Name: Pedococcus aerophilus 5516T-20
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 6303

Type strain:

Species: Pedococcus aerophilus

Strain Designation: 5516T-20

Culture col. no.: DSM 18548, KACC 20658, JCM 16378, NBRC 106307

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

NCBI tax ID(s): 436356 (species)

SI-ID 407070

DSM 18548

Special Collections

Section

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

Gram-positive
rod-shaped
aerobe
16S sequence
Bacteria

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Micrococcales*
	Family	*Intrasporangiaceae*
	Genus	*Pedococcus*
	Species	**Pedococcus aerophilus**
	Full Scientific Name (LPSN)	Pedococcus aerophilus (Weon et al. 2008) Nouioui et al. 2018

Synonym

Phycicoccus aerophilus

Information on morphological and physiological properties Morphology

[Ref.: #32254]	Gram stain	positive

[Ref.: #32254]	Cell length	1.1-1.5 µm

[Ref.: #32254]	Cell width	0.8-0.9 µm

[Ref.: #32254]	Cell shape	rod-shaped

[Ref.: #18320]	Colony color	Light ivory (1014)
[Ref.: #18320]	Incubation period	10-14 days
[Ref.: #18320]	Cultivation medium used	ISP 2

[Ref.: #18320]	Colony color	Light ivory (1014)
[Ref.: #18320]	Incubation period	10-14 days
[Ref.: #18320]	Cultivation medium used	ISP 3

[Ref.: #18320]	Colony color	Light ivory (1014)
[Ref.: #18320]	Incubation period	10-14 days
[Ref.: #18320]	Cultivation medium used	ISP 4

[Ref.: #18320]	Colony color	Light ivory (1014)
[Ref.: #18320]	Incubation period	10-14 days
[Ref.: #18320]	Cultivation medium used	ISP 5

[Ref.: #18320]	Colony color	Light ivory (1014)
[Ref.: #18320]	Incubation period	10-14 days
[Ref.: #18320]	Cultivation medium used	ISP 6

[Ref.: #18320]	Colony color	Light ivory (1014)
[Ref.: #18320]	Incubation period	10-14 days
[Ref.: #18320]	Cultivation medium used	ISP 7

[Ref.: #32254]

Pigment production

yes

[Ref.: #18320]	Multicellular complex forming ability	no
[Ref.: #18320]	Medium Name (multicellularity)	ISP 2

[Ref.: #18320]	Multicellular complex forming ability	no
[Ref.: #18320]	Medium Name (multicellularity)	ISP 3

[Ref.: #18320]	Multicellular complex forming ability	no
[Ref.: #18320]	Medium Name (multicellularity)	ISP 4

[Ref.: #18320]	Multicellular complex forming ability	no
[Ref.: #18320]	Medium Name (multicellularity)	ISP 5

[Ref.: #18320]	Multicellular complex forming ability	no
[Ref.: #18320]	Medium Name (multicellularity)	ISP 6

[Ref.: #18320]	Multicellular complex forming ability	no
[Ref.: #18320]	Medium Name (multicellularity)	ISP 7

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7585]

Culture medium

TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)

[Ref.: #7585]

Culture medium growth

[Ref.: #7585]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7585]

Culture medium composition

expand / minimize

[Ref.: #18320]

Culture medium

ISP 2

[Ref.: #18320]

Culture medium growth

[Ref.: #18320]

Culture medium composition

expand / minimize

[Ref.: #18320]

Culture medium

ISP 3

[Ref.: #18320]

Culture medium growth

[Ref.: #18320]

Culture medium composition

expand / minimize

[Ref.: #18320]

Culture medium

ISP 4

[Ref.: #18320]

Culture medium growth

[Ref.: #18320]

Culture medium composition

expand / minimize

[Ref.: #18320]

Culture medium

ISP 5

[Ref.: #18320]

Culture medium growth

[Ref.: #18320]

Culture medium composition

expand / minimize

[Ref.: #18320]

