Strain identifier

BacDive ID: 7449

Type strain: Yes

Species: Microbacterium agarici

Strain Designation: CC-SBCK 209

Strain history: CIP <- 2013, DSMZ <- P. Kämpfer, Giessen Univ., Giessen, Germany <- College of Agriculture and Natural Resources, Taichung Univ., Taiwan: strain CC-SBCK 209

NCBI tax ID(s): 630514 (species)

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General

@ref: 15961

BacDive-ID: 7449

DSM-Number: 21798

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

description: Microbacterium agarici CC-SBCK 209 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from stalk of the mushroom Agaricus blazei.

NCBI tax id

  • NCBI tax id: 630514
  • Matching level: species

strain history

@refhistory
15961<- P. Kämpfer, Univ. Giessen, Germany <- College of Agriculture and Natural Resources, University Taichung; CC-SBCK 209
67770CCM 7686 <-- P. Kämpfer CC-SBCK-209.
116147CIP <- 2013, DSMZ <- P. Kämpfer, Giessen Univ., Giessen, Germany <- College of Agriculture and Natural Resources, Taichung Univ., Taiwan: strain CC-SBCK 209

doi: 10.13145/bacdive7449.20230509.8.1

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 agarici
  • full scientific name: Microbacterium agarici Young et al. 2010

@ref: 15961

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Microbacterium

species: Microbacterium agarici

full scientific name: Microbacterium agarici Young et al. 2010 emend. Nouioui et al. 2018

strain designation: CC-SBCK 209

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapeconfidencemotility
29488positive2.5 µm1.1 µmrod-shaped
69480positive100
116147negativerod-shapedyes

colony morphology

@refcolony colorincubation periodmedium used
21360Maize yellow (1006)10-14 daysISP 2
2136010-14 daysISP 3
21360Dahlia yellow (1033)10-14 daysISP 4
2136010-14 daysISP 5
2136010-14 daysISP 7
21360Ochre yellow (1024)10-14 dayssuter with tyrosine
21360Sand yellow (1002)10-14 dayssuter without tyrosine
615721-2 days

multicellular morphology

@refforms multicellular complexmedium name
21360noISP 2
21360noISP 3
21360noISP 4
21360noISP 5
21360noISP 7
21360noSuter with tyrosine
21360noSuter without tyrosine

pigmentation

  • @ref: 29488
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15961TRYPTICASE 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
21360ISP 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
21360ISP 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
21360suter with tyrosineyesName: Synthetically suter medium (5337) with and without tyrosine - see Kutzner,H.J., R. M. Kroppensted and F. Korn-Wendisch. (1986) Composition: Glycerol 15.0 g/l Tyrosine 1.0 (optional, see preparation comment) L-arginine 5.0 g/l L-glutamic acid 5.0 g/l L-methionine 0.3 g/l L-isoleucine 0.3 g/l K2HPO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l Agar 20.0 g/l Trace element solution (5341) 1.0 ml Composition of Trace element solution (5341): CuSO4 x 5 H2O 10.0 g/l CaCl2 x 2 H2O 10.0 g/l FeSO4 x 7 H2O 10.0 g/l ZnSO4 x 7 H2O 10.0 g/l MnSO4 x 7 H2O 40.0 g/l Preparation: Control medium is prepared without tyrosine Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigment Organisms: All Actinomycetes
21360suter without tyrosineyesName: Synthetically suter medium (5337) with and without tyrosine - see Kutzner,H.J., R. M. Kroppensted and F. Korn-Wendisch. (1986) Composition: Glycerol 15.0 g/l Tyrosine 1.0 (optional, see preparation comment) L-arginine 5.0 g/l L-glutamic acid 5.0 g/l L-methionine 0.3 g/l L-isoleucine 0.3 g/l K2HPO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l Agar 20.0 g/l Trace element solution (5341) 1.0 ml Composition of Trace element solution (5341): CuSO4 x 5 H2O 10.0 g/l CaCl2 x 2 H2O 10.0 g/l FeSO4 x 7 H2O 10.0 g/l ZnSO4 x 7 H2O 10.0 g/l MnSO4 x 7 H2O 40.0 g/l Preparation: Control medium is prepared without tyrosine Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigment Organisms: All Actinomycetes
21360ISP 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:
21360ISP 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
21360ISP 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
41791MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
116147CIP Medium 338yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=338
116147CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
15961positivegrowth28mesophilic
29488positivegrowth25-30mesophilic
41791positivegrowth30mesophilic
61572positivegrowth30mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29488aerobe
61572aerobe

spore formation

@refspore formationconfidence
69481no92
69480no99.994

halophily

  • @ref: 21360
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 10 %

murein

  • @ref: 15961
  • murein short key: B12
  • type: B2alpha {Gly} [L-Orn] D-Glu-Gly-D-Orn

