Strain identifier

BacDive ID: 7983

Type strain: Yes

Species: Micromonospora auratinigra

Strain Designation: TT1-11

Strain history: CIP <- 2005, JCM <- C. Thawai: strain TT1-11

NCBI tax ID(s): 261654 (species)

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General

@ref: 12099

BacDive-ID: 7983

DSM-Number: 44815

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

description: Micromonospora auratinigra TT1-11 is a spore-forming, mesophilic, Gram-positive bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 261654
  • Matching level: species

strain history

@refhistory
12099<- Ch. Thawai; TT1-11 (Micromonospora aurantionigra)
67770C. Thawai TT1-11.
116566CIP <- 2005, JCM <- C. Thawai: strain TT1-11

doi: 10.13145/bacdive7983.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micromonosporales
  • family: Micromonosporaceae
  • genus: Micromonospora
  • species: Micromonospora auratinigra
  • full scientific name: Micromonospora auratinigra corrig. Thawai et al. 2004

  • synonyms

    • @ref: 20215
    • synonym: Micromonospora aurantionigra

@ref: 12099

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micromonosporaceae

genus: Micromonospora

species: Micromonospora auratinigra

full scientific name: Micromonospora auratinigra Thawai et al. 2004

strain designation: TT1-11

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480positive100
116566positiverod-shapedno

colony morphology

@refcolony colorincubation periodmedium used
19708Deep orange - Black brown10-14 daysISP 2
19708Deep orange10-14 daysISP 3
19708Deep orange10-14 daysISP 4
19708Brown orange10-14 daysISP 5
19708Honey yellow10-14 daysISP 6
19708Black brown10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
19708noISP 2
19708noISP 3
19708noISP 4
19708noISP 5
19708noISP 6
19708noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12099N-Z-AMINE-MEDIUM (DSMZ Medium 554)yeshttps://mediadive.dsmz.de/medium/554Name: N-Z-AMINE-MEDIUM (DSMZ Medium 554) Composition: Starch 20.0 g/l Agar 20.0 g/l Glucose 10.0 g/l N-Z amine 5.0 g/l Yeast extract 5.0 g/l CaCO3 1.0 g/l Distilled water
12099GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yeshttps://mediadive.dsmz.de/medium/65Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water
12099CZAPEK PEPTONE AGAR (DSMZ Medium 83)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium83.pdf
19708ISP 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
19708ISP 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:
19708ISP 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
19708ISP 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
19708ISP 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
19708ISP 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
36435MEDIUM 116 - for Streptomyces, Nocardia, Streptosporangium and Mycobacterium chlorophenolicumyesDistilled water make up to (1000.000 ml);Agar (20.000 g);Glucose (4.000g);Yeast extract (4.000 g);Malt extract (10.000 g)
116566CIP Medium 116yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=116

culture temp

@refgrowthtypetemperaturerange
19708positiveoptimum28mesophilic
36435positivegrowth30mesophilic
67770positivegrowth28mesophilic
12099positivegrowth28mesophilic
116566positivegrowth25-37mesophilic
116566nogrowth10psychrophilic
116566nogrowth41thermophilic
116566nogrowth45thermophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481yes100
69480yes100

halophily

@refsaltgrowthtested relationconcentration
116566NaClpositivegrowth0-2 %
116566NaClnogrowth4 %
116566NaClnogrowth6 %
116566NaClnogrowth8 %
116566NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: MK-10(H4), MK-9(H4), MK-10(H6)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1970817234glucose+
1970822599arabinose+/-
1970817992sucrose+/-
1970818222xylose-
1970817268myo-inositol-
1970829864mannitol-
1970828757fructose+
1970826546rhamnose-
1970816634raffinose+
1970816634raffinose+/-
11656616947citrate-carbon source
1165664853esculin+hydrolysis
116566606565hippurate+hydrolysis
11656617632nitrate-reduction
11656616301nitrite-reduction

metabolite production

  • @ref: 116566
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11656615688acetoin-
11656617234glucose-

enzymes

@refvalueactivityec
116566oxidase-
116566beta-galactosidase-3.2.1.23
116566alcohol dehydrogenase+1.1.1.1
116566gelatinase+
116566amylase+
116566DNase+
116566caseinase+3.4.21.50
116566catalase+1.11.1.6
116566tween esterase-
116566gamma-glutamyltransferase-2.3.2.2
116566lecithinase-
116566lipase+
116566lysine decarboxylase-4.1.1.18
116566ornithine decarboxylase-4.1.1.17
116566phenylalanine ammonia-lyase-4.3.1.24
116566tryptophan deaminase-
116566urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase+3.4.11.3
68382trypsin+3.4.21.4
68382alpha-chymotrypsin+3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase+3.2.1.22
68382beta-galactosidase+3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382alpha-mannosidase-3.2.1.24

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
19708+++-+++++++++-+++--
116566+++++++++++++-+++-+-

