Strain identifier

BacDive ID: 7759

Type strain: Yes

Species: Micrococcus endophyticus

Strain history: <- S-K Tang, Yunnan Inst. Microbiol, China

NCBI tax ID(s): 455343 (species)

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General

@ref: 7281

BacDive-ID: 7759

DSM-Number: 17945

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

description: Micrococcus endophyticus DSM 17945 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from surface-sterilized roots of Aquilaria sinensis collected in tropical rainforest.

NCBI tax id

  • NCBI tax id: 455343
  • Matching level: species

strain history

@refhistory
7281<- W.-J. Li, YIM <- H.-H. Chen; YIM 56238
67770KCTC 19156 <-- W.-J. Li YIM 56238.
67771<- S-K Tang, Yunnan Inst. Microbiol, China

doi: 10.13145/bacdive7759.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Micrococcaceae
  • genus: Micrococcus
  • species: Micrococcus endophyticus
  • full scientific name: Micrococcus endophyticus Chen et al. 2009

@ref: 7281

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micrococcaceae

genus: Micrococcus

species: Micrococcus endophyticus

full scientific name: Micrococcus endophyticus Chen et al. 2009

type strain: yes

Morphology

cell morphology

@refgram staincell shapeconfidencemotility
29104positivecoccus-shaped
67771positive
125439positive98.6
12543893.5no
125438positive92.657

colony morphology

@refcolony colorincubation periodmedium used
19758Lemon yellow (1012)10-14 daysISP 2
19758Sulfur yellow (1016)10-14 daysISP 3
19758Green beige (1000)10-14 daysISP 4
19758Green beige (1000)10-14 daysISP 5
19758Traffic yellow (1023)10-14 daysISP 6
19758Zinc yellow (1018)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
19758noISP 2
19758noISP 3
19758noISP 4
19758noISP 5
19758noISP 6
19758noISP 7

pigmentation

  • @ref: 29104
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7281TRYPTICASE 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
19758ISP 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
19758ISP 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:
19758ISP 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
19758ISP 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
19758ISP 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
19758ISP 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

@refgrowthtypetemperature
7281positivegrowth28
19758positiveoptimum28
29104positivegrowth15-37
29104positiveoptimum28
67770positivegrowth28
67771positivegrowth28

culture pH

@refabilitytypepHPH range
29104positivegrowth06-09alkaliphile
29104positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
29104aerobe
67771aerobe
125439facultative anaerobe91.3

spore formation

  • @ref: 29104
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
29104NaClpositivegrowth0-10 %
29104NaClpositiveoptimum5 %

observation

@refobservation
29104aggregates in clumps
67770quinones: MK-8(H2), MK-7(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
29104581435-dehydro-D-gluconate+carbon source
2910422599arabinose+carbon source
2910417057cellobiose+carbon source
2910428757fructose+carbon source
2910428260galactose+carbon source
2910417234glucose+carbon source
2910417306maltose+carbon source
2910437684mannose+carbon source
2910437657methyl D-glucoside+carbon source
29104506227N-acetylglucosamine+carbon source
2910416634raffinose+carbon source
2910433942ribose+carbon source
2910430911sorbitol+carbon source
2910417992sucrose+carbon source
2910427082trehalose+carbon source
291044853esculin+hydrolysis
2910417632nitrate+reduction
6837917992sucrose-fermentation
6837917716lactose-fermentation
6837916899D-mannitol-fermentation
6837965327D-xylose-fermentation
6837916988D-ribose-fermentation
6837917634D-glucose-fermentation
6837916199urea-hydrolysis
6837917632nitrate-reduction
6837928087glycogen-fermentation
6837917306maltose-fermentation
683795291gelatin+hydrolysis
683794853esculin-hydrolysis

enzymes

@refvalueactivityec
29104catalase+1.11.1.6
29104gelatinase+
29104cytochrome oxidase+1.9.3.1
68382alpha-fucosidase-3.2.1.51
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
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+
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase-3.1.3.2
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
68379beta-glucosidase-3.2.1.21
68379beta-galactosidase-3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase-3.1.3.1
68382alpha-galactosidase-3.2.1.22
68379gelatinase+
68379urease-3.5.1.5
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alpha-glucosidase-3.2.1.20
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase-3.5.1.B15

