Name: Nocardioides yefusunii HY056
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 164547

Type strain:

Species: Nocardioides yefusunii

Strain Designation: HY056

Culture col. no.: JCM 33399, CGMCC 4.7563

Strain history: J. Yang; Natl. Inst. for Commun. Dis. Control & Prev., China CDC, China; HY056.

NCBI tax ID(s): 2500546 (species)

Special Collections

Section

Nocardioides yefusunii HY056 is an aerobe, Gram-positive, rod-shaped bacterium that forms circular colonies and was isolated from Faeces of Equus kiang in Qinghai-Tibetan Plateau.

colony-forming
Gram-positive
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 yefusunii**
	Full Scientific Name (LPSN)	Nocardioides yefusunii Huang et al. 2019

Information on morphological and physiological properties Morphology

[Ref.: #68229]	Gram stain	positive

[Ref.: #68229]	Cell length	1.3-2.5 µm

[Ref.: #68229]	Cell width	0.2-0.5 µm

[Ref.: #68229]	Cell shape	rod-shaped

[Ref.: #68229]	Motility	no

[Ref.: #68229]	Colony size	1-2 mm
[Ref.: #68229]	Colony color	pale-yellow
[Ref.: #68229]	Colony shape	circular
[Ref.: #68229]	Incubation period	3 days
[Ref.: #68229]	Cultivation medium used	BHI 5.0 % sheep blood agar

Information on culture and growth conditions Culture and growth conditions

		Temperature
[Ref.: #67770]	growth	28 °C
[Ref.: #68229]	growth	16-37 °C
[Ref.: #68229]	optimum	28 °C

	pH	Kind of pH		pH
[Ref.: #68229]			optimum	7
[Ref.: #68229]			growth	5-11

Information on physiology and metabolism Physiology and metabolism

[Ref.: #68229]

Oxygen tolerance

aerobe

[Ref.: #68229]

Ability of spore formation

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #68229]		NaCl		growth	0-2	%(w/v)
[Ref.: #68229]		NaCl		optimum	0-0.5	%(w/v)

[Ref.: #67770]

Observation

quinones: MK-8(H₄)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68229]	2-dehydro-D-gluconate ChEBI	-	builds acid from
[Ref.: #68229]	5-dehydro-D-gluconate ChEBI	+	builds acid from
[Ref.: #68229]	amygdalin ChEBI	-	builds acid from
[Ref.: #68229]	arbutin ChEBI	-	builds acid from
[Ref.: #68229]	arginine ChEBI	-	assimilation
[Ref.: #68229]	cellobiose ChEBI	+/-	builds acid from
[Ref.: #68229]	D-arabinose ChEBI	-	builds acid from
[Ref.: #68229]	D-arabitol ChEBI	-	builds acid from
[Ref.: #68229]	D-fructose ChEBI	+	builds acid from
[Ref.: #68229]	D-fucose ChEBI	-	builds acid from
[Ref.: #68229]	D-galactose ChEBI	-	builds acid from
[Ref.: #68229]	D-glucose ChEBI	-	builds acid from
[Ref.: #68229]	D-mannitol ChEBI	-	builds acid from
[Ref.: #68229]	D-mannose ChEBI	-	builds acid from
[Ref.: #68229]	D-ribose ChEBI	+/-	builds acid from
[Ref.: #68229]	D-sorbitol ChEBI	-	builds acid from
[Ref.: #68229]	D-tagatose ChEBI	+	builds acid from
[Ref.: #68229]	D-trehalose ChEBI	+/-	builds acid from
[Ref.: #68229]	D-xylose ChEBI	-	builds acid from
[Ref.: #68229]	erythritol ChEBI	-	builds acid from
[Ref.: #68229]	esculin ChEBI	+	hydrolysis
[Ref.: #68229]	esculin ferric citrate	+	builds acid from
[Ref.: #68229]	galactitol ChEBI	-	builds acid from
[Ref.: #68229]	gelatin ChEBI	-	hydrolysis
[Ref.: #68229]	glycerol ChEBI	-	builds acid from
[Ref.: #68229]	glycogen ChEBI	-	builds acid from
[Ref.: #68229]	inulin ChEBI	-	builds acid from
[Ref.: #68229]	L-arabinose ChEBI	-	builds acid from
[Ref.: #68229]	L-arabitol ChEBI	-	builds acid from
[Ref.: #68229]	L-fucose ChEBI	-	builds acid from
[Ref.: #68229]	L-rhamnose ChEBI	-	builds acid from
[Ref.: #68229]	L-sorbose ChEBI	-	builds acid from
[Ref.: #68229]	lactose ChEBI	-	builds acid from
[Ref.: #68229]	maltose ChEBI	-	builds acid from
[Ref.: #68229]	melezitose ChEBI	-	builds acid from
[Ref.: #68229]	melibiose ChEBI	-	builds acid from
[Ref.: #68229]	myo-inositol ChEBI	-	builds acid from
[Ref.: #68229]	N-acetylglucosamine ChEBI	-	builds acid from
[Ref.: #68229]	nitrate ChEBI	+	reduction
[Ref.: #68229]	raffinose ChEBI	-	builds acid from
[Ref.: #68229]	salicin ChEBI	-	builds acid from
[Ref.: #68229]	sucrose ChEBI	-	builds acid from
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #68229]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #68229]	acid phosphatase	-	3.1.3.2
[Ref.: #68229]	alkaline phosphatase	+/-	3.1.3.1
[Ref.: #68229]	alpha-chymotrypsin	-	3.4.21.1
[Ref.: #68229]	alpha-fucosidase	-	3.2.1.51
[Ref.: #68229]	alpha-galactosidase	-	3.2.1.22
[Ref.: #68229]	alpha-glucosidase	-	3.2.1.20
[Ref.: #68229]	alpha-mannosidase	-	3.2.1.24
[Ref.: #68229]	beta-galactosidase	-	3.2.1.23
[Ref.: #68229]	beta-glucosidase	+	3.2.1.21
[Ref.: #68229]	beta-glucuronidase	-	3.2.1.31
[Ref.: #68229]	catalase	+	1.11.1.6
[Ref.: #68229]	cytochrome oxidase	-	1.9.3.1
[Ref.: #68229]	esterase (C 4)	+
[Ref.: #68229]	esterase Lipase (C 8)	+
[Ref.: #68229]	leucine arylamidase	+	3.4.11.1
[Ref.: #68229]	lipase	+/-
[Ref.: #68229]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #68229]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #68229]	trypsin	-	3.4.21.4
[Ref.: #68229]	urease	-	3.5.1.5
[Ref.: #68229]	valine arylamidase	+/-
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #68229]

