Strain identifier

BacDive ID: 7468

Type strain: Yes

Species: Mycetocola lacteus

Strain Designation: CM-10

Strain history: IFO 16278 <-- T. Tsukamoto CM-10.

NCBI tax ID(s): 76637 (species)

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General

@ref: 5742

BacDive-ID: 7468

DSM-Number: 15177

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

description: Mycetocola lacteus CM-10 is a mesophilic, Gram-positive bacterium that was isolated from cultivated mushroom Pleurotus ostreatus.

NCBI tax id

  • NCBI tax id: 76637
  • Matching level: species

strain history

@refhistory
5742<- NBRC <- T. Tsukamoto; CM-10
67770IFO 16278 <-- T. Tsukamoto CM-10.

doi: 10.13145/bacdive7468.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Microbacteriaceae
  • genus: Mycetocola
  • species: Mycetocola lacteus
  • full scientific name: Mycetocola lacteus Tsukamoto et al. 2001

@ref: 5742

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Mycetocola

species: Mycetocola lacteus

full scientific name: Mycetocola lacteus Tsukamoto et al. 2001

strain designation: CM-10

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: positive
  • confidence: 100

colony morphology

@refcolony colorincubation periodmedium used
18519Beige (1001)10-14 daysISP 2
18519Beige (1001)10-14 daysISP 3
1851910-14 daysISP 4
1851910-14 daysISP 5
1851910-14 daysISP 6
1851910-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
18519noISP 2
18519noISP 3
18519noISP 4
18519noISP 5
18519noISP 6
18519noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5742TRYPTICASE 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
18519ISP 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
18519ISP 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:
18519ISP 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
18519ISP 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
18519ISP 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
18519ISP 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

culture temp

@refgrowthtypetemperaturerange
18519positiveoptimum28mesophilic
5742positivegrowth28mesophilic
67770positivegrowth30mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no93
69480no99.996

observation

  • @ref: 67770
  • observation: quinones: MK-10, MK-9, MK-11

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1851962968cellulose-
1851916634raffinose-
1851926546rhamnose-
1851928757fructose+/-
1851929864mannitol+/-
1851917268myo-inositol-
1851918222xylose+
1851917992sucrose-
1851922599arabinose-
1851917234glucose-
683794853esculin+hydrolysis
683795291gelatin-hydrolysis
6837917992sucrose-fermentation

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
68379gelatinase-
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

@refPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELSAC
18519++--++-++/---

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
18519-++-+++--++++-+++--

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinentgeographic location
5742cultivated mushroom Pleurotus ostreatusPleurotus ostreatusJapanJPNAsia
67770Fruiting body of rotting cultivated mushroom PleurotusostreatusPleurotusostreatusJapanJPNAsiaGifu Pref.

isolation source categories

  • Cat1: #Host
  • Cat2: #Fungi
  • Cat3: #Mushroom

taxonmaps

  • @ref: 69479
  • File name: preview.99_3087.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_417;97_1928;98_2371;99_3087&stattab=map
  • Last taxonomy: Microbacterium
  • 16S sequence: AM410678
  • Sequence Identity:
  • Total samples: 1043
  • soil counts: 136
  • aquatic counts: 298
  • animal counts: 351
  • plant counts: 258

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
57421Risk group (German classification)
185191Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Mycetocola lacteus partial 16S rRNA gene, type strain DSM 15177AM4106781445ena76637
5742Mycetocola lacteus gene for 16S rRNAAB0126481445ena76637

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Mycetocola lacteus strain JCM 1165476637.3wgspatric76637
66792Mycetocola lacteus JCM 116542832382567draftimg76637
67770Mycetocola lacteus JCM 11654GCA_003667575contigncbi76637

GC content

@refGC-contentmethod
574264high performance liquid chromatography (HPLC)
6777063.9high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno93no
motileno91.587no
flagellatedno97.282no
gram-positiveyes93.905no
anaerobicno98.631no
halophileno76.802no
spore-formingno92.729no
glucose-utilyes62.214yes
aerobicyes88.965no
thermophileno99.424yes
glucose-fermentno76.664no

External links

@ref: 5742

culture collection no.: DSM 15177, IFO 16278, NBRC 16278, NRRL B-24121, JCM 11654, CGMCC 1.10732, IAM 15091, LMG 22187, MAFF 211326

straininfo link

  • @ref: 76913
  • straininfo: 62367

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny11411718Proposal of Mycetocola gen. nov. in the family Microbacteriaceae and three new species, Mycetocola saprophilus sp. nov., Mycetocola tolaasinivorans sp. nov. and Mycetocola lacteus sp. nov., isolated from cultivated mushroom, Pleurotus ostreatus.Tsukamoto T, Takeuchi M, Shida O, Murata H, Shirata AInt J Syst Evol Microbiol10.1099/00207713-51-3-9372001Actinomycetales/*classification/genetics/*physiology/ultrastructure, *Agaricales, DNA Primers, DNA, Ribosomal/genetics, Japan, Molecular Sequence Data, Peptidoglycan/chemistry/metabolism, *Phylogeny, RNA, Ribosomal, 16S/genetics, Vitamin K/metabolismGenetics
Phylogeny23291895Mycetocola miduiensis sp. nov., a psychrotolerant bacterium isolated from Midui glacier.Zhu L, Liu Q, Liu H, Zhou Y, Xin Y, Dong XInt J Syst Evol Microbiol10.1099/ijs.0.047985-02013Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Ice Cover/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil Microbiology, Tibet, Vitamin K 2/analysisGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5742Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15177)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15177
18519Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM15177.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
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/
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
76913Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID62367.1StrainInfo: A central database for resolving microbial strain identifiers