Strain identifier

BacDive ID: 12606

Type strain: Yes

Species: Promicromonospora umidemergens

Strain Designation: 09-Be-007

Strain history: CCM 7634 <-- P. Kämpfer 09-Be-007.

NCBI tax ID(s): 629679 (species)

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General

@ref: 16126

BacDive-ID: 12606

DSM-Number: 22081

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

description: Promicromonospora umidemergens 09-Be-007 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from wall colonized with moulds.

NCBI tax id

  • NCBI tax id: 629679
  • Matching level: species

strain history

@refhistory
16126<- P. Kämpfer, Univ. Giessen, Germany; 09-Be-007 <- C. Trautmann, Berlin, Germany
67770CCM 7634 <-- P. Kämpfer 09-Be-007.

doi: 10.13145/bacdive12606.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Promicromonosporaceae
  • genus: Promicromonospora
  • species: Promicromonospora umidemergens
  • full scientific name: Promicromonospora umidemergens Martin et al. 2010

@ref: 16126

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Promicromonosporaceae

genus: Promicromonospora

species: Promicromonospora umidemergens

full scientific name: Promicromonospora umidemergens Martin et al. 2010 emend. Nouioui et al. 2018

strain designation: 09-Be-007

type strain: yes

Morphology

cell morphology

  • @ref: 29492
  • gram stain: positive
  • motility: no

colony morphology

@refcolony colorincubation periodmedium used
19797Green beige10-14 daysISP 2
19797Light ivory10-14 daysISP 3
19797Ivory10-14 daysISP 4
19797Green beige10-14 daysISP 5
19797Green beige10-14 daysISP 6
19797Green beige10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
19797noISP 2
19797noISP 3
19797noISP 4
19797noISP 5
19797noISP 6
19797noISP 7

pigmentation

  • @ref: 29492
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16126GYM 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
19797ISP 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
19797ISP 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:
19797ISP 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
19797ISP 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
19797ISP 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
19797ISP 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
16126TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
16126RICH MEDIUM (DSMZ Medium 736)yeshttps://mediadive.dsmz.de/medium/736Name: RICH MEDIUM (DSMZ Medium 736) Composition: Agar 20.0 g/l Bacto peptone 10.0 g/l Yeast extract 5.0 g/l Malt extract 5.0 g/l Casamino acids 5.0 g/l Glycerol 2.0 g/l Meat extract 2.0 g/l MgSO4 x 7 H2O 1.0 g/l Tween 80 0.05 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
16126positivegrowth28mesophilic
19797positiveoptimum28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 29492
  • oxygen tolerance: aerobe

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1979762968cellulose-
1979716634raffinose-
1979726546rhamnose+
1979728757fructose+
1979729864mannitol+
1979717268myo-inositol-
1979718222xylose-
1979717992sucrose+
1979722599arabinose+
1979717234glucose+
29492370543-hydroxybutyrate+carbon source
2949222599arabinose+carbon source
2949235391aspartate+carbon source
2949217057cellobiose+carbon source
2949228757fructose+carbon source
2949217234glucose+carbon source
2949227570histidine+carbon source
2949224996lactate+carbon source
2949225115malate+carbon source
2949217306maltose+carbon source
2949237684mannose+carbon source
29492506227N-acetylglucosamine+carbon source
2949226271proline+carbon source
2949217272propionate+carbon source
2949215361pyruvate+carbon source
2949226546rhamnose+carbon source
2949233942ribose+carbon source
2949217814salicin+carbon source
2949230911sorbitol+carbon source
2949217992sucrose+carbon source
2949227082trehalose+carbon source
2949218222xylose+carbon source
294924853esculin+hydrolysis

enzymes

@refvalueactivityec
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
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
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- Fucosidase
19797+++-+-+--+++++++++-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
16126wall colonized with mouldsBerlinGermanyDEUEurope
61320Indoor wall material moistureBerlin/GiessenGermanyDEUEurope
67770Wall of a house with rising damp and colonized with mouldsGermanyDEUEurope

isolation source categories

Cat1Cat2
#Engineered#Built environment
#Host#Fungi

taxonmaps

  • @ref: 69479
  • File name: preview.99_18738.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_1939;97_2331;98_2876;99_18738&stattab=map
  • Last taxonomy: Promicromonospora
  • 16S sequence: FN293378
  • Sequence Identity:
  • Total samples: 1363
  • soil counts: 806
  • aquatic counts: 37
  • animal counts: 117
  • plant counts: 403

Safety information

risk assessment

  • @ref: 16126
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 16126
  • description: Promicromonospora umidemergens partial 16S rRNA gene, type strain 09-Be-007T
  • accession: FN293378
  • length: 1327
  • database: ena
  • NCBI tax ID: 629679

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Promicromonospora umidemergens DSM 220812596583659draftimg629679
66792Promicromonospora umidemergens DSM 22081GCA_024171995scaffoldncbi629679

GC content

  • @ref: 67770
  • GC-content: 70.8
  • method: genome sequence analysis

External links

@ref: 16126

culture collection no.: DSM 22081, CCM 7634, CCUG 57424, JCM 17975

straininfo link

  • @ref: 81820
  • straininfo: 400725

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19654362Promicromonospora umidemergens sp. nov., isolated from moisture from indoor wall material.Martin K, Schafer J, Kampfer PInt J Syst Evol Microbiol10.1099/ijs.0.014142-02009Actinomycetales/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, *Household Articles, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/geneticsMetabolism
Phylogeny26746665Promicromonospora alba sp. nov., an actinomycete isolated from the cuticle of Camponotus japonicas Mayr.Guo L, Liu C, Zhao J, Li C, Guo S, Fan J, Li J, Wang X, Xiang WInt J Syst Evol Microbiol10.1099/ijsem.0.0008852016
Phylogeny28879846Promicromonospora soli sp. nov., a novel actinomycete isolated from soil.Zheng W, Li D, Zhao J, Liu C, Zhao Y, Xiang W, Wang XInt J Syst Evol Microbiol10.1099/ijsem.0.0022072017Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
16126Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22081)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22081
19797Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM22081.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
29492Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2589228776041
61320Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 57424)https://www.ccug.se/strain?id=57424
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
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
81820Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID400725.1StrainInfo: A central database for resolving microbial strain identifiers