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
19758----------+--------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
19758-+++++----+---+----

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
7281surface-sterilized roots of Aquilaria sinensis collected in tropical rainforestAquilaria sinensissouth-west China, Yunnan ProvinceChinaCHNAsia
67771From plantYunnan ProvinceChinaCHNAsia
67770Surface-sterilized roots of Aquilaria sinensis from a tropical rainforestAquilaria sinensisYunnan Province, south-west ChinaChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Tree
#Host Body-Site#Plant#Root (Rhizome)
#Host Body-Site#Plant#Sterilized plant part
#Climate#Hot#Tropical

taxonmaps

  • @ref: 69479
  • File name: preview.99_746.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_453;97_519;98_597;99_746&stattab=map
  • Last taxonomy: Micrococcus
  • 16S sequence: EU005372
  • Sequence Identity:
  • Total samples: 56744
  • soil counts: 6060
  • aquatic counts: 9695
  • animal counts: 37863
  • plant counts: 3126

Safety information

risk assessment

  • @ref: 7281
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 7281
  • description: Micrococcus endophyticus strain YIM 56238 16S ribosomal RNA gene, partial sequence
  • accession: EU005372
  • length: 1438
  • database: nuccore
  • NCBI tax ID: 455343

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Micrococcus endophyticus DSM 17945GCA_014205115contigncbi455343
66792Micrococcus endophyticus strain DSM 17945455343.4wgspatric455343
66792Micrococcus endophyticus DSM 179452870801768draftimg455343

GC content

@refGC-contentmethod
728172.9high performance liquid chromatography (HPLC)
2910472.9

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes92.657yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.248yes
125438spore-formingspore-formingAbility to form endo- or exosporesno82.371yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes88.02yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno94.5yes
125438motile2+flagellatedAbility to perform flagellated movementno93.5no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno68
125439BacteriaNetmotilityAbility to perform movementno76.3
125439BacteriaNetgram_stainReaction to gram-stainingpositive98.6
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthfacultative anaerobe91.3

External links

@ref: 7281

culture collection no.: DSM 17945, KCTC 19156, YIM 56238, JCM 16951

straininfo link

  • @ref: 77202
  • straininfo: 404163

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19406795Micrococcus endophyticus sp. nov., isolated from surface-sterilized Aquilaria sinensis roots.Chen HH, Zhao GZ, Park DJ, Zhang YQ, Xu LH, Lee JC, Kim CJ, Li WJInt J Syst Evol Microbiol10.1099/ijs.0.006296-02009Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, DNA, Bacterial/analysis/genetics, Fatty Acids/analysis, Genes, rRNA, Micrococcus/*classification/genetics/isolation & purification/physiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity, Thymelaeaceae/classification/*microbiologyGenetics
Phylogeny25048212Description of Micrococcus aloeverae sp. nov., an endophytic actinobacterium isolated from Aloe vera.Prakash O, Nimonkar Y, Munot H, Sharma A, Vemuluri VR, Chavadar MS, Shouche YSInt J Syst Evol Microbiol10.1099/ijs.0.063339-02014Aloe/*microbiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, India, Micrococcus/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny36362904Micrococcus porci sp. nov., Isolated from Feces of Black Pig (Sus scrofa).Lee AY, Chen CH, Liou JS, Lin YC, Hamada M, Wang YT, Peng LL, Chang SC, Chen CC, Lin CF, Huang L, Huang CHLife (Basel)10.3390/life121117492022

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7281Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17945)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17945
19758Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM17945.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
29104Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2553328776041
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/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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
77202Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID404163.1StrainInfo: A central database for resolving microbial strain identifiers
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1