Strain identifier

BacDive ID: 7369

Type strain: Yes

Species: Microbacterium oxydans

Strain Designation: X98

Strain history: CIP <- 1966, Lab. Ident. Inst. Pasteur, Paris, France: strain X98

NCBI tax ID(s): 82380 (species)

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General

@ref: 8928

BacDive-ID: 7369

DSM-Number: 20578

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

description: Microbacterium oxydans X98 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from air.

NCBI tax id

  • NCBI tax id: 82380
  • Matching level: species

strain history

@refhistory
8928<- NCIB <- CIP <- R. Chatelain and L. Second, X98
376121966, Lab. Ident. Inst. Pasteur, Paris, France: strain X98
67770NBRC 15586 <-- IFO 15586 <-- DSM 20578 <-- NCIB 9944 <-- CIP 66.12 <-- R. Chatelain and L. Second strain X98.
67771<- DSM <- NCIMB <- CIP <- R. Chatelain and L. Second, X 98
121487CIP <- 1966, Lab. Ident. Inst. Pasteur, Paris, France: strain X98

doi: 10.13145/bacdive7369.20230509.8.1

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 oxydans
  • full scientific name: Microbacterium oxydans (Chatelain and Second 1966) Schumann et al. 1999

  • synonyms

    • @ref: 20215
    • synonym: Brevibacterium oxydans

@ref: 8928

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Microbacterium

species: Microbacterium oxydans

full scientific name: Microbacterium oxydans (Chatelain and Second 1966) Schumann et al. 1999

strain designation: X98

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotility
67771positive
121487positiverod-shapedyes

colony morphology

@refcolony colorincubation periodmedium used
18450Beige (1001)10-14 daysISP 2
18450Zinc yellow (1018)10-14 daysISP 3
18450Beige (1001)10-14 daysISP 4
18450Beige (1001)10-14 daysISP 5
18450Beige (1001)10-14 daysISP 6
18450Beige (1001)10-14 daysISP 7
121487

multicellular morphology

@refforms multicellular complexmedium name
18450noISP 2
18450noISP 3
18450noISP 4
18450noISP 5
18450noISP 6
18450noISP 7

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
18450ISP 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
18450ISP 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
18450ISP 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:
18450ISP 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
18450ISP 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
18450ISP 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
8928CORYNEBACTERIUM AGAR (DSMZ Medium 53)yesName: CORYNEBACTERIUM AGAR (DSMZ Medium 53) Composition: Agar 15.0 g/l Casein peptone 10.0 g/l NaCl 5.0 g/l Glucose 5.0 g/l Yeast extract 5.0 g/l Distilled waterhttps://mediadive.dsmz.de/medium/53
37612MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
121487CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
18450positiveoptimum28mesophilic
8928positivegrowth30mesophilic
37612positivegrowth30mesophilic
61577positivegrowth37mesophilic
67770positivegrowth28mesophilic
67771positivegrowth30mesophilic
121487positivegrowth10-37
121487nogrowth41thermophilic
121487nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
61577aerobe
67771aerobe
121487obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
121487NaClpositivegrowth0-6 %
121487NaClnogrowth8 %
121487NaClnogrowth10 %

murein

  • @ref: 8928
  • murein short key: B06
  • type: B2ß {Gly} [L-Hsr] D-Glu(Hyg)-Gly-D-Orn

observation

  • @ref: 67770
  • observation: quinones: MK-11, MK-12

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
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
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
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
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
121487citrate+carbon source16947
121487esculin+hydrolysis4853
121487hippurate+hydrolysis606565
121487nitrate-reduction17632
121487nitrite-reduction16301
121487nitrate-respiration17632
68379nitrate-reduction17632
68379esculin+hydrolysis4853
68379gelatin+hydrolysis5291
68379D-glucose-fermentation17634
68379D-ribose-fermentation16988
68379D-xylose-fermentation65327
68379D-mannitol-fermentation16899
68379maltose-fermentation17306
68379lactose-fermentation17716
68379sucrose-fermentation17992
68379glycogen-fermentation28087

antibiotic resistance

  • @ref: 121487
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 121487
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12148715688acetoin-
12148717234glucose-

