Name: Nocardioides humi DSM 23133
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 11146

Type strain:

Species: Nocardioides humi

Culture col. no.: DSM 23133, KCTC 19265, LMG 24128, DCY 24, JCM 14942, JCM 17026

Strain history: <- DC Yang, Kyunghee Univ.

NCBI tax ID(s): 449461 (species)

SI-ID 307678

LMG 24128, KCTC 19265, JCM 14942, JCM 17026, DSM 23133

Section

Nocardioides humi DSM 23133 is an aerobe, Gram-positive, motile bacterium that was isolated from surface soil of a ginseng field.

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

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 humi**
	Full Scientific Name (LPSN)	Nocardioides humi Kim et al. 2009

Information on morphological and physiological properties Morphology

[Ref.: #29218]	Gram stain	positive
[Ref.: #67771]	Gram stain	positive

[Ref.: #29218]	Cell length	0.9 µm

[Ref.: #29218]	Cell width	0.4 µm

[Ref.: #29218]	Cell shape	rod-shaped

[Ref.: #29218]	Motility	yes

[Ref.: #18349]	Colony color	Light grey (7035)
[Ref.: #18349]	Incubation period	10-14 days
[Ref.: #18349]	Cultivation medium used	ISP 2

[Ref.: #18349]	Colony color	Light grey (7035)
[Ref.: #18349]	Incubation period	10-14 days
[Ref.: #18349]	Cultivation medium used	ISP 3

[Ref.: #18349]	Colony color	Light grey (7035)
[Ref.: #18349]	Incubation period	10-14 days
[Ref.: #18349]	Cultivation medium used	ISP 4

[Ref.: #18349]	Colony color	Light grey (7035)
[Ref.: #18349]	Incubation period	10-14 days
[Ref.: #18349]	Cultivation medium used	ISP 5

[Ref.: #18349]	Colony color	Green beige (1000)
[Ref.: #18349]	Incubation period	10-14 days
[Ref.: #18349]	Cultivation medium used	ISP 6

[Ref.: #18349]	Colony color	Cream (9001)
[Ref.: #18349]	Incubation period	10-14 days
[Ref.: #18349]	Cultivation medium used	ISP 7

[Ref.: #29218]

Pigment production

yes

[Ref.: #18349]	Multicellular complex forming ability	no
[Ref.: #18349]	Medium Name (multicellularity)	ISP 2

[Ref.: #18349]	Multicellular complex forming ability	no
[Ref.: #18349]	Medium Name (multicellularity)	ISP 3

[Ref.: #18349]	Multicellular complex forming ability	no
[Ref.: #18349]	Medium Name (multicellularity)	ISP 4

[Ref.: #18349]	Multicellular complex forming ability	no
[Ref.: #18349]	Medium Name (multicellularity)	ISP 5

[Ref.: #18349]	Multicellular complex forming ability	no
[Ref.: #18349]	Medium Name (multicellularity)	ISP 6

[Ref.: #18349]	Multicellular complex forming ability	no
[Ref.: #18349]	Medium Name (multicellularity)	ISP 7

Information on culture and growth conditions Culture and growth conditions

[Ref.: #16723]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #16723]

Culture medium growth

[Ref.: #16723]

Culture medium link

Medium recipe at MediaDive

[Ref.: #16723]

Culture medium composition

expand / minimize

[Ref.: #18349]

Culture medium

ISP 2

[Ref.: #18349]

Culture medium growth

[Ref.: #18349]

Culture medium composition

expand / minimize

[Ref.: #18349]

Culture medium

ISP 3

[Ref.: #18349]

Culture medium growth

[Ref.: #18349]

Culture medium composition

expand / minimize

[Ref.: #18349]

Culture medium

ISP 4

[Ref.: #18349]

Culture medium growth

[Ref.: #18349]

Culture medium composition

expand / minimize

[Ref.: #18349]

Culture medium

ISP 5

[Ref.: #18349]

Culture medium growth

[Ref.: #18349]

