Strain identifier

BacDive ID: 7989

Type strain: Yes

Species: Micromonospora citrea

Strain Designation: 71-97

Strain history: CIP <- 2005, DSMZ <- JCM <- KCC <- X. Yan: strain 71-97

NCBI tax ID(s): 47855 (species)

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General

@ref: 11378

BacDive-ID: 7989

DSM-Number: 43903

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

description: Micromonospora citrea 71-97 is a spore-forming, mesophilic bacterium that was isolated from lake mud.

NCBI tax id

  • NCBI tax id: 47855
  • Matching level: species

strain history

@refhistory
11378<- JCM (Micromonospora citrea) <- KCC <- X. Yan, 71-97
67770KCC A-0256 <-- X. Yan 71-97.
118294CIP <- 2005, DSMZ <- JCM <- KCC <- X. Yan: strain 71-97

doi: 10.13145/bacdive7989.20230509.8.1

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 citrea
  • full scientific name: Micromonospora citrea Kroppenstedt et al. 2005

@ref: 11378

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micromonosporaceae

genus: Micromonospora

species: Micromonospora citrea

full scientific name: Micromonospora citrea Kroppenstedt et al. 2005

strain designation: 71-97

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no90.238
69480100positive
118294nopositiverod-shaped

colony morphology

@refcolony colorincubation periodmedium used
19613Pastel orange10-14 daysISP 2
19613Salmon pink10-14 daysISP 3
19613Pastel yellow10-14 daysISP 4
1961310-14 daysISP 5
19613Yellow orange10-14 daysISP 6
1961310-14 daysISP 7
118294

multicellular morphology

@refforms multicellular complexmedium name
19613noISP 2
19613noISP 3
19613noISP 4
19613noISP 5
19613noISP 6
19613noISP 7

multimedia

  • @ref: 11378
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_43903.jpg
  • caption: Medium 554 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11378N-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
11378GYM 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
19613ISP 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
19613ISP 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:
19613ISP 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
19613ISP 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
19613ISP 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
19613ISP 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
118294CIP Medium 57yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=57

culture temp

@refgrowthtypetemperaturerange
11378positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481yes100
69480yes100

compound production

  • @ref: 19613
  • compound: Citreamicin

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1961317234glucose+
1961322599arabinose+
1961317992sucrose+
1961318222xylose-
1961317268myo-inositol-
1961329864mannitol-
1961328757fructose-
1961326546rhamnose-
1961316634raffinose-
1961362968cellulose+
11829417632nitrate+reduction
11829416301nitrite-reduction

metabolite production

  • @ref: 118294
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
118294oxidase-
118294alcohol dehydrogenase-1.1.1.1
118294catalase+1.11.1.6
118294lysine decarboxylase+4.1.1.18
118294ornithine decarboxylase-4.1.1.17
118294urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382cystine arylamidase-3.4.11.3
68382trypsin+3.4.21.4
68382alpha-chymotrypsin+3.4.21.1
68382acid phosphatase+3.1.3.2
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
68382alpha-fucosidase-3.2.1.51

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
19613+++-++-++++++-+-+--
118294+++-+--+++--+-+-+---

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
11378lake mud
67770Lake mudChinaCHNAsia
118294Environment, Lake, mudChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Lake (large)
#Environmental#Aquatic#Sediment

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
113781Risk group (German classification)
196131Risk group (German classification)
1182941Risk group (French classification)

Sequence information

16S sequences

  • @ref: 11378
  • description: Micromonospora citrea 16S rRNA gene, type strain DSM 43903
  • accession: X92617
  • length: 1476
  • database: ena
  • NCBI tax ID: 47855

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Micromonospora citrea strain DSM 4390347855.4wgspatric47855
66792Micromonospora citrea DSM 439032623620569draftimg47855
67770Micromonospora citrea DSM 43903GCA_900090315contigncbi47855

GC content

  • @ref: 67770
  • GC-content: 73.82
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
gram-positiveyes91.656no
anaerobicno99.134no
halophileno90.974no
spore-formingyes96.486no
glucose-utilyes86.799yes
aerobicyes93.554no
motileno93.676no
flagellatedno97.674no
thermophileno98.698yes
glucose-fermentno92.258no

External links

@ref: 11378

culture collection no.: DSM 43903, ATCC 35571, CIP 108947, IFO 14025, JCM 3256, KCC A-0256, NBRC 14025, NRRL B-16101, BCRC 12535, CGMCC 4.1269, IMSNU 21289, KCTC 9367

straininfo link

  • @ref: 77419
  • straininfo: 308587

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15997706Eight new species of the genus Micromonospora, Micromonospora citrea sp. nov., Micromonospora echinaurantiaca sp. nov., Micromonospora echinofusca sp. nov. Micromonospora fulviviridis sp. nov., Micromonospora inyonensis sp. nov., Micromonospora peucetia sp. nov., Micromonospora sagamiensis sp. nov., and Micromonospora viridifaciens sp. nov.Kroppenstedt RM, Mayilraj S, Wink JM, Kallow W, Schumann P, Secondini C, Stackebrandt ESyst Appl Microbiol10.1016/j.syapm.2004.12.0112005Carbohydrates/analysis, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Isomerism, Micromonospora/*classification/cytology/genetics/physiology, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Ribotyping, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, Vitamin K 2/analysis
Phylogeny33174828Micromonospora fluminis sp. nov., isolated from mountain river sediment.Camacho Pozo MI, Wieme AD, Rodriguez Perez S, Llaurado Maury G, Peeters C, Snauwaert C, Lescaylle Veranes Y, Pena Zamora L, Schumann P, Vandamme PAInt J Syst Evol Microbiol10.1099/ijsem.0.0045542020Bacterial Typing Techniques, Base Composition, Cuba, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Micromonospora/*classification/isolation & purification, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rivers/*microbiology, Sequence Analysis, DNA, Vitamin K 2/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitle
11378Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43903)https://www.dsmz.de/collection/catalogue/details/culture/DSM-43903
19613Wink, J.Micromonospora citreaCompendium 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
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
77419Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID308587.1StrainInfo: A central database for resolving microbial strain identifiers
118294Curators of the CIPCollection of Institut Pasteur (CIP 108947)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108947