enzymes

@refvalueactivityec
68382alpha-mannosidase+3.2.1.24
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382alpha-galactosidase-3.2.1.22
68382acid phosphatase+3.1.3.2
68382leucine arylamidase+3.4.11.1
68382esterase lipase (C 8)+
68382esterase (C 4)+
68379catalase+1.11.1.6
68379gelatinase+
68379beta-glucosidase+3.2.1.21
68379alpha-glucosidase+3.2.1.20
68379beta-glucuronidase-3.2.1.31
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase-3.5.1.B15
121487oxidase-
121487beta-galactosidase+3.2.1.23
121487alcohol dehydrogenase-1.1.1.1
121487gelatinase+
121487amylase+
121487DNase+
121487caseinase+3.4.21.50
121487catalase+1.11.1.6
121487tween esterase-
121487gamma-glutamyltransferase-2.3.2.2
121487lecithinase-
121487lipase-
121487lysine decarboxylase-4.1.1.18
121487ornithine decarboxylase-4.1.1.17
121487phenylalanine ammonia-lyase-4.3.1.24
121487protease+
121487tryptophan deaminase-
121487urease-3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYGControlCAT
18450------+-+++--------
61577---+-++++-+---------+

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
18450-++-++++++--+-++-++
61577+++-+----++---++++--
121487+++++++++++-+-+++++-

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
8928-+---+/-----++++-+--+--+-++++++--++-+----++---------
121487-------------------------------------------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121487+++++--+-++----++-++--++++--+--+-+++--+--+-------+---++-+-+++-----------+--+--+++-----+---++-+--++-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
8928air
61577Air contaminant,hospitalParisFranceFRAEurope
67770Air
121487Environment, Contaminating airParisFranceFRAEurope

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Air

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: Y17227
  • Sequence Identity:
  • Total samples: 42253
  • soil counts: 10113
  • aquatic counts: 9581
  • animal counts: 16954
  • plant counts: 5605

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
89281Risk group (German classification)
184501German classification
1214871Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Microbacterium oxydans strain DSM 20578 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceHQ853347500ena82380
20218Microbacterium oxydans 16S rRNA geneY172271466ena82380
8928Microbacterium oxydans strain DSM 20578 16S ribosomal RNA, partial sequenceNR_0449311466nuccore82380

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Microbacterium oxydans strain DSM 2057882380.43wgspatric82380
66792Microbacterium oxydans strain NBRC 1558682380.42wgspatric82380
67770Microbacterium oxydans NBRC 15586GCA_006540085contigncbi82380
67770Microbacterium oxydans DSM 20578GCA_008868025contigncbi82380

GC content

@refGC-contentmethod
892867.0
6777070high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes56.961no
flagellatedno91.95no
gram-positiveyes91.66yes
anaerobicno99.176yes
halophileno90.941no
spore-formingno90.437no
thermophileno99.62no
glucose-utilyes79.481no
aerobicyes93.693yes
glucose-fermentno90.321no

External links

@ref: 8928

culture collection no.: DSM 20578, CIP 6612, NCIB 9944, NRRL B-24236, CCUG 58056, JCM 12414, CIP 66.12, KCTC 3256, BCRC 12117, CGMCC 1.8870, IAM 15197, IFO 15586, NBRC 15586, NCIMB 9944, VKM Ac-2116, IFO (now NBRC) 15586, NCIB (now NCIMB) 9944

straininfo link

  • @ref: 76818
  • straininfo: 49650

literature

  • topic: Phylogeny
  • Pubmed-ID: 33263510
  • title: Microbacterium algeriense sp. nov., a novel actinobacterium isolated from Algerian oil production waters.
  • authors: Lenchi N, Anzil A, Servais P, Kebbouche-Gana S, Gana ML, Lliros M
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.004434
  • year: 2020
  • mesh: Algeria, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Microbacterium/*classification/isolation & purification, Nucleic Acid Hybridization, Oil and Gas Fields/*microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/chemistry, Water
  • topic2: Transcriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8928Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20578)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20578
18450Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM20578.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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
37612Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/10234
61577Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 58056)https://www.ccug.se/strain?id=58056
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)
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/
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
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
76818Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID49650.1StrainInfo: A central database for resolving microbial strain identifiers
121487Curators of the CIPCollection of Institut Pasteur (CIP 66.12)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2066.12