Strain identifier

BacDive ID: 7446

Type strain: Yes

Species: Microbacterium invictum

Strain Designation: DC-200

Strain history: CIP <- 2009, DSMZ

NCBI tax ID(s): 515415 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 8203

BacDive-ID: 7446

DSM-Number: 19600

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

description: Microbacterium invictum DC-200 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from homemade compost from kitchen refuse.

NCBI tax id

  • NCBI tax id: 515415
  • Matching level: species

strain history

@refhistory
378992009, DSMZ
8203<- C. M. Manaia, Escola Superior de Biotecnol., Univ. Católica Portuguesa, Porto, Portugal <- I. Vaz-Moreira; DC-200
67770LMG 24557 <-- C. M. Manaia DC-200.
120276CIP <- 2009, DSMZ

doi: 10.13145/bacdive7446.20230509.8.1

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 invictum
  • full scientific name: Microbacterium invictum Vaz-Moreira et al. 2009

@ref: 8203

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Microbacterium

species: Microbacterium invictum

full scientific name: Microbacterium invictum Vaz-Moreira et al. 2009

strain designation: DC-200

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29076positive0.74 µm0.54 µmrod-shapedyes
69480positive100
120276positiverod-shapedyes

colony morphology

@refcolony colorincubation periodmedium used
19784Sand yellow (1002)10-14 daysISP 2
19784Ivory (1014)10-14 daysISP 3
19784Lemon yellow (1012)10-14 daysISP 6

multicellular morphology

@refforms multicellular complexmedium name
19784noISP 2
19784noISP 3
19784noISP 6

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8203TRYPTICASE 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
19784ISP 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
19784ISP 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:
19784ISP 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
37899MEDIUM 328- for nutrient agaryesDistilled water make up to (1000.000 ml);Agar (15.000 g);Peptone (5.000g);Beef extract (3.000 g)
120276CIP Medium 328yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=328

culture temp

@refgrowthtypetemperaturerange
8203positivegrowth28mesophilic
19784positiveoptimum28mesophilic
29076positivegrowth10-37
29076positiveoptimum23.5psychrophilic
37899positivegrowth30mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
29076positivegrowth6.0-9.5alkaliphile
29076positiveoptimum7.8

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29076aerobe
120276facultative anaerobe

spore formation

@refspore formationconfidence
29076no
69481no100
69480no99.969

halophily

  • @ref: 29076
  • salt: NaCl
  • growth: positive
  • tested relation: optimum
  • concentration: 5 %

murein

  • @ref: 8203
  • murein short key: B01
  • type: B1alpha {Gly} [L-Lys] D-Glu(Hyg)-Gly-L-Lys

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2907622599arabinose+carbon source
2907617057cellobiose+carbon source
2907628757fructose+carbon source
2907617234glucose+carbon source
2907617306maltose+carbon source
2907629864mannitol+carbon source
2907637684mannose+carbon source
29076506227N-acetylglucosamine+carbon source
2907626546rhamnose+carbon source
2907617814salicin+carbon source
2907630911sorbitol+carbon source
2907617151xylitol+carbon source
2907618222xylose+carbon source
290764853esculin+hydrolysis
2907617632nitrate+reduction
12027617632nitrate+reduction
12027616301nitrite-reduction
6837917632nitrate-reduction
683794853esculin+hydrolysis
6837916199urea-hydrolysis
683795291gelatin-hydrolysis
6837917634D-glucose+fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837917716lactose-fermentation
6837917992sucrose+fermentation
6837928087glycogen-fermentation

metabolite production

  • @ref: 120276
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
29076acid phosphatase+3.1.3.2
29076alkaline phosphatase+3.1.3.1
29076catalase+1.11.1.6
29076gelatinase+
68382alpha-fucosidase-3.2.1.51
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382beta-glucosidase+3.2.1.21
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
68382cystine arylamidase-3.4.11.3
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
120276oxidase-
120276catalase+1.11.1.6
120276urease-3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
19784-+--+++-+--+--+/-+/--+-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
19784++++++-+-++-++++++-
120276++--++---++-++-++---