Culture medium

ISP 6

[Ref.: #18320]

Culture medium growth

[Ref.: #18320]

Culture medium composition

expand / minimize

[Ref.: #18320]

Culture medium

ISP 7

[Ref.: #18320]

Culture medium growth

[Ref.: #18320]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #7585]	growth	28 °C
[Ref.: #18320]	optimum	28 °C
[Ref.: #32254]	growth	05-37 °C
[Ref.: #32254]	optimum	30 °C
[Ref.: #67770]	growth	28 °C

	pH	Kind of pH		pH
[Ref.: #32254]			optimum	06-07
[Ref.: #32254]			growth	05-09

Information on physiology and metabolism Physiology and metabolism

[Ref.: #32254]

Oxygen tolerance

aerobe

[Ref.: #32254]

Ability of spore formation

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #32254]		NaCl		growth	0-7	%
[Ref.: #32254]		NaCl		optimum	0-7	%

[Ref.: #7585]	Murein short key	A31
[Ref.: #7585]	Murein types	A1gamma m-Dpm-direct

[Ref.: #32254]	Observation	aggregates in chains
[Ref.: #67770]	Observation	quinones: MK-8(H₄)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #32254]	3-hydroxybutyrate ChEBI	+	carbon source
[Ref.: #68379]	D-glucose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	D-mannitol ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	D-ribose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	D-xylose ChEBI	-	fermentation	* from API Coryne
[Ref.: #32254]	esculin ChEBI	+	hydrolysis
[Ref.: #68379]	esculin ChEBI	+	hydrolysis	* from API Coryne
[Ref.: #32254]	fucose ChEBI	+	carbon source
[Ref.: #68379]	gelatin ChEBI	+	hydrolysis	* from API Coryne
[Ref.: #32254]	glucose ChEBI	+	carbon source
[Ref.: #32254]	glycogen ChEBI	+	carbon source
[Ref.: #68379]	glycogen ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	lactose ChEBI	-	fermentation	* from API Coryne
[Ref.: #32254]	malate ChEBI	+	carbon source
[Ref.: #68379]	maltose ChEBI	-	fermentation	* from API Coryne
[Ref.: #32254]	mannitol ChEBI	+	carbon source
[Ref.: #32254]	mannose ChEBI	+	carbon source
[Ref.: #32254]	melibiose ChEBI	+	carbon source
[Ref.: #32254]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #68379]	nitrate ChEBI	-	reduction	* from API Coryne
[Ref.: #32254]	propionate ChEBI	+	carbon source
[Ref.: #32254]	salicin ChEBI	+	carbon source
[Ref.: #32254]	sucrose ChEBI	+	carbon source
[Ref.: #68379]	sucrose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	urea ChEBI	+	hydrolysis	* from API Coryne
	Only first 10 entries are displayed. Click here to see all.

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym, API Coryne
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	+	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	+	3.2.1.20	* from API zym, API Coryne
[Ref.: #68382]	alpha-mannosidase	+	3.2.1.24	* from API zym
[Ref.: #68382]	beta-galactosidase	+	3.2.1.23	* from API zym, API Coryne
[Ref.: #68382]	beta-glucosidase	+	3.2.1.21	* from API zym, API Coryne
[Ref.: #68382]	beta-glucuronidase	+	3.2.1.31	* from API zym, API Coryne
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #68379]	gelatinase	+		* from API Coryne
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym, API Coryne
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #68379]	pyrazinamidase	-	3.5.1.B15	* from API Coryne
[Ref.: #68379]	pyrrolidonyl arylamidase	+	3.4.19.3	* from API Coryne
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #68379]	urease	+	3.5.1.5	* from API Coryne
[Ref.: #68382]	valine arylamidase	+		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® Coryne:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Reduction of nitrateNIT	PyrazinamidasePYZ	Pyrrolidonyl arylamidasePYRA	Alkaline phosphatasePAL	beta-Glucuronidasebeta GUR	beta-Galactosidasebeta GAL	alpha-Glucosidasealpha GLU	N-Acetyl-beta-Glucosidasebeta NAG	Esculin hydrolysis/beta-GlucosidaseESC	Urease/urea hydrolysisURE	Gelatinase/gelatin hydrolysisGEL	Control fermentationControl	Fermentation of D-glucoseGLU	Fermentation of D-riboseRIB	Fermentation of D-xyloseXYL	Fermentation of D-mannitolMAN	Fermentation of maltoseMAL	Fermentation of lactoseLAC	Fermentation of sucroseSAC	Fermentation of glycogenGLYG	CatalaseCAT
[Ref.: #18320]	15	-	-	+	+	+	+	+	-	+	+	+	not determinedn.d.	-	-	-	-	-	-	-	-	not determinedn.d.

