Nocardia xishanensis (DSM 44895, CGMCC 4.1860, IFM 10549)

Name: Nocardia xishanensis (DSM 44895, CGMCC 4.1860, IFM 10549)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 10797

Type strain

Strain Designation 276

Culture col. no. DSM 44895 CGMCC 4.1860 IFM 10549 JCM 12160 276 1 more

NCBI tax ID(s) 1210101 238964

Special Collections DSMZ JCM Wink compendium Literature strains

History <- Y. Mikami, IFM, Chiba University, Japan <- Z. Liu; 276 Z. Liu 276.

Links

Nocardia xishanensis 276 is an aerobe, Gram-positive, ovoid-shaped bacterium that builds an aerial mycelium and was isolated from soil.

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

Name and taxonomic classification

SI-ID 134457

CGMCC 4.1860,JCM 12160,AS 4.1860,DSM 44895,NBRC 101358

@ref 20215

Last LPSN update 2026-02-09 11:20:21

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Mycobacteriales

Family Nocardiaceae

Genus Nocardia

Species Nocardia xishanensis

Full scientific name Nocardia xishanensis Zhang et al. 2004

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
31251	positive	ovoid-shaped
125438	positive		91.675
125439	positive		99.3

Colony morphology

@ref	Colony color	Medium used
69366	Colourless	ISP 2
69366	Colourless	ISP 3
69366	Beige (1001)	ISP 7
69366	Beige (1001)	suter with tyrosine
69366	Beige (1001)	suter without tyrosine
69366	Ivory (1014)	ISP 5
69366	Ivory (1014)	ISP 6

Multicellular morphology

@ref	Complex name	Complex color	Medium name
69366	Aerial mycelium	Cream (9001)	ISP 2
69366	Aerial mycelium	Pure white (9010)	ISP 3
69366	Aerial mycelium		ISP 5
69366	Aerial mycelium	Cream (9001)	ISP 6
69366	Aerial mycelium		ISP 7
69366	Aerial mycelium	Light ivory (1015)	suter with tyrosine
69366	Aerial mycelium		suter without tyrosine

Pigmentation

@ref	Color	Name
31251
69366		melanin pigment
69366	Brown beige (1011), ochre brown (8001)	soluble pigment

Multimedia

@ref:	69366
multimedia content:	DSM_44895_image3.jpeg
multimedia.multimedia content:	DSM_44895_image3.jpeg
caption:	Plates (65, ISP2, ISP3, ISP4, ISP5, ISP7)
intellectual property rights:	Helmholtz-Zentrum für Infektionsforschung GmbH
manual_annotation:	1

@ref:	69366
multimedia content:	DSM_44895_image4.jpeg
multimedia.multimedia content:	DSM_44895_image4.jpeg
caption:	Plates (65, ISP2, ISP3, ISP4, ISP5, ISP7)
intellectual property rights:	Helmholtz-Zentrum für Infektionsforschung GmbH
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
12180	GPHF-MEDIUM (DSMZ Medium 553)		Medium recipe at MediaDive	Name: GPHF-MEDIUM (DSMZ Medium 553) Composition: Agar 20.0 g/l Glucose 10.0 g/l Beef extract 5.0 g/l Yeast extract 5.0 g/l Casein peptone 5.0 g/l CaCl2 x 2 H2O 0.74 g/l Distilled water
12180	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)
12180	positive	growth	28
31251	positive	growth	22-38
31251	positive	optimum	30
67770	positive	growth	28

Culture pH

@ref	Ability	Type	PH	PH range
31251	positive	optimum	7.75
31251	positive	growth	5.5-10	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
31251	aerobe
125438	aerobe	90.71
125439	obligate aerobe	99.3

Spore formation

31251

Spore formationno

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31251	NaCl	positive	growth	0-3 %
31251	NaCl	positive	optimum	1.5 %
69366	NaCl	positive	growth	0-2.5 %

