Strain identifier

BacDive ID: 11055

Type strain: Yes

Species: Aeromicrobium erythreum

Strain history: NRRL B-3381 <-- J. C. French.

NCBI tax ID(s): 2041 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 3325

BacDive-ID: 11055

DSM-Number: 8599

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, antibiotic compound production

description: Aeromicrobium erythreum DSM 8599 is a mesophilic bacterium that produces antibiotic compounds and was isolated from soil.

NCBI tax id

  • NCBI tax id: 2041
  • Matching level: species

strain history

@refhistory
3325<- H. Prauser <- NRRL <- J.C. French (Arthrobacter sp.)
67770NRRL B-3381 <-- J. C. French.

doi: 10.13145/bacdive11055.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Propionibacteriales
  • family: Nocardioidaceae
  • genus: Aeromicrobium
  • species: Aeromicrobium erythreum
  • full scientific name: Aeromicrobium erythreum Miller et al. 1991

@ref: 3325

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardioidaceae

genus: Aeromicrobium

species: Aeromicrobium erythreum

full scientific name: Aeromicrobium erythreum Miller et al. 1991 emend. Nouioui et al. 2018

type strain: yes

Morphology

colony morphology

@refcolony colorincubation periodmedium used
19730Saffron yellow10-14 days5006
19730Saffron yellow10-14 days5425
19730Saffron yellow10-14 days5428
19730Saffron yellow10-14 days5530
19730Saffron yellow10-14 daysISP 2

multicellular morphology

@refforms multicellular complexmedium name
19730noISP 2
19730no5006
19730no5425
19730no5428
19730no5530

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3325TRYPTICASE 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
19730ISP 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
197305006yesMedium: 5006 Name: Composition (g/l) Sucrose 3,0 Dextrin 15,0 Meat extract 1,0 Yeast extract 2,0 Tryptone soy broth (Oxoid) 5,0 NaCl 0,5 K2HPO4 0,5 MgSO4 x 7 H2O 0,5 FeSO4 x 7 H2O 0,01 Agar 20,0 Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7,3 Usage: Maintenance Organisms: All Actinomycetes
197305425yesName: Brain Heart Infusion (BHI) Agar; 5425 Composition: Calf brain infusion 200.0 g/l Beef heart infusion 250.0 g/l Casein (meat) peptone 10.0 g/l Glucose 2.0 g/l NaCl 5.0 g/l Na2HPO4 2.5 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.4 Usage: Maintenance and revitalization Organisms: Dermatophilus congolensis, Nocardia brasieliensis, N. asteroides, Rhodococcus equi, R. fascians, R. rhodochrous, Streptomyces thermoviol aceus subsp. apingens, Coryneform species
197305428yes
197305530yes

culture temp

@refgrowthtypetemperaturerange
19730positiveoptimum37mesophilic
3325positivegrowth28mesophilic
67770positivegrowth30mesophilic

Physiology and metabolism

compound production

  • @ref: 3325
  • compound: erythromycin A

murein

  • @ref: 3325
  • murein short key: A41.01
  • type: A3gamma LL-Dpm-Gly

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate+assimilation
6836818257ornithine+degradation
6836825094lysine+degradation
6836829016arginine+hydrolysis
6837917632nitrate-reduction
683794853esculin+hydrolysis
6837916199urea+hydrolysis
683795291gelatin+hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837928087glycogen-fermentation

metabolite production

@refChebi-IDmetaboliteproduction
6777048923erythromycinyes
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

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

enzymes

@refvalueactivityec
68379gelatinase+
68379urease+3.5.1.5
68379beta-glucosidase+3.2.1.21
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alpha-glucosidase+3.2.1.20
68379beta-galactosidase-3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase+3.1.3.1
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase-3.5.1.B15
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
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 coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
19730---+--+-+++--------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
19730++++++++++----++---

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19730-++++-+---+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
3325soilPuerto RicoPuerto RicoPRIMiddle and South America
67770SoilPuerto RicoUSAUSANorth America

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_4049.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_142;96_1793;97_2145;98_3066;99_4049&stattab=map
  • Last taxonomy: Aeromicrobium erythreum subclade
  • 16S sequence: AF005021
  • Sequence Identity:
  • Total samples: 200
  • soil counts: 85
  • aquatic counts: 61
  • animal counts: 27
  • plant counts: 27

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
33251Risk group (German classification)
197301Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Aeromicrobium erythreum strain NRRL B-3381 16S ribosomal RNA gene, partial sequenceAF0050211474ena2041
20218Aeromicrobium erythreum strain NRRL B-3381 16S-23S internal transcribed spacer, complete sequenceAF017508349ena2041
67770A.erythreus small subunit ribosomal RNAM372001463ena2041

