Strain identifier

BacDive ID: 6303

Type strain: Yes

Species: Pedococcus aerophilus

Strain Designation: 5516T-20

Strain history: KACC 20658 <-- H.-Y. Weon 5516T-20.

NCBI tax ID(s): 436356 (species)

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General

@ref: 7585

BacDive-ID: 6303

DSM-Number: 18548

keywords: 16S sequence, Bacteria, aerobe, Gram-positive, rod-shaped

description: Pedococcus aerophilus 5516T-20 is an aerobe, Gram-positive, rod-shaped bacterium that was isolated from air sample.

NCBI tax id

  • NCBI tax id: 436356
  • Matching level: species

strain history

@refhistory
7585<- Soon Wo Kwon; 5516T-20
67770KACC 20658 <-- H.-Y. Weon 5516T-20.

doi: 10.13145/bacdive6303.20240510.9

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Intrasporangiaceae
  • genus: Pedococcus
  • species: Pedococcus aerophilus
  • full scientific name: Pedococcus aerophilus (Weon et al. 2008) Nouioui et al. 2018

  • synonyms

    • @ref: 20215
    • synonym: Phycicoccus aerophilus

@ref: 7585

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Intrasporangiaceae

genus: Pedococcus

species: Pedococcus aerophilus

full scientific name: Pedococcus aerophilus (Weon et al. 2008) Nouioui et al. 2018

strain designation: 5516T-20

type strain: yes

Morphology

cell morphology

  • @ref: 32254
  • gram stain: positive
  • cell length: 1.1-1.5 µm
  • cell width: 0.8-0.9 µm
  • cell shape: rod-shaped

colony morphology

@refcolony colorincubation periodmedium used
18320Light ivory (1014)10-14 daysISP 2
18320Light ivory (1014)10-14 daysISP 3
18320Light ivory (1014)10-14 daysISP 4
18320Light ivory (1014)10-14 daysISP 5
18320Light ivory (1014)10-14 daysISP 6
18320Light ivory (1014)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
18320noISP 2
18320noISP 3
18320noISP 4
18320noISP 5
18320noISP 6
18320noISP 7

pigmentation

  • @ref: 32254
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7585TRYPTICASE 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
18320ISP 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
18320ISP 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:
18320ISP 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
18320ISP 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
18320ISP 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
18320ISP 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

culture temp

@refgrowthtypetemperature
18320positiveoptimum28
7585positivegrowth28
32254positivegrowth05-37
32254positiveoptimum30
67770positivegrowth28

culture pH

@refabilitytypepHPH range
32254positivegrowth05-09alkaliphile
32254positiveoptimum06-07

Physiology and metabolism

oxygen tolerance

  • @ref: 32254
  • oxygen tolerance: aerobe

spore formation

  • @ref: 32254
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
32254NaClpositivegrowth0-7 %
32254NaClpositiveoptimum0-7 %

murein

  • @ref: 7585
  • murein short key: A31
  • type: A1gamma m-Dpm-direct

observation

@refobservation
32254aggregates in chains
67770quinones: MK-8(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
32254370543-hydroxybutyrate+carbon source
3225433984fucose+carbon source
3225417234glucose+carbon source
3225428087glycogen+carbon source
3225425115malate+carbon source
3225429864mannitol+carbon source
3225437684mannose+carbon source
3225428053melibiose+carbon source
32254506227N-acetylglucosamine+carbon source
3225417272propionate+carbon source
3225417814salicin+carbon source
3225417992sucrose+carbon source
322544853esculin+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

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase+3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase+3.2.1.31
68382beta-galactosidase+3.2.1.23
68382alpha-galactosidase+3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
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

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
18320--+++++-+++--------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
18320+++-++---+++++++-+-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7585air sampleTaeanRepublic of KoreaKORAsia
67770AirTaean regionRepublic of KoreaKORAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Air

taxonmaps

  • @ref: 69479
  • File name: preview.99_116780.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_670;97_776;98_900;99_116780&stattab=map
  • Last taxonomy: Pedococcus aerophilus
  • 16S sequence: EF493847
  • Sequence Identity:
  • Total samples: 27
  • soil counts: 19
  • aquatic counts: 2
  • animal counts: 4
  • plant counts: 2

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
183201German classification
75851Risk group (German classification)

Sequence information

16S sequences

  • @ref: 7585
  • description: Phycicoccus aerophilum strain 5516T-20 16S ribosomal RNA gene, partial sequence
  • accession: EF493847
  • length: 1394
  • database: nuccore
  • NCBI tax ID: 436356

GC content

@refGC-contentmethod
758570.5high performance liquid chromatography (HPLC)
3225470.5

External links

@ref: 7585

culture collection no.: DSM 18548, KACC 20658, JCM 16378, NBRC 106307

straininfo link

  • @ref: 75778
  • straininfo: 407070

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18842861Phycicoccus aerophilus sp. nov., isolated from air.Weon HY, Yoo SH, Kim BY, Schumann P, Kroppenstedt RM, Hong SK, Kwon SWInt J Syst Evol Microbiol10.1099/ijs.0.65202-02008Actinomycetales/chemistry/*classification/*genetics/isolation & purification, *Air Microbiology, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Genes, rRNA, Molecular Sequence Data, Phenotype, Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny20382795Phycicoccus ginsenosidimutans sp. nov., isolated from soil of a ginseng field.Wang L, An DS, Jin FX, Lee ST, Im WT, Bae HMInt J Syst Evol Microbiol10.1099/ijs.0.022137-02010Actinomycetales/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, China, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Panax, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyGenetics
Phylogeny25872959Phycicoccus soli sp. nov., isolated from soil.Singh H, Won K, Ngo HTT, Du J, Kook M, Yi THInt J Syst Evol Microbiol10.1099/ijs.0.0002652015Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny27666743Phycicoccus ginsengisoli sp. nov., isolated from cultivated ginseng soil.Kang JP, Kim YJ, Nguyen NL, Hoang VA, Farh ME, Joo SC, Quan LH, Yang DCInt J Syst Evol Microbiol10.1099/ijsem.0.0015152016Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Panax/*microbiology, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7585Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18548)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18548
18320Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM18548.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
32254Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2849528776041
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
75778Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID407070.1StrainInfo: A central database for resolving microbial strain identifiers