Strain identifier

BacDive ID: 7469

Type strain: Yes

Species: Mycetocola saprophilus

Strain Designation: CM-01

Strain history: IFO 16274 <-- T. Tsukamoto CM-01.

NCBI tax ID(s): 76636 (species)

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General

@ref: 5743

BacDive-ID: 7469

DSM-Number: 15178

keywords: genome sequence, 16S sequence, Bacteria, mesophilic

description: Mycetocola saprophilus CM-01 is a mesophilic bacterium that was isolated from cultivated mushroom Pleurotus ostreatus.

NCBI tax id

  • NCBI tax id: 76636
  • Matching level: species

strain history

@refhistory
5743<- NBRC <- T. Tsukamoto; CM-01
67770IFO 16274 <-- T. Tsukamoto CM-01.

doi: 10.13145/bacdive7469.20230509.8.1

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 saprophilus
  • full scientific name: Mycetocola saprophilus Tsukamoto et al. 2001

@ref: 5743

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Mycetocola

species: Mycetocola saprophilus

full scientific name: Mycetocola saprophilus Tsukamoto et al. 2001 emend. Nouioui et al. 2018

strain designation: CM-01

type strain: yes

Morphology

colony morphology

@refcolony colorincubation periodmedium used
18520Beige (1001)10-14 daysISP 2
18520Beige (1001)10-14 daysISP 3
1852010-14 daysISP 4
1852010-14 daysISP 5
1852010-14 daysISP 6
1852010-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
18520noISP 2
18520noISP 3
18520noISP 4
18520noISP 5
18520noISP 6
18520noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5743TRYPTICASE 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
18520ISP 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
18520ISP 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:
18520ISP 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
18520ISP 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
18520ISP 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
18520ISP 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
18520positiveoptimum28mesophilic
5743positivegrowth28mesophilic
67770positivegrowth30mesophilic

Physiology and metabolism

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1852062968cellulose-
1852016634raffinose-
1852026546rhamnose-
1852028757fructose+/-
1852029864mannitol+/-
1852017268myo-inositol-
1852018222xylose+
1852017992sucrose+/-
1852022599arabinose-
1852017234glucose-
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
18520++--++--+/---

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
18520-++-+++----++-+++--

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinentgeographic location
5743cultivated mushroom Pleurotus ostreatusPleurotus ostreatusJapanJPNAsia
67770Fruiting body of rotting cultivated mushroom PleurotusostreatusPleurotusostreatusJapanJPNAsiaYamagata 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: AM410677
  • 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
57431Risk group (German classification)
185201Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Mycetocola saprophilus partial 16S rRNA gene, type strain DSM 15178AM4106771444ena76636
5743Mycetocola saprophilus gene for 16S rRNAAB0126471444ena76636

Genome sequences

  • @ref: 67770
  • description: Mycetocola saprophilus NRRL B-24119
  • accession: GCA_000718085
  • assembly level: contig
  • database: ncbi
  • NCBI tax ID: 76636

GC content

@refGC-contentmethod
574365.2high performance liquid chromatography (HPLC)
6777066.1genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno93.357no
flagellatedno97.187no
gram-positiveyes94.288no
anaerobicno98.772no
halophileno78.545no
spore-formingno93.194no
glucose-utilyes62.891yes
aerobicyes89.671no
thermophileno99.076yes
glucose-fermentno81.839no

External links

@ref: 5743

culture collection no.: DSM 15178, IFO 16274, NBRC 16274, NRRL B-24119, JCM 11655, CGMCC 1.10735, IAM 15092, LMG 22188, MAFF 211324

straininfo link

  • @ref: 76914
  • straininfo: 62363

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
Phylogeny35316169Mycetocola spongiae sp. nov., isolated from deep-sea sponge Cacospongia mycofijiensis.Chen Y, Sang J, Sun W, Song Q, Li ZInt J Syst Evol Microbiol10.1099/ijsem.0.0052912022Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, *Fatty Acids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5743Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15178)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15178
18520Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM15178.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
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
76914Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID62363.1StrainInfo: A central database for resolving microbial strain identifiers