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116566-----------------------+---------------------------------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
12099soilPattalung PrefectureThailandTHAAsia
67770Soil in a peat swamp forestThatien, PattalungThailandTHAAsia
116566Environment, Soil in a peat swamp forestThatien, PattalungThailandTHAAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
120991Risk group (German classification)
197081Risk group (German classification)
1165661Risk group (French classification)

Sequence information

16S sequences

  • @ref: 12099
  • description: Micromonospora auratinigra gene for 16S rRNA, partial sequence
  • accession: AB159779
  • length: 1482
  • database: ena
  • NCBI tax ID: 261654

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Micromonospora auratinigra DSM 44815GCA_900089595chromosomencbi261654
66792Micromonospora auratinigra strain DSM 44815261654.4completepatric261654
66792Micromonospora auratinigra DSM 448152617270871draftimg261654

GC content

@refGC-contentmethod
1209972.8
6777072.8high performance liquid chromatography (HPLC)
6777073.62genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno94.369no
gram-positiveyes91.04no
anaerobicno98.926no
aerobicyes94.644no
halophileno94.87no
spore-formingyes93.359no
glucose-utilyes87.849yes
flagellatedno97.894no
thermophileno99.207yes
glucose-fermentno93.017no

External links

@ref: 12099

culture collection no.: DSM 44815, JCM 12357, PCU 239, CGMCC 4.5704, CIP 108632, NBRC 101913, TISTR 1532

straininfo link

  • @ref: 77416
  • straininfo: 134298

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18398196Micromonospora chaiyaphumensis sp. nov., isolated from Thai soils.Jongrungruangchok S, Tanasupawat S, Kudo TInt J Syst Evol Microbiol10.1099/ijs.0.65594-02008Carbohydrate Metabolism, Genes, Bacterial, Micromonospora/*classification/genetics/*isolation & purification/metabolism, Microscopy, Electron, Scanning, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Soil Microbiology, Terminology as Topic, ThailandMetabolism
Phylogeny21398502Micromonospora yangpuensis sp. nov., isolated from a sponge.Zhang L, Xi L, Ruan J, Huang YInt J Syst Evol Microbiol10.1099/ijs.0.029439-02011Animals, Bacterial Typing Techniques, Base Composition, China, DNA Gyrase/genetics, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Genotype, Lipids/analysis, Micromonospora/*classification/genetics/isolation & purification/physiology, Molecular Sequence Data, Phenotype, Phylogeny, Porifera/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species SpecificityGenetics
Phylogeny21873512Description of Verrucosispora qiuiae sp. nov., isolated from mangrove swamp sediment, and emended description of the genus Verrucosispora.Xi L, Zhang L, Ruan J, Huang YInt J Syst Evol Microbiol10.1099/ijs.0.033787-02011Bacterial Typing Techniques, Base Composition, Carbohydrates/analysis, China, Cluster Analysis, DNA Gyrase/genetics, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, *Environmental Microbiology, Micromonosporaceae/*classification/genetics/*isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, WetlandsGenetics
Phylogeny22634700Micromonospora equina sp. nov., isolated from soil from a racecourse.Everest GJ, Meyers PRInt J Syst Evol Microbiol10.1099/ijs.0.042929-02012Animals, Bacterial Typing Techniques, DNA, Bacterial/genetics, Horses, Micromonospora/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, South AfricaGenetics
Phylogeny25966850Micromonospora endophytica sp. nov., an endophytic actinobacteria of Thai upland rice (Oryza sativa).Thanaboripat D, Thawai C, Kittiwongwattana C, Laosinwattana C, Koohakan P, Parinthawong NJ Antibiot (Tokyo)10.1038/ja.2015.572015Micromonospora/chemistry/genetics/*growth & development, Oryza/*microbiology, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics
Phylogeny26358439Micromonospora fluostatini sp. nov., isolated from marine sediment.Phongsopitanun W, Kudo T, Mori M, Shiomi K, Pittayakhajonwut P, Suwanborirux K, Tanasupawat SInt J Syst Evol Microbiol10.1099/ijsem.0.0005892015Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Micromonospora/*classification/genetics/isolation & purification, Molecular Sequence Data, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Thailand, Vitamin K 2/chemistryGenetics
Phylogeny33666807Micromonospora rubida sp. nov., a novel actinobacterium isolated from soil of Harbin.Sun X, Qiu S, Luo X, Jin P, Zhao J, Wu X, Yang J, Wang X, Song J, Xiang WAntonie Van Leeuwenhoek10.1007/s10482-021-01550-62021Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, *Micromonospora/genetics, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil, Soil Microbiology, Vitamin K 2Transcriptome

Reference

@idauthorscataloguedoi/urltitle
12099Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44815)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44815
19708Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44815.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
36435Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6282
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/
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
77416Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID134298.1StrainInfo: A central database for resolving microbial strain identifiers
116566Curators of the CIPCollection of Institut Pasteur (CIP 108632)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108632