Observation

67770

Observationquinones: MK-8(H₆, ω-cycl)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31251	30089 ChEBI	acetate	+	carbon source
31251	17128 ChEBI	adipate	+	carbon source
69366	22599 ChEBI	arabinose	-	growth
31251	17057 ChEBI	cellobiose	+	carbon source
69366	62968 ChEBI	cellulose	-	growth
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
31251	4853 ChEBI	esculin	+	hydrolysis
68379	4853 ChEBI	esculin	-	hydrolysis	from API Coryne
31251	28757 ChEBI	fructose	+	carbon source
69366	28757 ChEBI	fructose	-	growth
31251	33984 ChEBI	fucose	+	carbon source
31251	28260 ChEBI	galactose	+	carbon source
68379	5291 ChEBI	gelatin	-	hydrolysis	from API Coryne
31251	17234 ChEBI	glucose	+	carbon source
69366	17234 ChEBI	glucose	+	growth
31251	17754 ChEBI	glycerol	+	carbon source
68379	28087 ChEBI	glycogen	-	fermentation	from API Coryne
69366	17268 ChEBI	inositol	-	growth
31251	24996 ChEBI	lactate	+	carbon source
68379	17716 ChEBI	lactose	-	fermentation	from API Coryne
31251	25115 ChEBI	malate	+	carbon source
31251	17306 ChEBI	maltose	+	carbon source
68379	17306 ChEBI	maltose	-	fermentation	from API Coryne
31251	37684 ChEBI	mannose	+	carbon source
69366	37684 ChEBI	mannose	-	growth
31251	28053 ChEBI	melibiose	+	carbon source
31251	17632 ChEBI	nitrate	+	reduction
31251	15361 ChEBI	pyruvate	+	carbon source
69366	16634 ChEBI	raffinose	-	growth
31251	26546 ChEBI	rhamnose	+	carbon source
69366	26546 ChEBI	rhamnose	-	growth
31251	33942 ChEBI	ribose	+	carbon source
31251	17814 ChEBI	salicin	+	carbon source
31251	30911 ChEBI	sorbitol	+	carbon source
31251	30031 ChEBI	succinate	+	carbon source
31251	17992 ChEBI	sucrose	+	carbon source
68379	17992 ChEBI	sucrose	-	fermentation	from API Coryne
69366	17992 ChEBI	sucrose	-	growth
69366	18222 ChEBI	xylose	-	growth

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	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
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
31251	catalase	+	1.11.1.6
68382	esterase lipase (C 8)	+		from API zym
68379	gelatinase	-		from API Coryne
68382	leucine arylamidase	+	3.4.11.1	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
68379	pyrazinamidase	-	3.5.1.B15	from API Coryne
68379	pyrrolidonyl arylamidase	-	3.4.19.3	from API Coryne
31251	urease	+	3.5.1.5

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
69366	+/-	-	-	+	-	-	+	-	-	+/-	-	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
69366	not determinedn.d.	+/-	+/-	+	+/-	+	+/-	+/-	+/-	-	+	+/-	-	-	-	+	+/-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
12180	soil	Beijing, Xishan Mountain	China	CHN	Asia
67770	Soil	Xishan Mountain, Beijing	China	CHN	Asia

Taxonmaps

69479

Global distribution of 16S sequence GQ853067 (>99% sequence identity) for Nocardia from Microbeatlas

Aquatic Samples	3
Soil Samples	20
Animal Samples	5
Plant Samples	2
Total Samples	30

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
12180	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	ASM161336v1 assembly for Nocardia xishanensis NBRC 101358	contig	GCA_001613365	1210101.4	2731957752	1210101	52.38

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Nocardia xishanensis strain W9867 16S ribosomal RNA gene, partial sequence	GQ853067	1441		238964
12180	Nocardia xishanensis 16S ribosomal RNA gene, partial sequence	AY333115	1411		238964

GC content

@ref	GC-content (mol%)	Method
12180	68.8
67770	68.8	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Nocardia xishanensis NBRC 101358
NCBI: GCA_001613365

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	73.30	no
125439	motility	BacteriaNetⓘ	no	85.10	no
125439	gram_stain	BacteriaNetⓘ	positive	99.30	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.30	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Nocardia xishanensis NBRC 101358
PATRIC: 1210101.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	91.68	yes
125438	anaerobic	anaerobicⓘ	no	97.24	no
125438	spore-forming	spore-formingⓘ	no	50.54	yes
125438	aerobic	aerobicⓘ	yes	90.71	no
125438	thermophilic	thermophileⓘ	no	96.90	yes
125438	flagellated	motile2+ⓘ	no	89.00	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pseudonocardia mongoliensis sp. nov. and Pseudonocardia khuvsgulensis sp. nov., isolated from soil.	Ara I, Tsetseg B, Daram D, Suto M, Ando K.	Int J Syst Evol Microbiol	10.1099/ijs.0.019562-0	2011
Phylogeny	Nocardia xishanensis sp. nov., a novel actinomycete isolated from soil.	Zhang J, Liu Z, Goodfellow M	Int J Syst Evol Microbiol	10.1099/ijs.0.63133-0	2004

References

#12180	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 44895
#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 )
#20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )
#27574	IJSEM 2301 2004 ( DOI 10.1099/ijs.0.63133-0 , PubMed 15545475 )
#31251	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 #27574
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68379	Automatically annotated from API Coryne .
#68382	Automatically annotated from API zym .
#69366	Wink, J.: Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig .
#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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Nocardia xishanensis (DSM 44895, CGMCC 4.1860, IFM 10549)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Multicellular morphology

Pigmentation

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Enzymes

API coryne

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_001613365

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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