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #18320]	30	not determinedn.d.	+	+	+	-	+	+	-	-	-	+	+	+	+	+	+	+	-	+	-

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #7585]	Sample type/isolated from	air sample
[Ref.: #7585]	Geographic location (country and/or sea, region)	Taean
[Ref.: #7585]	Country	Republic of Korea
[Ref.: #7585]	Country ISO 3 Code	KOR
[Ref.: #7585]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Air
[Ref.: #67770]	Geographic location (country and/or sea, region)	Taean region
[Ref.: #67770]	Country	Republic of Korea
[Ref.: #67770]	Country ISO 3 Code	KOR
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental

#Air

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence EF493847 (>99% sequence identity) for Pedococcus aerophilus from Microbeatlas

Aquatic Samples	2
Soil Samples	19
Animal Samples	4
Plant Samples	2
Total Samples	27

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #18320]	Biosafety level	1	German classification
[Ref.: #7585]	Biosafety level	1	Risk group (German classification) According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #7585]	Phycicoccus aerophilum strain 5516T-20 16S ribosomal RNA gene, partial sequence	EF493847	1394	GenBank ENA	436356 tax ID

[Ref.: #7585]	GC-content	70.5 mol%	high performance liquid chromatography (HPLC)
[Ref.: #32254]	GC-content	70.5 mol%

Availability in culture collections External links

[Ref.: #7585]

Culture collection no.

DSM 18548, KACC 20658, JCM 16378, NBRC 106307

[Ref.: #75778]

SI-ID 407070

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Phycicoccus ginsengisoli sp. nov., isolated from cultivated ginseng soil.	Kang JP, Kim YJ, Nguyen NL, Hoang VA, Farh ME, Joo SC, Quan LH, Yang DC	Int J Syst Evol Microbiol	10.1099/ijsem.0.001515	2016	*
Phylogeny	Phycicoccus soli sp. nov., isolated from soil.	Singh H, Won K, Ngo HTT, Du J, Kook M, Yi TH	Int J Syst Evol Microbiol	10.1099/ijs.0.000265	2015	*
Phylogeny	Phycicoccus ginsenosidimutans sp. nov., isolated from soil of a ginseng field.	Wang L, An DS, Jin FX, Lee ST, Im WT, Bae HM	Int J Syst Evol Microbiol	10.1099/ijs.0.022137-0	2010	*
Phylogeny	Phycicoccus aerophilus sp. nov., isolated from air.	Weon HY, Yoo SH, Kim BY, Schumann P, Kroppenstedt RM, Hong SK, Kwon SW	Int J Syst Evol Microbiol	10.1099/ijs.0.65202-0	2008	*

References

#7585

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18548

#18320

Wink, J.: Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig .

#20215

Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.: List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )

#32254

Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #28495 (see below)

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#68379

Automatically annotated from API Coryne .

#68382

Automatically annotated from API zym .

#69479

João 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.: MicrobeAtlas 1.0 beta .

#75778

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID407070.1 )

#28495

IJSEM 2389 2008 ( DOI 10.1099/ijs.0.65202-0 , PubMed 18842861 )

* These data were automatically processed and therefore are not curated

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