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
8203homemade compost from kitchen refusePortugalPRTEurope
67770Homemade compost produced by thermal digestion of kitchen refusePortugalPRTEurope
120276Environment, Homemade compost

isolation source categories

Cat1Cat2Cat3
#Engineered#Biodegradation#Composting
#Engineered#Waste#Domestic waste

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
82031Risk group (German classification)
1202761Risk group (French classification)

Sequence information

16S sequences

  • @ref: 8203
  • description: Microbacterium invictum partial 16S rRNA gene, culture collection DSM 19600, type strain DC-200T
  • accession: AM949677
  • length: 1486
  • database: ena
  • NCBI tax ID: 515415

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Microbacterium invictum JCM 17023GCA_015278285contigncbi515415
66792Microbacterium invictum strain DSM 19600515415.3wgspatric515415
66792Microbacterium invictum strain JCM 17023515415.4wgspatric515415
66792Microbacterium invictum DSM 196002831315640draftimg515415
66792Microbacterium invictum DSM 19600GCA_023155715scaffoldncbi515415

GC content

@refGC-contentmethod
820370.1high performance liquid chromatography (HPLC)
2907670
6777069.8-70.4high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveyes93.627no
anaerobicno99.655yes
halophileno88.209no
spore-formingno92.956no
glucose-utilyes87.023no
aerobicyes91.378no
thermophileno98.417yes
motileno88.063yes
flagellatedno98.026no
glucose-fermentno83.434no

External links

@ref: 8203

culture collection no.: DSM 19600, CIP 110032, LMG 24557, JCM 17023

straininfo link

  • @ref: 76894
  • straininfo: 343585

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19567581Microbacterium invictum sp. nov., isolated from homemade compost.Vaz-Moreira I, Lopes AR, Faria C, Sproer C, Schumann P, Nunes OC, Manaia CMInt J Syst Evol Microbiol10.1099/ijs.0.005561-02009Actinomycetales/*classification/genetics/*isolation & purification/physiology, Aerobiosis, Base Composition, Catalase/metabolism, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Locomotion, Molecular Sequence Data, Nucleic Acid Hybridization, Oxidoreductases/metabolism, Peptidoglycan/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, *Soil Microbiology, Temperature, Vitamin K 2/analysisMetabolism
Phylogeny26296337Microbacterium rhizomatis sp. nov., a beta-glucosidase-producing bacterium isolated from rhizome of Korean mountain ginseng.Hoang VA, Kim YJ, Nguyen NL, Kang CH, Kang JP, Singh P, Farh ME, Yang DU, Yang DCInt J Syst Evol Microbiol10.1099/ijsem.0.0003992015*Actinomycetales/classification, Bacterial Typing Techniques, Base Composition, Cellulases/genetics, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genotype, Glucosidases, Glycolipids/chemistry, Lipids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization/genetics, Panax/microbiology, Peptidoglycan/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rhizome, Sequence Analysis, DNA, Soil MicrobiologyGenetics
Phylogeny36167780Microbacterium kunmingensis sp. nov., an attached bacterium of Microcystis aeruginosa.Xiao Y, Chen M, Chen J, Mao LN, Peng YR, Gui SS, Zhang BHJ Antibiot (Tokyo)10.1038/s41429-022-00568-w2022RNA, Ribosomal, 16S/genetics, *Microcystis, Microbacterium, DNA, Bacterial/genetics, Bacterial Typing Techniques, Phylogeny, Sequence Analysis, DNA, *Actinomycetales, Fatty Acids/chemistry, Vitamin K 2/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
8203Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19600)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19600
19784Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM19600.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
29076Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2550628776041
37899Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7844
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/
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
76894Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID343585.1StrainInfo: A central database for resolving microbial strain identifiers
120276Curators of the CIPCollection of Institut Pasteur (CIP 110032)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110032