Strain identifier

BacDive ID: 7964

Type strain: Yes

Species: Micromonospora halophytica

Strain history: KCC A-0125 <-- NRRL 2998 <-- Schering Corp..

NCBI tax ID(s): 47864 (species)

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General

@ref: 10839

BacDive-ID: 7964

DSM-Number: 43171

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

description: Micromonospora halophytica DSM 43171 is a spore-forming, mesophilic, Gram-positive bacterium that builds an aerial mycelium and produces antibiotic compounds.

NCBI tax id

  • NCBI tax id: 47864
  • Matching level: species

strain history

@refhistory
10839<- KCC <- NRRL <- Schering AG
67770KCC A-0125 <-- NRRL 2998 <-- Schering Corp..

doi: 10.13145/bacdive7964.20230509.8.1

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 halophytica
  • full scientific name: Micromonospora halophytica Weinstein et al. 1968 (Approved Lists 1980)

@ref: 10839

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micromonosporaceae

genus: Micromonospora

species: Micromonospora halophytica

full scientific name: Micromonospora halophytica Weinstein et al. 1968

type strain: yes

Morphology

cell morphology

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

colony morphology

@refcolony colorincubation periodmedium used
19553Orange10-14 daysISP 2
19553Orange - Black10-14 daysISP 3
19553Orange10-14 daysISP 4
19553Orange10-14 daysISP 5
19553Orange10-14 daysISP 6
19553Orange10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium namecomplex namecomplex color
19553noISP 2
19553noISP 3
19553noISP 4
19553yesISP 5Aerial MyceliumWhite
19553noISP 6
19553noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
10839CZAPEK PEPTONE AGAR (DSMZ Medium 83)yeshttps://mediadive.dsmz.de/medium/83Name: CZAPEK PEPTONE AGAR (DSMZ Medium 83) Composition: Sucrose 30.0 g/l Agar 20.0 g/l Peptone 5.0 g/l NaNO3 3.0 g/l Yeast extract 2.0 g/l K2HPO4 1.0 g/l MgSO4 x 7 H2O 0.5 g/l KCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Distilled water
19553ISP 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
19553ISP 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:
19553ISP 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
19553ISP 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
19553ISP 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
19553ISP 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
10839GYM 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

culture temp

@refgrowthtypetemperaturerange
19553positiveoptimum28mesophilic
10839positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481yes100
69480yes98.381

compound production

  • @ref: 10839
  • compound: halomycin

halophily

  • @ref: 19553
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 2.5 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1955317234glucose+
1955322599arabinose+
1955317992sucrose+
1955318222xylose-
1955317268myo-inositol-
1955329864mannitol-
1955328757fructose+/-
1955326546rhamnose-
1955316634raffinose+
1955362968cellulose-
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis

metabolite production

@refmetaboliteproductionChebi-ID
67770halomicinyes
68368acetoinno15688
68368indoleno35581
68368hydrogen sulfideno16136

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin-
6836835581indole-

enzymes

@refvalueactivityec
68368gelatinase+
68368tryptophan deaminase-4.1.99.1
68368urease-3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase-3.5.3.6
68368beta-galactosidase-3.2.1.23

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19553----------+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
10839salt poolNew York, SyracuseUSAUSANorth America
67770Mud, bottom of a salt poolSyracuse, NYUSAUSANorth America

isolation source categories

Cat1Cat2Cat3
#Engineered#Built environment#Water reservoir (Aquarium/pool)
#Condition#Saline

taxonmaps

  • @ref: 69479
  • File name: preview.99_1923.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_94;96_404;97_1111;98_1509;99_1923&stattab=map
  • Last taxonomy: Micromonospora
  • 16S sequence: X92601
  • Sequence Identity:
  • Total samples: 804
  • soil counts: 470
  • aquatic counts: 188
  • animal counts: 133
  • plant counts: 13

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
108391Risk group (German classification)
195531Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Micromonospora halophytica subsp. halophytica 16S-23S ribosomal RNA spacer regionAF004002382ena47864
10839Micromonospora halophytica 16S rRNA gene (isolate DSM 43171)X926011476ena47864

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Micromonospora halophytica strain DSM 4317147864.4wgspatric47864
66792Micromonospora halophytica DSM 431712622736531draftimg47864
67770Micromonospora halophytica DSM 43171GCA_900090245scaffoldncbi47864

GC content

@refGC-contentmethod
6777072.5high performance liquid chromatography (HPLC)
6777072.94genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
gram-positiveyes90.994no
anaerobicno99.126no
halophileno92.124no
spore-formingyes94.466no
glucose-utilyes86.93yes
aerobicyes93.034no
thermophileno97.945no
motileno93.65no
flagellatedno97.708no
glucose-fermentno92.189no

External links

@ref: 10839

culture collection no.: DSM 43171, ATCC 27596, JCM 3125, KCC A-0125, NRRL 2998, BCRC 11658, CBS 336.76, CECT 3293, CGMCC 4.1078, CGMCC 4.1490, IFM 1276, IFO 14112, KCTC 9551, NBRC 14112, NCIMB 2223

straininfo link

  • @ref: 77398
  • straininfo: 45819

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny20562246Micromonospora humi sp. nov., isolated from peat swamp forest soil.Songsumanus A, Tanasupawat S, Thawai C, Suwanborirux K, Kudo TInt J Syst Evol Microbiol10.1099/ijs.0.024281-02010DNA, Bacterial/genetics, Micromonospora/*classification/genetics/*isolation & purification, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Thailand, Trees/microbiologyGenetics
Phylogeny22523171Micromonospora maritima sp. nov., isolated from mangrove soil.Songsumanus A, Tanasupawat S, Igarashi Y, Kudo TInt J Syst Evol Microbiol10.1099/ijs.0.039180-02012Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Micromonospora/*classification/genetics/metabolism, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Thailand, Vitamin K 2/analysisGenetics
Phylogeny25957972Two new species of the genus Micromonospora: Micromonospora palomenae sp. nov. and Micromonospora harpali sp. nov. isolated from the insects.Fang B, Liu C, Guan X, Song J, Zhao J, Liu H, Li C, Ning W, Wang X, Xiang WAntonie Van Leeuwenhoek10.1007/s10482-015-0472-92015Animals, Bacterial Typing Techniques, China, Cluster Analysis, DNA Gyrase/genetics, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Insecta/*microbiology, Micromonospora/*classification/genetics/*isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Phylogeny27220280Micromonospora sediminis sp. nov., isolated from mangrove sediment.Phongsopitanun W, Kudo T, Ohkuma M, Pittayakhajonwut P, Suwanborirux K, Tanasupawat SInt J Syst Evol Microbiol10.1099/ijsem.0.0011752016Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Micromonospora/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Thailand, Vitamin K 2/chemistry, *WetlandsTranscriptome
Phylogeny30528275A study of three bacteria isolated from marine sediment and description of Micromonospora globispora sp. nov.Carro L, Veyisoglu A, Cetin D, Igual JM, Klenk HP, Trujillo ME, Sahin NSyst Appl Microbiol10.1016/j.syapm.2018.11.0032018Bacterial Typing Techniques, Black Sea, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Genes, Bacterial, Geologic Sediments/*microbiology, Micromonospora/*classification/isolation & purification, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Turkey, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
10839Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43171)https://www.dsmz.de/collection/catalogue/details/culture/DSM-43171
19553Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM43171.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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68368Automatically annotated from API 20E
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
77398Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID45819.1StrainInfo: A central database for resolving microbial strain identifiers