Strain identifier

BacDive ID: 11064

Type strain: Yes

Species: Aeromicrobium flavum

Strain Designation: TYLN1, TYLNI

Strain history: CIP <- 2012, CCTCC <- Wuhan Univ., Wuhan, China: strain TYLNI

NCBI tax ID(s): 416568 (species)

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General

@ref: 8069

BacDive-ID: 11064

DSM-Number: 19355

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, spore-forming, mesophilic, Gram-positive, rod-shaped

description: Aeromicrobium flavum TYLN1 is a facultative anaerobe, spore-forming, mesophilic bacterium that was isolated from air.

NCBI tax id

  • NCBI tax id: 416568
  • Matching level: species

strain history

@refhistory
8069<- C. Fang, Wuhan Univ., China; TYLN1
67770DSM 19355 <-- C. Fang TYLN1.
119382CIP <- 2012, CCTCC <- Wuhan Univ., Wuhan, China: strain TYLNI

doi: 10.13145/bacdive11064.20230509.8.1

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 flavum
  • full scientific name: Aeromicrobium flavum Tang et al. 2008

@ref: 8069

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardioidaceae

genus: Aeromicrobium

species: Aeromicrobium flavum

full scientific name: Aeromicrobium flavum Tang et al. 2008

strain designation: TYLN1, TYLNI

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32405positive0.3-1.2 µm0.2-0.4 µmrod-shapedno
69480no97.391
69480positive100
119382positiverod-shapedno

colony morphology

@refcolony colorincubation periodmedium used
18335Traffic yellow (1023)10-14 daysISP 2
18335Traffic yellow (1023)10-14 daysISP 3
18335Traffic yellow (1023)10-14 daysISP 4
18335Traffic yellow (1023)10-14 daysISP 5
18335Traffic yellow (1023)10-14 daysISP 6
18335Traffic yellow (1023)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
18335noISP 2
18335noISP 3
18335noISP 4
18335noISP 5
18335noISP 6
18335noISP 7

pigmentation

  • @ref: 32405
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8069TRYPTICASE 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
18335ISP 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
18335ISP 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:
18335ISP 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
18335ISP 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
18335ISP 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
18335ISP 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
40084MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromatiyesDistilled water make up to (1000.000 ml);R2A agar (18.200 g)
119382CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566

culture temp

@refgrowthtypetemperaturerange
8069positivegrowth28mesophilic
18335positiveoptimum28mesophilic
32405positivegrowth25-37mesophilic
32405positiveoptimum30mesophilic
40084positivegrowth25mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
32405positivegrowth05-10alkaliphile
32405positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 32405
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
32405yes
69481yes100
69480no99.998

halophily

@refsaltgrowthtested relationconcentration
32405NaClpositivegrowth01-04 %
32405NaClpositiveoptimum01-02 %

observation

@refobservation
32405aggregates in chains
67770quinones: MK-9(H4), MK-8(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3240530089acetate+carbon source
3240528757fructose+carbon source
3240517234glucose+carbon source
3240517754glycerol+carbon source
3240517306maltose+carbon source
3240515361pyruvate+carbon source
3240533942ribose+carbon source
3240517992sucrose+carbon source
3240527082trehalose+carbon source
324054853esculin+hydrolysis
3240517632nitrate+reduction
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

enzymes

@refvalueactivityec
32405catalase+1.11.1.6
32405cytochrome oxidase+1.9.3.1
32405urease+3.5.1.5
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
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
18335--+---+--+-------+-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
18335-++-+----++---++---

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
8069airWuhan University campus, ChinaChinaCHNAsia
67770Air at the campus of Wuhan Univ.WuhanChinaCHNAsia
119382Environment, Air sampleWuhanChinaCHNAsia2007

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Air

taxonmaps

  • @ref: 69479
  • File name: preview.99_106185.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_142;96_1793;97_2595;98_3218;99_106185&stattab=map
  • Last taxonomy: Aeromicrobium
  • 16S sequence: EF133690
  • Sequence Identity:
  • Total samples: 147
  • soil counts: 35
  • aquatic counts: 23
  • animal counts: 56
  • plant counts: 33

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
80691Risk group (German classification)
183351German classification
1193821Risk group (French classification)

Sequence information

16S sequences

  • @ref: 8069
  • description: Aeromicrobium flavum strain TYLN1 16S ribosomal RNA gene, partial sequence
  • accession: EF133690
  • length: 1427
  • database: ena
  • NCBI tax ID: 416568

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Aeromicrobium flavum NBRC 107625GCA_007992115contigncbi416568
66792Aeromicrobium flavum strain NBRC 107625416568.3wgspatric416568

GC content

@refGC-contentmethod
806973.3
6777073.3thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
gram-positiveyes90.499yes
anaerobicno98.945yes
halophileno90.643no
spore-formingno89.855yes
glucose-utilyes89.088no
aerobicyes89.604yes
flagellatedno98.827yes
thermophileno98.455yes
motileno96.527yes
glucose-fermentno87.847no

External links

@ref: 8069

culture collection no.: DSM 19355, CCTCC AB 206046, JCM 16538, NBRC 107625, CIP 110459

straininfo link

  • @ref: 80313
  • straininfo: 396815

literature

  • topic: Phylogeny
  • Pubmed-ID: 18676469
  • title: Aeromicrobium flavum sp. nov., isolated from air.
  • authors: Tang Y, Zhou G, Zhang L, Mao J, Luo X, Wang M, Fang C
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.65443-0
  • year: 2008
  • mesh: Actinomycetales/*classification/genetics/isolation & purification/physiology, *Air Microbiology, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
8069Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19355)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19355
18335Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM19355.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
32405Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2862928776041
40084Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/8320
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/
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
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
80313Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID396815.1StrainInfo: A central database for resolving microbial strain identifiers
119382Curators of the CIPCollection of Institut Pasteur (CIP 110459)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110459