Nocardioides sediminis (DSM 19263, JCM 19559, KCTC 19271)

Name: Nocardioides sediminis (DSM 19263, JCM 19559, KCTC 19271)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 11144

Type strain

Culture col. no. DSM 19263 JCM 19559 KCTC 19271 MSL 01

NCBI tax ID(s) 433648

Special Collections DSMZ JCM KCTC Wink compendium Literature strains

History DSMZ <- C.-J. Kim <- S. G. Dastager <- Y. J. Ju, Korea Res. Inst. Biosci. & Biotechnol. (KRIBB), Taejon, South Korea; MSL 01 JCM <-- DSM 19263 <-- C.-J. Kim <-- S. G. Dastager <-- Y. J. Ju MSL-01. KCTC <- CJ Kim, KRIBB

Links

Nocardioides sediminis DSM 19263 is an aerobe, Gram-positive, motile bacterium that was isolated from sediment.

Gram-positive motile rod-shaped aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 407644

KCTC 19271,JCM 19559,DSM 19263

@ref 20215

Last LPSN update 2026-05-29 08:27:29

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Propionibacteriales

Family Nocardioidaceae

Genus Nocardioides

Species Nocardioides sediminis

Full scientific name Nocardioides sediminis Dastager et al. 2009

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
28939	positive	0.9-1.4 µm	0.3-0.8 µm	rod-shaped
67771	positive
125438					90.1
125438	positive				91.518
125439	positive				97.827

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
7912	R2A MEDIUM (DSMZ Medium 830)		Medium recipe at MediaDive	Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
7912	positive	growth	28
18614	positive	optimum	28
28939	positive	growth	20-37
28939	positive	optimum	28
67770	positive	growth	28
67771	positive	growth	30

Culture pH

@ref	Ability	Type	PH
28939	positive	optimum	7.25
28939	positive	growth	7.0-7.5

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
28939	aerobe
67771	aerobe
125438	aerobe	93.121
125439	obligate aerobe	98.287

Spore formation

28939

Spore formationno

Observation

@ref	Observation
28939	aggregates in clumps
67770	quinones: MK-8(H₄)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
28939	17057 ChEBI	cellobiose	+	carbon source
68379	17634 ChEBI	D-glucose	-	fermentation	from API Coryne
68379	16899 ChEBI	D-mannitol	-	fermentation	from API Coryne
68379	16988 ChEBI	D-ribose	-	fermentation	from API Coryne
68379	65327 ChEBI	D-xylose	-	fermentation	from API Coryne
68379	4853 ChEBI	esculin	-	hydrolysis	from API Coryne
28939	28757 ChEBI	fructose	+	carbon source
28939	28260 ChEBI	galactose	+	carbon source
68379	5291 ChEBI	gelatin	+	hydrolysis	from API Coryne
28939	17234 ChEBI	glucose	+	carbon source
68379	28087 ChEBI	glycogen	-	fermentation	from API Coryne
28939	17716 ChEBI	lactose	+	carbon source
68379	17716 ChEBI	lactose	-	fermentation	from API Coryne
28939	17306 ChEBI	maltose	+	carbon source
68379	17306 ChEBI	maltose	-	fermentation	from API Coryne
28939	29864 ChEBI	mannitol	+	carbon source
28939	28053 ChEBI	melibiose	+	carbon source
28939	17268 ChEBI	myo-inositol	+	carbon source
28939	17632 ChEBI	nitrate	+	reduction
68379	17632 ChEBI	nitrate	-	reduction	from API Coryne
28939	26546 ChEBI	rhamnose	+	carbon source
28939	17992 ChEBI	sucrose	+	carbon source
68379	17992 ChEBI	sucrose	+	fermentation	from API Coryne
28939	27082 ChEBI	trehalose	+	carbon source
68379	16199 ChEBI	urea	-	hydrolysis	from API Coryne
28939	18222 ChEBI	xylose	+	carbon source

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
28939	alkaline phosphatase	+	3.1.3.1
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68379	alkaline phosphatase	+	3.1.3.1	from API Coryne
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	+	3.2.1.20	from API zym
68379	alpha-glucosidase	+	3.2.1.20	from API Coryne
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68382	beta-galactosidase	+	3.2.1.23	from API zym
68379	beta-galactosidase	-	3.2.1.23	from API Coryne
68382	beta-glucosidase	+	3.2.1.21	from API zym
68379	beta-glucosidase	-	3.2.1.21	from API Coryne
68382	beta-glucuronidase	-	3.2.1.31	from API zym
68379	beta-glucuronidase	-	3.2.1.31	from API Coryne
28939	catalase	+	1.11.1.6
68382	cystine arylamidase	+	3.4.11.3	from API zym
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
28939	gelatinase	+
68379	gelatinase	+		from API Coryne
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68379	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API Coryne
68382	naphthol-AS-BI-phosphohydrolase	-		from API zym
68379	pyrazinamidase	-	3.5.1.B15	from API Coryne
68379	pyrrolidonyl arylamidase	-	3.4.19.3	from API Coryne
68382	trypsin	-	3.4.21.4	from API zym
68379	urease	-	3.5.1.5	from API Coryne
68382	valine arylamidase	+		from API zym