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Aeromicrobium erythreum strain AR182041.4completepatric2041
67770Aeromicrobium erythreum AR18GCA_001509405completencbi2041

GC content

@refGC-contentmethod
332571
6777072.1genome sequence analysis
6777070thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno95.705no
gram-positiveyes94.177no
anaerobicno99.055no
halophileno91.083no
spore-formingno84.506no
glucose-utilyes88.106no
flagellatedno98.543no
aerobicyes95.43no
thermophileno98.513yes
glucose-fermentno91.102no

External links

@ref: 3325

culture collection no.: DSM 8599, ATCC 51598, NRRL B-3381, JCM 8359, GTC 01565, IFO 15406, KCCM 41104, KCTC 9586, LMG 16472, NBRC 15406, NCIMB 13258

straininfo link

  • @ref: 80304
  • straininfo: 8163

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny1883712Description of the erythromycin-producing bacterium Arthrobacter sp. strain NRRL B-3381 as Aeromicrobium erythreum gen. nov., sp. nov.Miller ES, Woese CR, Brenner SInt J Syst Bacteriol10.1099/00207713-41-3-3631991Amino Acids/analysis, Arthrobacter/*classification/metabolism, Bacteria, Aerobic/*classification/metabolism, Base Composition, Base Sequence, Erythromycin/*metabolism, Fatty Acids/analysis, Gram-Positive Bacteria/*classification/metabolism, Microscopy, Electron, Molecular Sequence Data, Peptidoglycan/chemistry, Phenotype, RNA, Ribosomal, 16S/genetics, Sequence Homology, Nucleic Acid, Soil Microbiology, Vitamin K/analysisMetabolism
Phylogeny14657123Aeromicrobium marinum sp. nov., an abundant pelagic bacterium isolated from the German Wadden Sea.Bruns A, Philipp H, Cypionka H, Brinkhoff TInt J Syst Evol Microbiol10.1099/ijs.0.02735-02003DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Germany, Microscopy, Electron, Molecular Sequence Data, Nocardiaceae/*classification/*genetics/growth & development/isolation & purification, Nucleic Acid Hybridization, *Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Seawater/*microbiologyGenetics
Phylogeny18398207Aeromicrobium ponti sp. nov., isolated from seawater.Lee DW, Lee SDInt J Syst Evol Microbiol10.1099/ijs.0.65575-02008Actinomycetales/*classification/genetics/*isolation & purification/metabolism, Base Composition, DNA, Bacterial/chemistry/genetics, Fatty Acids/metabolism, Genes, Bacterial, Korea, Molecular Sequence Data, Phenotype, Phospholipids/metabolism, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Species Specificity, Terminology as Topic, Vitamin K 2/metabolismMetabolism
Phylogeny20081024Aeromicrobium halocynthiae sp. nov., a taurocholic acid-producing bacterium isolated from the marine ascidian Halocynthia roretzi.Kim SH, Yang HO, Sohn YC, Kwon HCInt J Syst Evol Microbiol10.1099/ijs.0.016618-02010Actinomycetales/*classification/genetics/isolation & purification, Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Taurocholic Acid/*biosynthesis, Urochordata/*microbiology, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny26354190Aeromicrobium camelliae sp. nov., isolated from Pu'er tea.Niu L, Xiong M, Tang T, Song L, Hu X, Zhao M, Zhang KInt J Syst Evol Microbiol10.1099/ijsem.0.0005832015Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Tea/*microbiology, Vitamin K 2/analogs & derivatives/chemistryGenetics
Genetics27103725Genome Sequence of Aeromicrobium erythreum NRRL B-3381, an Erythromycin-Producing Bacterium of the Nocardioidaceae.Harrell EA, Miller ESGenome Announc10.1128/genomeA.00300-162016
Phylogeny31124044Aeromicrobium endophyticum sp. nov., an endophytic actinobacterium isolated from reed (Phragmites australis).Li FN, Liao SL, Liu SW, Jin T, Sun CHJ Microbiol10.1007/s12275-019-8705-72019Actinobacteria/classification/genetics/*isolation & purification/metabolism, Bacterial Typing Techniques, Cell Wall/chemistry/metabolism, China, DNA, Bacterial/genetics, Endophytes/classification/genetics/*isolation & purification/metabolism, Fatty Acids/chemistry/metabolism, Peptidoglycan/chemistry/metabolism, Phylogeny, Poaceae/*microbiology, RNA, Ribosomal, 16S/geneticsMetabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3325Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 8599)https://www.dsmz.de/collection/catalogue/details/culture/DSM-8599
19730Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM8599.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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68368Automatically annotated from API 20E
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
80304Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID8163.1StrainInfo: A central database for resolving microbial strain identifiers