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2136017234glucose+/-
2136022599arabinose+
2136017992sucrose+
2136018222xylose+/-
2136017268myo-inositol+
2136037684mannose+
2136028757fructose+
2136026546rhamnose+
2136016634raffinose-
2136062968cellulose+/-
2948822599arabinose+carbon source
2948835391aspartate+carbon source
2948828260galactose+carbon source
2948825115malate+carbon source
2948817148putrescine+carbon source
2948826546rhamnose+carbon source
2948833942ribose+carbon source
2948817814salicin+carbon source
2948830911sorbitol+carbon source
2948818222xylose+carbon source
294884853esculin+hydrolysis
683794853esculin+hydrolysis
6837916199urea+hydrolysis
683795291gelatin+hydrolysis
6837917634D-glucose+fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose+fermentation
6837928087glycogen-fermentation

enzymes

@refvalueactivityec
29488catalase+1.11.1.6
29488cytochrome oxidase+1.9.3.1
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
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 (C 4)+
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

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
21360+/-+---+++++++-----+-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
21360+/-++/--+----+-+/-+-++++-

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinent
15961stalk of the mushroom Agaricus blazeiAgaricus blazeiTaiwanTWNAsia
61572Stalk of the mushroom Agaricus brasiliensiTaiwanTWNAsia
67770Stalk of the edible mushroom Agaricus blazei grown in the laboratoryAgaricus blazei
116147Stalk of the mushroom, Agaricus blazeiTaiwanTWNAsia

isolation source categories

Cat1Cat2Cat3
#Host#Fungi#Mushroom
#Host Body-Site

taxonmaps

  • @ref: 69479
  • File name: preview.99_156044.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_27915;97_45951;98_102879;99_156044&stattab=map
  • Last taxonomy: Microbacterium
  • 16S sequence: FJ807673
  • Sequence Identity:
  • Total samples: 224
  • soil counts: 138
  • aquatic counts: 24
  • animal counts: 30
  • plant counts: 32

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
159611Risk group (German classification)
1161471Risk group (French classification)

Sequence information

16S sequences

  • @ref: 15961
  • description: Microbacterium agarici strain CC-SBCK-209 16S ribosomal RNA gene, partial sequence
  • accession: FJ807673
  • length: 1480
  • database: ena
  • NCBI tax ID: 630514

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Microbacterium agarici strain DSM 21798630514.3wgspatric630514
66792Microbacterium agarici DSM 217982627853600draftimg630514
67770Microbacterium agarici DSM 21798GCA_002563955contigncbi630514

GC content

  • @ref: 67770
  • GC-content: 64.5
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno92no
gram-positiveyes89.132no
anaerobicno99.57no
halophileno62.133no
spore-formingno92.178no
glucose-utilyes89.911no
thermophileno97.128yes
flagellatedno94.068no
aerobicyes90.967yes
motileyes51.113no
glucose-fermentno86.273yes

External links

@ref: 15961

culture collection no.: DSM 21798, CCM 7686, CIP 110690, CCUG 58051, JCM 18705

straininfo link

  • @ref: 76897
  • straininfo: 400174

literature

  • topic: Phylogeny
  • Pubmed-ID: 19661494
  • title: Microbacterium agarici sp. nov., Microbacterium humi sp. nov. and Microbacterium pseudoresistens sp. nov., isolated from the base of the mushroom Agaricus blazei.
  • authors: Young CC, Busse HJ, Langer S, Chu JN, Schumann P, Arun AB, Shen FT, Rekha PD, Kampfer P
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.014092-0
  • year: 2009
  • mesh: Actinomycetales/*classification/genetics/*isolation & purification/physiology, *Agaricus, Bacterial Typing Techniques, DNA, Ribosomal/analysis/genetics, Fatty Acids/analysis, Genes, rRNA, Genotype, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, Plant Stems/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
15961Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21798)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21798
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
21360Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM21798.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
29488Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2588828776041
41791Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/30495
61572Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 58051)https://www.ccug.se/strain?id=58051
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 updates33211880Nucleic Acids Res. 49: D498-D508 2020
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
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
76897Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID400174.1StrainInfo: A central database for resolving microbial strain identifiers
116147Curators of the CIPCollection of Institut Pasteur (CIP 110690)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110690