API coryne

@ref	Reduction of nitrateNIT	PYZ	PYRA	PAL	beta GUR	beta GAL	alpha GLU	beta NAG	ESC	URE	GEL	Control fermentationControl	GLU	RIB	XYL	MAN	MAL	LAC	SAC	GLYG	CAT
18614	-	-	-	+	-	-	+	-	-	-	+	not determinedn.d.	-	-	-	-	-	-	+	-	not determinedn.d.

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
18614	not determinedn.d.	+	+	+	-	+	+	+	-	-	+	-	-	+	-	+	+	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Sediment
#Environmental	#Terrestrial	#Sediment

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
7912	sediment	Bigeum Island	Republic of Korea	KOR	Asia
67770	Sediment from Bigeum Island		Republic of Korea	KOR	Asia
67771	From farming field	Bikeum island	Republic of Korea	KOR	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7912	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
67770	ASM304729v1 assembly for Nocardioides sediminis KCTC 19271	contig	GCA_003047295	433648.4	2866221110	433648	72.62

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
7912	Nocardioides sediminis strain MSL-01 16S ribosomal RNA gene, partial sequence	EF466110	1437		433648

GC content

@ref	GC-content (mol%)	Method
7912	71.5	high performance liquid chromatography (HPLC)
28939	71.5

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM304729v1 assembly for Nocardioides sediminis KCTC 19271
NCBI: GCA_003047295

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.29	no
125439	motility	BacteriaNetⓘ	no	76.03	no
125439	gram_stain	BacteriaNetⓘ	positive	97.83	no
125439	spore_formation	BacteriaNetⓘ	no	87.73	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Nocardioides sediminis strain KCTC 19271
PATRIC: 433648.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	91.52	yes
125438	anaerobic	anaerobicⓘ	no	96.97	no
125438	spore-forming	spore-formingⓘ	no	67.18	yes
125438	aerobic	aerobicⓘ	yes	93.12	yes
125438	thermophilic	thermophileⓘ	no	95.61	yes
125438	flagellated	motile2+ⓘ	no	90.10	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Targeting antimalarial metabolites from the actinomycetes associated with the Red Sea sponge Callyspongia siphonella using a metabolomic method.	Gamaleldin NM, Bahr HS, Millan-Aguinaga N, Danesh M, Othman EM, Dandekar T, Hassan HM, Abdelmohsen UR.	BMC Microbiol	10.1186/s12866-023-03094-3	2023
Phylogeny	Nocardioides allogilvus sp. nov., a novel actinobacterium isolated from a karst cave.	Zhang LY, Ming H, Zhao ZL, Ji WL, Salam N, Jiao JY, Fang BZ, Li WJ, Nie GX.	Int J Syst Evol Microbiol	10.1099/ijsem.0.002863	2018
Metabolism	Nocardioides panaciterrulae sp. nov., isolated from soil of a ginseng field, with ginsenoside converting activity.	Kim JK, Liu QM, Park HY, Kang MS, Kim SC, Im WT, Yoon MH.	Antonie Van Leeuwenhoek	10.1007/s10482-013-9919-z	2013
Phylogeny	Nocardioides hungaricus sp. nov., isolated from a drinking water supply system.	Toth EM, Keki Z, Makk J, Homonnay ZG, Marialigeti K, Schumann P.	Int J Syst Evol Microbiol	10.1099/ijs.0.022939-0	2011
Phylogeny	Nocardioides ginsengisegetis sp. nov., isolated from soil of a ginseng field.	Im WT, Kim SY, Liu QM, Yang JE, Lee ST, Yi TH.	J Microbiol	10.1007/s12275-010-0001-5	2010
Phylogeny	Nocardioides gansuensis sp. nov., isolated from geopark soil.	Wu S, Xia X, Zhou Z, Wang D, Wang G	Int J Syst Evol Microbiol	10.1099/ijsem.0.003157	2018
Phylogeny	Nocardioides sediminis sp. nov., isolated from a sediment sample.	Dastager SG, Lee JC, Ju YJ, Park DJ, Kim CJ	Int J Syst Evol Microbiol	10.1099/ijs.0.002162-0	2009

References

#7912	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19263
#18614	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 )
#25378	IJSEM 280 2009 ( DOI 10.1099/ijs.0.002162-0 , PubMed 19196766 )
#28939	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 #25378
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#68379	Automatically annotated from API Coryne .
#68382	Automatically annotated from API zym .
#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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Nocardioides sediminis (DSM 19263, JCM 19559, KCTC 19271)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Observation

Metabolite utilization

Enzymes

API coryne

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_003047295

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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