Name: Nocardioides panacihumi DSM 18660
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 11122

Type strain:

Species: Nocardioides panacihumi

Culture col. no.: DSM 18660, KCTC 19187, Gsoil 616, JCM 15309, CIP 109747

Strain history: CIP <- 2007, KCTC <- S.T. Lee, KAIST, Daejon, Korea: strain Gsoil 616

NCBI tax ID(s): 400774 (species)

SI-ID 292499

LMG 23811, DSM 18660, KCTC 19187, CIP 109747, JCM 15309

Section

Nocardioides panacihumi DSM 18660 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from soil, ginseng field.

Gram-positive
rod-shaped
aerobe
mesophilic
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	*Propionibacteriales*
	Family	*Nocardioidaceae*
	Genus	*Nocardioides*
	Species	**Nocardioides panacihumi**
	Full Scientific Name (LPSN)	Nocardioides panacihumi An et al. 2007

Information on morphological and physiological properties Morphology

[Ref.: #32010]	Gram stain	positive
[Ref.: #67771]	Gram stain	positive
[Ref.: #121524]	Gram stain	positive

[Ref.: #32010]	Cell length	0.7-1.2 µm

[Ref.: #32010]	Cell width	0.3-0.5 µm

[Ref.: #32010]	Cell shape	rod-shaped
[Ref.: #121524]	Cell shape	oval-shaped

[Ref.: #32010]	Motility	no
[Ref.: #121524]	Motility	no

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7643]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #7643]

Culture medium growth

[Ref.: #7643]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7643]

Culture medium composition

expand / minimize

[Ref.: #37831]

Culture medium

MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromati

[Ref.: #37831]

Culture medium growth

[Ref.: #37831]

Culture medium composition

expand / minimize

[Ref.: #7643]

Culture medium

TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)

[Ref.: #7643]

Culture medium growth

[Ref.: #7643]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7643]

Culture medium composition

expand / minimize

[Ref.: #121524]

Culture medium

CIP Medium 566

[Ref.: #121524]

Culture medium growth

[Ref.: #121524]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #7643]	growth	28 °C
[Ref.: #19769]	optimum	28 °C
[Ref.: #32010]	growth	15-30 °C
[Ref.: #32010]	optimum	30 °C
[Ref.: #37831]	growth	30 °C
[Ref.: #67770]	growth	28 °C
[Ref.: #67771]	growth	30 °C

[Ref.: #7643]	Temperature range	mesophilic
[Ref.: #19769]	Temperature range	mesophilic
[Ref.: #32010]	Temperature range	mesophilic
[Ref.: #37831]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #32010]			optimum	7
[Ref.: #32010]			growth	5.0-8.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #32010]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #32010]

Ability of spore formation

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #32010]		NaCl		growth	0-1	%
[Ref.: #32010]		NaCl		optimum	0.5	%

[Ref.: #7643]	Murein short key	A41.01
[Ref.: #7643]	Murein types	A3gamma LL-Dpm-Gly

[Ref.: #67770]

