydans CF36 is an aerobe, mesophilic, Gram-positive human pathogen that was isolated from blood of a child with acute lymphoblastic leukemia.
NCBI tax id
NCBI tax id | Matching level |
---|---|
199592 | species |
1223529 | strain |
strain history
@ref | history |
---|---|
5670 | <- G. Wauters; CF36 <- J. Gigi |
67770 | CCUG 46601 <-- G. Wauters CF36 <-- J. Gigi. |
121572 | CIP <- 2003, DSMZ <- G. Wauters: strain CF36 <- J. Gigi |
doi: 10.13145/bacdive7414.20230509.8.1
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 paraoxydans
- full scientific name: Microbacterium paraoxydans Laffineur et al. 2003
@ref: 5670
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Microbacteriaceae
genus: Microbacterium
species: Microbacterium paraoxydans
full scientific name: Microbacterium paraoxydans Laffineur et al. 2003 emend. Buczolits et al. 2008
strain designation: CF36
type strain: yes
Morphology
cell morphology
- @ref: 121572
- gram stain: positive
- cell shape: rod-shaped
- motility: yes
colony morphology
@ref | incubation period |
---|---|
57279 | 1-2 days |
121572 |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
5670 | 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 |
5670 | COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) | yes | https://mediadive.dsmz.de/medium/693 | Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base |
40483 | MEDIUM 45 - for Columbia agar with sheep blood | yes | Distilled water make up to (1000.000 ml);Columbia agar (39.000 g);Sheepblood (100.000 ml) | |
121572 | CIP Medium 45 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=45 | |
121572 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
5670 | positive | growth | 37 | mesophilic |
40483 | positive | growth | 37 | mesophilic |
57279 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
121572 | positive | growth | 15-37 | |
121572 | no | growth | 10 | psychrophilic |
121572 | no | growth | 41 | thermophilic |
121572 | no | growth | 45 | thermophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
57279 | aerobe |
121572 | obligate aerobe |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
121572 | NaCl | positive | growth | 0-6 % |
121572 | NaCl | no | growth | 8 % |
121572 | NaCl | no | growth | 10 % |
metabolite utilization
@ref | metabolite | utilization activity | kind of utilization tested | Chebi-ID |
---|---|---|---|---|
68371 | Potassium 5-ketogluconate | - | builds acid from | |
68371 | Potassium 2-ketogluconate | - | builds acid from | |
68371 | L-arabitol | - | builds acid from | 18403 |
68371 | D-arabitol | - | builds acid from | 18333 |
68371 | D-fucose | - | builds acid from | 28847 |
68371 | D-tagatose | - | builds acid from | 16443 |
68371 | D-lyxose | - | builds acid from | 62318 |
68371 | xylitol | - | builds acid from | 17151 |
68371 | glycogen | - | builds acid from | 28087 |
68371 | starch | - | builds acid from | 28017 |
68371 | raffinose | - | builds acid from | 16634 |
68371 | inulin | - | builds acid from | 15443 |
68371 | melibiose | - | builds acid from | 28053 |
68371 | lactose | - | builds acid from | 17716 |
68371 | salicin | - | builds acid from | 17814 |
68371 | arbutin | - | builds acid from | 18305 |
68371 | amygdalin | - | builds acid from | 27613 |
68371 | N-acetylglucosamine | - | builds acid from | 59640 |
68371 | methyl alpha-D-glucopyranoside | - | builds acid from | 320061 |
68371 | methyl alpha-D-mannoside | - | builds acid from | 43943 |
68371 | D-sorbitol | - | builds acid from | 17924 |
68371 | myo-inositol | - | builds acid from | 17268 |
68371 | galactitol | - | builds acid from | 16813 |
68371 | L-rhamnose | - | builds acid from | 62345 |
68371 | L-sorbose | - | builds acid from | 17266 |
68371 | methyl beta-D-xylopyranoside | - | builds acid from | 74863 |
68371 | ribitol | - | builds acid from | 15963 |
68371 | L-xylose | - | builds acid from | 65328 |
68371 | D-xylose | - | builds acid from | 65327 |
68371 | D-ribose | - | builds acid from | 16988 |
68371 | L-arabinose | - | builds acid from | 30849 |
68371 | erythritol | - | builds acid from | 17113 |
121572 | citrate | - | carbon source | 16947 |
121572 | esculin | + | hydrolysis | 4853 |
121572 | hippurate | - | hydrolysis | 606565 |
121572 | nitrate | - | reduction | 17632 |
121572 | nitrite | - | reduction | 16301 |
121572 | nitrate | - | respiration | 17632 |
antibiotic resistance
- @ref: 121572
- metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
- is antibiotic: yes
- is sensitive: yes
- is resistant: no
metabolite production
- @ref: 121572
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
@ref | Chebi-ID | metabolite | voges-proskauer-test | methylred-test |
---|---|---|---|---|
121572 | 15688 | acetoin | - | |
121572 | 17234 | glucose | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
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 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | trypsin | + | 3.4.21.4 |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | valine arylamidase | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | lipase (C 14) | - | |
68382 | esterase lipase (C 8) | - | |
68382 | esterase (C 4) | - | |
68382 | alkaline phosphatase | - | 3.1.3.1 |
121572 | oxidase | - | |
121572 | beta-galactosidase | + | 3.2.1.23 |
121572 | alcohol dehydrogenase | - | 1.1.1.1 |
121572 | gelatinase | + | |
121572 | amylase | - | |
121572 | DNase | + | |
121572 | caseinase | + | 3.4.21.50 |
121572 | catalase | + | 1.11.1.6 |
121572 | tween esterase | - | |
121572 | gamma-glutamyltransferase | - | 2.3.2.2 |
121572 | lecithinase | - | |
121572 | lipase | - | |
121572 | lysine decarboxylase | - | 4.1.1.18 |
121572 | ornithine decarboxylase | - | 4.1.1.17 |