Fatty acid	Percentage
C18:1 w9c	28.7
C18:0 10-methyl	15.3
C16:0 iso	11.1
C18:0	9.7
C16:1 w7c/C16:1 w6c	5.3
C16:0 10-methyl/C17:1 iso w9c	2
C19:1 w11c / C19:1 w9c	1.3
C18:0 iso	1

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

[Ref.: #67770]	Sample type/isolated from	Faeces of Equus kiang (Tibetan wild ass) in Qinghai-Tibetan Plateau
[Ref.: #67770]	Host species	Equus kiang
[Ref.: #67770]	Country	China
[Ref.: #67770]	Country ISO 3 Code	CHN
[Ref.: #67770]	Continent	Asia

[Ref.: #68229]	Sample type/isolated from	Faecal samples of Tibetan wild ass (Equus kiang)
[Ref.: #68229]	Sampling date	2017-09-01
[Ref.: #68229]	Geographic location (country and/or sea, region)	Qinghai-Tibet Plateau
[Ref.: #68229]	Country	China
[Ref.: #68229]	Country ISO 3 Code	CHN
[Ref.: #68229]	Continent	Asia
[Ref.: #68229]	Enrichment culture	BHI
[Ref.: #68229]	Enrichment culture composition	supplemented with 5.0 % sheep blood
[Ref.: #68229]	Enrichment culture duration	7 days
[Ref.: #68229]	Enrichment culture temperature	28 ̊C
* marker position based on {}

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.: #68229]	Nocardioides yefusunii strain HY056 16S ribosomal RNA gene, partial sequence	MH607119	1481	GenBank ENA	35761 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Nocardioides yefusunii HY056	GCA_004014875	complete	GenBank ENA	2500546 tax ID

[Ref.: #67770]

GC-content

68.9 mol%

genome sequence analysis

Data predicted using genome information as a basis Genome-based predictions

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Nocardioides yefusunii HY056 NCBI: GCA_004014875.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	yes	87.922	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	95.343	yes
[Ref.: #69480]	aerobic	aerobicⓘ	yes	83.402	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	66.483	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	no	92.521	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	no	65.5	no

Availability in culture collections External links

[Ref.: #67770]

Culture collection no.

JCM 33399, CGMCC 4.7563

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Nocardioides yefusunii sp. nov., isolated from Equus kiang (Tibetan wild ass) faeces.	Huang Y, Wang X, Yang J, Lu S, Lai XH, Jin D, Pu J, Huang Y, Ren Z, Zhu W, Meng J, Dong K, Ge Y, Zhou J, Zhang G, Zhang S, Lei W, Liang H, Xu J	Int J Syst Evol Microbiol	10.1099/ijsem.0.003674	2019	*

References

#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 )

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#68229

Yuyuan Huang, Xiaoxia Wang, Jing Yang, Shan Lu, Xin-He Lai, Dong Jin, Ji Pu, Ying Huang, Zhihong Ren, Wentao Zhu, Jiajia Meng, Kui Dong, Yajun Ge, Juan Zhou, Gui Zhang, Sihui Zhang, Wenjing Lei, Hao Liang and Jianguo Xu: Nocardioides yefusunii sp. nov., isolated from Equus kiang (Tibetan wild ass) faeces. IJSEM 69: 3629 - 3635 2019 ( DOI 10.1099/ijsem.0.003674 )

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

* These data were automatically processed and therefore are not curated

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