Strain identifier

BacDive ID: 7414

Type strain: Yes

Species: Microbacterium paraoxydans

Strain Designation: CF36

Strain history: CIP <- 2003, DSMZ <- G. Wauters: strain CF36 <- J. Gigi

For citation purpose refer to the digital object identifier (doi) of the current version.
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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 idMatching level
199592species
1223529strain

strain history

@refhistory
5670<- G. Wauters; CF36 <- J. Gigi
67770CCUG 46601 <-- G. Wauters CF36 <-- J. Gigi.
121572CIP <- 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

@refincubation period
572791-2 days
121572

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5670TRYPTICASE 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
5670COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://mediadive.dsmz.de/medium/693Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
40483MEDIUM 45 - for Columbia agar with sheep bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Sheepblood (100.000 ml)
121572CIP Medium 45yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=45
121572CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
5670positivegrowth37mesophilic
40483positivegrowth37mesophilic
57279positivegrowth37mesophilic
67770positivegrowth37mesophilic
121572positivegrowth15-37
121572nogrowth10psychrophilic
121572nogrowth41thermophilic
121572nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
57279aerobe
121572obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
121572NaClpositivegrowth0-6 %
121572NaClnogrowth8 %
121572NaClnogrowth10 %

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371inulin-builds acid from15443
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371salicin-builds acid from17814
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose-builds acid from16988
68371L-arabinose-builds acid from30849
68371erythritol-builds acid from17113
121572citrate-carbon source16947
121572esculin+hydrolysis4853
121572hippurate-hydrolysis606565
121572nitrate-reduction17632
121572nitrite-reduction16301
121572nitrate-respiration17632

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

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12157215688acetoin-
12157217234glucose-

enzymes

@refvalueactivityec
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
121572oxidase-
121572beta-galactosidase+3.2.1.23
121572alcohol dehydrogenase-1.1.1.1
121572gelatinase+
121572amylase-
121572DNase+
121572caseinase+3.4.21.50
121572catalase+1.11.1.6
121572tween esterase-
121572gamma-glutamyltransferase-2.3.2.2
121572lecithinase-
121572lipase-
121572lysine decarboxylase-4.1.1.18
121572ornithine decarboxylase-4.1.1.17
121572phenylalanine ammonia-lyase-4.3.1.24
121572protease+
121572tryptophan deaminase-
121572urease-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
121572-----+--+-++-+-+++++

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
121572+/--+/-------+/-+/-+/-+/-----+/-------+/--+/-+/---+/-+/--+/-----+/-+/----+/---+/---

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentsampling dateisolation date
5670blood of a child with acute lymphoblastic leukemiaBelgiumBELEurope
57279Human blood,5-yr-old boy,leukemiaBelgiumBELEurope1997-03-01
67770Blood of a child with acute lymphoblastic leukemia
121572Human, BloodBelgiumBELEurope1997

isolation source categories

Cat1Cat2Cat3
#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

@refpathogenicity humanbiosafety levelbiosafety level comment
5670yes, in single cases1Risk group (German classification)
1215721Risk 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

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Microbacterium paraoxydans DSM 15019GCA_900105335chromosomencbi199592
66792Microbacterium paraoxydans NBRC 1030761223529.4wgspatric1223529
66792Microbacterium paraoxydans strain DSM 15019199592.7completepatric199592
66792Microbacterium paraoxydans DSM 150192634166897draftimg199592
66792Microbacterium paraoxydans NBRC 1030762731957588draftimg1223529
67770Microbacterium paraoxydans NBRC 103076GCA_001552495contigncbi1223529
66792Microbacterium paraoxydans DSM 15019GCA_025002625contigncbi199592

GC content

  • @ref: 5670
  • GC-content: 69.9

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes59.447no
gram-positiveyes90.576no
anaerobicno99.06yes
halophileno89.094no
spore-formingno85.497no
glucose-utilyes81.267no
flagellatedno91.432no
aerobicyes94.704yes
thermophileno99.483yes
glucose-fermentno89.826no

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

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12734292Bacteremia 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 MJ Clin Microbiol10.1128/JCM.41.5.2242-2246.20032003Actinomycetales/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 SpecificityPathogenicity
Phylogeny15774639Microbacterium oleivorans sp. nov. and Microbacterium hydrocarbonoxydans sp. nov., novel crude-oil-degrading Gram-positive bacteria.Schippers A, Bosecker K, Sproer C, Schumann PInt J Syst Evol Microbiol10.1099/ijs.0.63305-02005Actinomycetales/*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 SpecificityMetabolism

Reference

@idauthorscataloguedoi/urltitle
5670Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15019)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15019
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
40483Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5665
57279Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 46601)https://www.ccug.se/strain?id=46601
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
76863Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID113575.1StrainInfo: A central database for resolving microbial strain identifiers
121572Curators of the CIPCollection of Institut Pasteur (CIP 108082)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108082