Observation

quinones: MK-8(H₄)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #32010]	3-hydroxybenzoate ChEBI	+	carbon source
[Ref.: #32010]	3-hydroxybutyrate ChEBI	+	carbon source
[Ref.: #32010]	4-hydroxybenzoate ChEBI	+	carbon source
[Ref.: #32010]	acetate ChEBI	+	carbon source
[Ref.: #32010]	alanine ChEBI	+	carbon source
[Ref.: #68371]	arbutin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-arabinose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-arabitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-fucose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-galactose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68379]	D-glucose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68371]	D-lyxose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-mannitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68379]	D-mannitol ChEBI	-	fermentation	* from API Coryne
[Ref.: #68371]	D-mannose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-ribose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68379]	D-ribose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68371]	D-sorbitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-tagatose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-xylose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68379]	D-xylose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68371]	erythritol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #32010]	esculin ChEBI	+	hydrolysis
[Ref.: #68379]	esculin ChEBI	+	hydrolysis	* from API Coryne
[Ref.: #68371]	galactitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68379]	gelatin ChEBI	-	hydrolysis	* from API Coryne
[Ref.: #68371]	gentiobiose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #32010]	gluconate ChEBI	+	carbon source
[Ref.: #68371]	gluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	glycerol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #32010]	glycogen ChEBI	+	carbon source
[Ref.: #68371]	glycogen ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68379]	glycogen ChEBI	-	fermentation	* from API Coryne
[Ref.: #68371]	inulin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-arabinose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-arabitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-fucose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-sorbose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-xylose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	lactose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68379]	lactose ChEBI	-	fermentation	* from API Coryne
[Ref.: #32010]	maltose ChEBI	+	carbon source
[Ref.: #68379]	maltose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68371]	melezitose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	melibiose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl alpha-D-glucopyranoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl alpha-D-mannoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl beta-D-xylopyranoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	myo-inositol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	N-acetylglucosamine ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #32010]	nitrate ChEBI	+	reduction
[Ref.: #121524]	nitrate ChEBI	+	reduction
[Ref.: #68379]	nitrate ChEBI	-	reduction	* from API Coryne
[Ref.: #121524]	nitrite ChEBI	-	reduction
[Ref.: #32010]	phenylacetate ChEBI	+	carbon source
[Ref.: #68371]	Potassium 2-ketogluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	Potassium 5-ketogluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #32010]	proline ChEBI	+	carbon source
[Ref.: #32010]	propionate ChEBI	+	carbon source
[Ref.: #32010]	rhamnose ChEBI	+	carbon source
[Ref.: #68371]	ribitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #32010]	salicin ChEBI	+	carbon source
[Ref.: #68371]	starch ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68379]	sucrose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68371]	trehalose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68379]	urea ChEBI	-	hydrolysis	* from API Coryne
[Ref.: #32010]	valerate ChEBI	+	carbon source
[Ref.: #68371]	xylitol ChEBI	-	builds acid from	* from API 50CH acid
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #121524]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #32010]	acid phosphatase	+	3.1.3.2
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #32010]	alkaline phosphatase	+	3.1.3.1
[Ref.: #68379]	alkaline phosphatase	-	3.1.3.1	* from API Coryne, API zym
[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.: #68379]	alpha-glucosidase	+	3.2.1.20	* from API Coryne, API zym
[Ref.: #68379]	beta-galactosidase	-	3.2.1.23	* from API Coryne, API zym
[Ref.: #68379]	beta-glucosidase	+	3.2.1.21	* from API Coryne, API zym
[Ref.: #68379]	beta-glucuronidase	-	3.2.1.31	* from API Coryne, API zym
[Ref.: #121524]	catalase	+	1.11.1.6
[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.: #68379]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API Coryne
[Ref.: #121524]	oxidase	-
[Ref.: #68379]	pyrazinamidase	-	3.5.1.B15	* from API Coryne
[Ref.: #68379]	pyrrolidonyl arylamidase	-	3.4.19.3	* from API Coryne
[Ref.: #121524]	urease	-	3.5.1.5
[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® 50CH acid:

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

	API ID	ControlQ	Acid from glycerolGLY	Acid from erythritolERY	Acid from D-arabinoseDARA	Acid from L-arabinoseLARA	Acid from D-riboseRIB	Acid from D-xyloseDXYL	Acid from L-xyloseLXYL	Acid from D-adonitolADO	Acid from methyl beta-D-xylopyranosideMDX	Acid from D-galactoseGAL	Acid from D-glucoseGLU	Acid from D-fructoseFRU	Acid from D-mannoseMNE	Acid from L-sorboseSBE	Acid from L-rhamnoseRHA	Acid from dulcitolDUL	Acid from inositolINO	Acid from D-mannitolMAN	Acid from D-sorbitolSOR	Acid from methyl alpha-D-mannopyranosideMDM	Acid from methyl alpha-D-glucopyranosideMDG	Acid from N-acetyl-glucosamineNAG	Acid from amygdalinAMY	Acid from arbutinARB	Acid from esculinESC	Acid from salicinSAL	Acid from cellobioseCEL	Acid from maltoseMAL	Acid from lactoseLAC	Acid from melibioseMEL	Acid from sucroseSAC	Acid from trehaloseTRE	Acid from inulinINU	Acid from melezitoseMLZ	Acid from raffinoseRAF	Acid from starchAMD	Acid from glycogenGLYG	Acid from xylitolXLT	Acid from gentiobioseGEN	Acid from turanoseTUR	Acid from D-lyxoseLYX	Acid from D-tagatoseTAG	Acid from D-fucoseDFUC	Acid from L-fucoseLFUC	Acid from D-arabitolDARL	Acid from L-arabitolLARL	Acid from gluconateGNT	Acid from 2-Ketogluconate2KG	Acid from 5-Ketogluconate5KG
[Ref.: #121524]	11647	not determinedn.d.	-	-	-	-	-	-	-	-	-	-	+/-	+/-	-	-	+/-	-	-	-	-	-	-	-	+/-	-	+/-	+/-	+/-	+/-	-	-	+/-	-	-	-	+/-	-	-	-	-	+/-	-	-	-	-	-	-	-	-	-