121572 | phenylalanine ammonia-lyase | - | 4.3.1.24 |
121572 | protease | + | |
121572 | tryptophan deaminase | - | |
121572 | urease | - | 3.5.1.5 |
API zym
@ref | Control | 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
121572 | - | - | - | - | - | + | - | - | + | - | + | + | - | + | - | + | + | + | + | + |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
121572 | +/- | - | +/- | - | - | - | - | - | - | +/- | +/- | +/- | +/- | - | - | - | - | +/- | - | - | - | - | - | - | +/- | - | +/- | +/- | - | - | +/- | +/- | - | +/- | - | - | - | - | +/- | +/- | - | - | - | +/- | - | - | +/- | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | country | origin.country | continent | sampling date | isolation date |
---|---|---|---|---|---|---|
5670 | blood of a child with acute lymphoblastic leukemia | Belgium | BEL | Europe | ||
57279 | Human blood,5-yr-old boy,leukemia | Belgium | BEL | Europe | 1997-03-01 | |
67770 | Blood of a child with acute lymphoblastic leukemia | |||||
121572 | Human, Blood | Belgium | BEL | Europe | 1997 |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Infection | #Patient | |
#Host | #Human | #Child |
#Host Body Product | #Fluids | #Blood |
taxonmaps
- @ref: 69479
- File name: preview.99_191.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_137;97_148;98_165;99_191&stattab=map
- Last taxonomy: Microbacterium
- 16S sequence: AJ491806
- Sequence Identity:
- Total samples: 42253
- soil counts: 10113
- aquatic counts: 9581
- animal counts: 16954
- plant counts: 5605
Safety information
risk assessment
@ref | pathogenicity human | biosafety level | biosafety level comment |
---|---|---|---|
5670 | yes, in single cases | 1 | Risk group (German classification) |
121572 | 1 | Risk group (French classification) |
Sequence information
16S sequences
- @ref: 5670
- description: Microbacterium paraoxydans partial 16S rRNA gene, strain CF36
- accession: AJ491806
- length: 1490
- database: ena
- NCBI tax ID: 199592
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Microbacterium paraoxydans DSM 15019 | GCA_900105335 | chromosome | ncbi | 199592 |
66792 | Microbacterium paraoxydans NBRC 103076 | 1223529.4 | wgs | patric | 1223529 |
66792 | Microbacterium paraoxydans strain DSM 15019 | 199592.7 | complete | patric | 199592 |
66792 | Microbacterium paraoxydans DSM 15019 | 2634166897 | draft | img | 199592 |
66792 | Microbacterium paraoxydans NBRC 103076 | 2731957588 | draft | img | 1223529 |
67770 | Microbacterium paraoxydans NBRC 103076 | GCA_001552495 | contig | ncbi | 1223529 |
66792 | Microbacterium paraoxydans DSM 15019 | GCA_025002625 | contig | ncbi | 199592 |
GC content
- @ref: 5670
- GC-content: 69.9
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | yes | 59.447 | no |
gram-positive | yes | 90.576 | no |
anaerobic | no | 99.06 | yes |
halophile | no | 89.094 | no |
spore-forming | no | 85.497 | no |
glucose-util | yes | 81.267 | no |
flagellated | no | 91.432 | no |
aerobic | yes | 94.704 | yes |
thermophile | no | 99.483 | yes |
glucose-ferment | no | 89.826 | no |
External links
@ref: 5670
culture collection no.: DSM 15019, CCUG 46601, CIP 108082, NRRL B-24275, JCM 12372, IAM 15196, IFM 10517, LMG 23172, NBRC 103076, VTT E-072721
straininfo link
- @ref: 76863
- straininfo: 113575
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 12734292 | Bacteremia due to a novel Microbacterium species in a patient with leukemia and description of Microbacterium paraoxydans sp. nov. | Laffineur K, Avesani V, Cornu G, Charlier J, Janssens M, Wauters G, Delmee M | J Clin Microbiol | 10.1128/JCM.41.5.2242-2246.2003 | 2003 | Actinomycetales/classification/genetics/isolation & purification/*pathogenicity, Actinomycetales Infections/*complications/*microbiology, Bacteremia/*complications/*microbiology, Base Composition, Child, Preschool, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Humans, Male, Molecular Sequence Data, Phenotype, Phylogeny, Precursor Cell Lymphoblastic Leukemia-Lymphoma/*complications, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Species Specificity | Pathogenicity |
Phylogeny | 15774639 | Microbacterium oleivorans sp. nov. and Microbacterium hydrocarbonoxydans sp. nov., novel crude-oil-degrading Gram-positive bacteria. | Schippers A, Bosecker K, Sproer C, Schumann P | Int J Syst Evol Microbiol | 10.1099/ijs.0.63305-0 | 2005 | Actinomycetales/*classification/genetics/metabolism/ultrastructure, Bacterial Typing Techniques, Biodegradation, Environmental, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Gram-Positive Bacteria/classification/metabolism, Molecular Sequence Data, Petroleum/*metabolism, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity | Metabolism |
Reference
@id | authors | catalogue | doi/url | title |
---|---|---|---|---|
5670 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15019) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-15019 | |
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 | |
40483 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/5665 | ||
57279 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 46601) | https://www.ccug.se/strain?id=46601 | |
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/ | ||
68371 | Automatically annotated from API 50CH acid | |||
68382 | Automatically annotated from API zym | |||
69479 | João 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 | |
76863 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID113575.1 | StrainInfo: A central database for resolving microbial strain identifiers | |
121572 | Curators of the CIP | Collection of Institut Pasteur (CIP 108082) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108082 |