Pedococcus badiiscoriae (DSM 23987, KACC 15111, KCTC 19807)

Name: Pedococcus badiiscoriae (DSM 23987, KACC 15111, KCTC 19807)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 23071

Type strain

Strain Designation Sco-B23

Culture col. no. DSM 23987 KACC 15111 KCTC 19807 NBRC 107918 Sco-B23

NCBI tax ID(s) 642776

Special Collections DSMZ KCTC Literature strains

History <- S. D. Lee, Jeju National Univ., Rep. of Korea; Sco-B23 <- SD Lee, Cheju Univ.

Links

Pedococcus badiiscoriae Sco-B23 is an aerobe, Gram-positive, coccus-shaped bacterium that was isolated from volcanic ash .

Gram-positive coccus-shaped aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 399376

KCTC 19807,NBRC 107918,DSM 23987

@ref 20215

Last LPSN update 2026-02-09 11:23:39

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Micrococcales

Family Intrasporangiaceae

Genus Pedococcus

Species Pedococcus badiiscoriae

Full scientific name Pedococcus badiiscoriae (Lee 2013) Nouioui et al. 2018

Synonyms (1)

Phycicoccus badiiscoriae

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
30673	positive	0.2 µm	0.2 µm	coccus-shaped
67771				coccus-shaped
67771	positive
125439	positive				93.5
125438					90
125438	positive				90.16

Pigmentation

30673

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
19266	GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)		Medium recipe at MediaDive	Name: 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

Culture temp

@ref	Growth	Type	Temperature (°C)
19266	positive	growth	28
30673	positive	growth	20-35
30673	positive	optimum	30
67771	positive	growth	30

Culture pH

@ref	Ability	Type	PH	PH range
30673	positive	optimum	8.6
30673	positive	growth	5.1-11.1	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
30673	aerobe
67771	aerobe
125438	aerobe	92.294
125439	obligate aerobe	92.5

Spore formation

30673

Spore formationno

Halophily

@ref	Salt	Growth	Tested relation	Concentration
30673	NaCl	positive	growth	0-1 %

Observation

67771

Observationquinones: MK-8(H4)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
30673	4853 ChEBI	esculin	+	hydrolysis
30673	17234 ChEBI	glucose	+	carbon source
30673	25115 ChEBI	malate	+	carbon source
30673	17306 ChEBI	maltose	+	carbon source
30673	37684 ChEBI	mannose	+	carbon source
30673	506227 ChEBI	N-acetylglucosamine	+	carbon source

Enzymes

@ref	Value	Activity	Ec
30673	acid phosphatase	+	3.1.3.2
30673	alkaline phosphatase	+	3.1.3.1
30673	catalase	+	1.11.1.6
30673	gelatinase	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Dust
#Environmental	#Terrestrial	#Volcanic

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
19266	volcanic ash (scoria)	Jeju, near the small mountain Darangshi Oreum	Republic of Korea	KOR	Asia
67771	From volcanic ash (scoria)	Jeju	Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence FN386744 (>99% sequence identity) for Pedococcus from Microbeatlas

Aquatic Samples	473
Soil Samples	3476
Animal Samples	999
Plant Samples	606
Total Samples	5554

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
19266	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM1340892v1 assembly for Pedococcus badiiscoriae DSM 23987	contig	GCA_013408925	642776.3	2844619028	642776	75.15

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
19266	Phycicoccus badiiscoriae partial 16S rRNA gene, type strain Sco-B23T	FN386744	1433		642776

GC content

@ref	GC-content (mol%)	Method
19266	69.7	high performance liquid chromatography (HPLC)
30673	69.7

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Pedococcus badiiscoriae DSM 23987
NCBI: GCA_013408925

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	89.80	no
125439	motility	BacteriaNetⓘ	no	50.30	no
125439	gram_stain	BacteriaNetⓘ	positive	93.50	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	92.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Phycicoccus badiiscoriae strain DSM 23987
PATRIC: 642776.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	90.16	no
125438	anaerobic	anaerobicⓘ	no	96.99	yes
125438	spore-forming	spore-formingⓘ	no	74.35	no
125438	aerobic	aerobicⓘ	yes	92.29	yes
125438	thermophilic	thermophileⓘ	no	96.15	yes
125438	flagellated	motile2+ⓘ	no	90.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Genome-Based Taxonomic Classification of the Phylum Actinobacteria.	Nouioui I, Carro L, Garcia-Lopez M, Meier-Kolthoff JP, Woyke T, Kyrpides NC, Pukall R, Klenk HP, Goodfellow M, Goker M.	Front Microbiol	10.3389/fmicb.2018.02007	2018
Phylogeny	Phycicoccus badiiscoriae sp. nov., a novel actinomycete isolated from scoria.	Lee SD	Int J Syst Evol Microbiol	10.1099/ijs.0.041699-0	2012

References

#19266	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 23987
#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 )
#27004	IJSEM 989 2013 ( DOI 10.1099/ijs.0.041699-0 , PubMed 22685104 )
#30673	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 #27004
#66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#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 .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Pedococcus badiiscoriae (DSM 23987, KACC 15111, KCTC 19807)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_013408925

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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