Culture medium composition

expand / minimize

[Ref.: #18349]

Culture medium

ISP 6

[Ref.: #18349]

Culture medium growth

[Ref.: #18349]

Culture medium composition

expand / minimize

[Ref.: #18349]

Culture medium

ISP 7

[Ref.: #18349]

Culture medium growth

[Ref.: #18349]

Culture medium composition

expand / minimize

[Ref.: #16723]

Culture medium

TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)

[Ref.: #16723]

Culture medium growth

[Ref.: #16723]

Culture medium link

Medium recipe at MediaDive

[Ref.: #16723]

Culture medium composition

expand / minimize

[Ref.: #16723]

Culture medium

GPHF-MEDIUM (DSMZ Medium 553)

[Ref.: #16723]

Culture medium growth

[Ref.: #16723]

Culture medium link

Medium recipe at MediaDive

[Ref.: #16723]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #16723]	growth	28 °C
[Ref.: #18349]	optimum	28 °C
[Ref.: #29218]	growth	25-42 °C
[Ref.: #29218]	optimum	33.5 °C
[Ref.: #67770]	growth	28 °C
[Ref.: #67771]	growth	30 °C

	pH	Kind of pH		pH
[Ref.: #29218]			optimum	8
[Ref.: #29218]			growth	05-11

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29218]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #67770]	Observation	quinones: MK-8(H₄)
[Ref.: #67771]	Observation	quinones: MK-8(H4)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #29218]	2-dehydro-D-gluconate ChEBI	+	carbon source
[Ref.: #29218]	3-hydroxybutyrate ChEBI	+	carbon source
[Ref.: #29218]	acetate ChEBI	+	carbon source
[Ref.: #29218]	alanine ChEBI	+	carbon source
[Ref.: #18349]	arabinose ChEBI	-
[Ref.: #18349]	cellulose ChEBI	+
[Ref.: #29218]	esculin ChEBI	+	hydrolysis
[Ref.: #68379]	esculin ChEBI	+	hydrolysis	* from API Coryne
[Ref.: #18349]	fructose ChEBI	+
[Ref.: #68379]	gelatin ChEBI	+	hydrolysis	* from API Coryne
[Ref.: #29218]	gluconate ChEBI	+	carbon source
[Ref.: #18349]	glucose ChEBI	+
[Ref.: #29218]	glucose ChEBI	+	carbon source
[Ref.: #29218]	glycogen ChEBI	+	carbon source
[Ref.: #68379]	glycogen ChEBI	-	fermentation	* from API Coryne
[Ref.: #29218]	itaconate ChEBI	+	carbon source
[Ref.: #29218]	malate ChEBI	+	carbon source
[Ref.: #18349]	mannitol ChEBI	+
[Ref.: #29218]	mannitol ChEBI	+	carbon source
[Ref.: #29218]	melibiose ChEBI	+	carbon source
[Ref.: #18349]	myo-inositol ChEBI	+
[Ref.: #29218]	nitrate ChEBI	+	reduction
[Ref.: #29218]	proline ChEBI	+	carbon source
[Ref.: #29218]	propionate ChEBI	+	carbon source
[Ref.: #18349]	raffinose ChEBI	-
[Ref.: #18349]	rhamnose ChEBI	+
[Ref.: #29218]	rhamnose ChEBI	+	carbon source
[Ref.: #29218]	ribose ChEBI	+	carbon source
[Ref.: #29218]	serine ChEBI	+	carbon source
[Ref.: #18349]	sucrose ChEBI	+
[Ref.: #29218]	sucrose ChEBI	+	carbon source
[Ref.: #68379]	sucrose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	urea ChEBI	-	hydrolysis	* from API Coryne
[Ref.: #29218]	valerate ChEBI	+	carbon source
[Ref.: #18349]	xylose ChEBI	-
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #29218]		indole ChEBI	yes