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.: #19769]	309	-	-	-	-	-	-	+	-	+	-	-	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.: #19769]	593	not determinedn.d.	-	+	+	-	+	+	-	-	-	+	+	-	-	-	+	+	-	-	-
[Ref.: #121524]	12083	-	-	+	+	-	+	+	-	+	-	+	-	-	-	-	+	+	+	+	-

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

[Ref.: #7643]	Sample type/isolated from	soil, ginseng field
[Ref.: #7643]	Geographic location (country and/or sea, region)	Pocheon province
[Ref.: #7643]	Country	Republic of Korea
[Ref.: #7643]	Country ISO 3 Code	KOR
[Ref.: #7643]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Soil of a ginseng field
[Ref.: #67770]	Geographic location (country and/or sea, region)	Pocheon Province
[Ref.: #67770]	Country	Republic of Korea
[Ref.: #67770]	Country ISO 3 Code	KOR
[Ref.: #67770]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From soil, ginseng field
[Ref.: #67771]	Country	Republic of Korea
[Ref.: #67771]	Country ISO 3 Code	KOR
[Ref.: #67771]	Continent	Asia

[Ref.: #121524]	Sample type/isolated from	Environment, Soil, ginseng field
[Ref.: #121524]	Geographic location (country and/or sea, region)	Pocheon
[Ref.: #121524]	Country	Republic of Korea
[Ref.: #121524]	Country ISO 3 Code	KOR
[Ref.: #121524]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered	#Agriculture	#Field
#Environmental	#Terrestrial	#Soil
#Host	#Plants	#Herbaceous plants (Grass,Crops)

What are isolation sources categories?

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

[Ref.: #7643]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #19769]	Biosafety level	1	Risk group (German classification)
[Ref.: #121524]	Biosafety level	1	Risk group (French classification)

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.: #7643]	Nocardioides panacihumi gene for 16S rRNA, partial sequence	AB271053	1457	ENA	400774 tax ID

[Ref.: #7643]	GC-content	73 mol%
[Ref.: #67770]	GC-content	73 mol%	high performance liquid chromatography (HPLC)

Availability in culture collections External links

[Ref.: #7643]

Culture collection no.

DSM 18660, KCTC 19187, Gsoil 616, JCM 15309, CIP 109747

[Ref.: #80371]

SI-ID 292499

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Nocardioides cynanchi sp. nov., isolated from soil of rhizosphere of Cynanchum wilfordii.	Suh MK, Lee KC, Kim JS, Han KI, Kim HS, Eom MK, Shin YK, Lee JS	Int J Syst Evol Microbiol	10.1099/ijsem.0.004640	2021	*
Phylogeny	Nocardioides opuntiae sp. nov., isolated from soil of a cactus.	Lee SD, Seong CN	Int J Syst Evol Microbiol	10.1099/ijs.0.060400-0	2014	*
Phylogeny	Nocardioides terrae sp. nov., isolated from forest soil.	Zhang JY, Liu XY, Liu SJ	Int J Syst Evol Microbiol	10.1099/ijs.0.010785-0	2009	*
Phylogeny	Nocardioides panacihumi sp. nov., isolated from soil of a ginseng field.	An DS, Im WT, Lee ST, Yoon MH	Int J Syst Evol Microbiol	10.1099/ijs.0.64806-0	2007	*

References

#7643

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18660

#19769

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 )

#32010

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 #28264 (see below)

#37831 ; Curators of the CIP;
#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#68371

Automatically annotated from API 50CH acid .

#68379

Automatically annotated from API Coryne .

#68382

Automatically annotated from API zym .

#80371

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-ID292499.1 )

#121524 Collection of Institut Pasteur ; Curators of the CIP; CIP 109747

#28264

IJSEM 2143 2007 ( DOI 10.1099/ijs.0.64806-0 , PubMed 17766888 )

* These data were automatically processed and therefore are not curated

Change proposal

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