	Physiological tests	Metabolite	Indole test
[Ref.: #29218]		indole ChEBI	+

	Enzyme	Enzyme activity	EC number
[Ref.: #29218]	acid phosphatase	+	3.1.3.2
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #29218]	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.: #29218]	alpha-galactosidase	+	3.2.1.22
[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.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #68382]	beta-galactosidase	+	3.2.1.23	* from API zym
[Ref.: #68379]	beta-galactosidase	-	3.2.1.23	* from API Coryne
[Ref.: #68379]	beta-glucosidase	+	3.2.1.21	* from API Coryne, API zym
[Ref.: #68379]	beta-glucuronidase	+	3.2.1.31	* from API Coryne
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #29218]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	+	3.4.11.3	* from API zym
[Ref.: #29218]	cytochrome oxidase	+	1.9.3.1
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #29218]	gelatinase	+
[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, API zym
[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.: #29218]	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® 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.: #18349]	38	+/-	-	+	+	+	-	+	-	+	-	+	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.: #18349]	59	not determinedn.d.	+	+	+	+	+	+	+	-	-	+	+	-	+	-	+	+	-	-	-

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

[Ref.: #16723]	Sample type/isolated from	surface soil of a ginseng field
[Ref.: #16723]	Country	Republic of Korea
[Ref.: #16723]	Country ISO 3 Code	KOR
[Ref.: #16723]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Soil of a ginseng field
[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
[Ref.: #67771]	Country	Republic of Korea
[Ref.: #67771]	Country ISO 3 Code	KOR
[Ref.: #67771]	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?

[Ref.: #69479]

Global distribution of 16S sequence EF623863 (>99% sequence identity) for Nocardioides humi subclade from Microbeatlas

Aquatic Samples	17
Soil Samples	130
Animal Samples	20
Plant Samples	36
Total Samples	203

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

[Ref.: #16723]

Biosafety level

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.: #16723]	Nocardioides humi strain DCY24 16S ribosomal RNA gene, partial sequence	EF623863	1478	GenBank ENA	449461 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Nocardioides humi DCY24	GCA_006494775	complete	GenBank ENA	449461 tax ID

[Ref.: #16723]	GC-content	71.0 mol%	high performance liquid chromatography (HPLC)
[Ref.: #29218]	GC-content	71 mol%
[Ref.: #67770]	GC-content	71 mol%	high performance liquid chromatography (HPLC)
[Ref.: #67771]	GC-content	71.0 mol%

Availability in culture collections External links

[Ref.: #16723]

Culture collection no.

DSM 23133, KCTC 19265, LMG 24128, DCY 24, JCM 14942, JCM 17026

[Ref.: #80395]

SI-ID 307678

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Nocardioides sambongensis sp. nov., isolated from Dokdo Islands soil.	Hwang YJ, Son JS, Lee SY, He Y, Jo Y, Shin JH, Ghim SY	Int J Syst Evol Microbiol	10.1099/ijsem.0.003689	2020	*
Phylogeny	Nocardioides pelophilus sp. nov., isolated from freshwater mud.	Yan ZF, Lin P, Li CT, Kook M, Yi TH	Int J Syst Evol Microbiol	10.1099/ijsem.0.002776	2018	*
Phylogeny	Nocardioides ultimimeridianus sp. nov. and Nocardioides maradonensis sp. nov., isolated from rhizosphere soil.	Lee DW, Lee SY, Yoon JH, Lee SD	Int J Syst Evol Microbiol	10.1099/ijs.0.022715-0	2010	*
Phylogeny	Nocardioides humi sp. nov., a beta-glucosidase-producing bacterium isolated from soil of a ginseng field.	Kim MK, Srinivasan S, Park MJ, Sathiyaraj G, Kim YJ, Yang DC	Int J Syst Evol Microbiol	10.1099/ijs.0.008821-0	2009	*

References

#16723

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 23133

#18349

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 )

#29218

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 #25639 (see below)

#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 .

#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 .

#80395

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-ID307678.1 )

#25639

IJSEM 2724 2009 ( DOI 10.1099/ijs.0.008821-0 , PubMed 19625430 )

* These data were automatically processed and therefore are not curated

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